Starting phenix.real_space_refine on Mon Jul 6 22:41:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o7r_12754/07_2026/7o7r_12754.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7r_12754/07_2026/7o7r_12754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7o7r_12754/07_2026/7o7r_12754.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o7r_12754/07_2026/7o7r_12754.cif" model { file = "/net/cci-nas-00/data/ceres_data/7o7r_12754/07_2026/7o7r_12754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7r_12754/07_2026/7o7r_12754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o7r_12754/07_2026/7o7r_12754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7r_12754/07_2026/7o7r_12754.map" } resolution = 3.9 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 81 residue(s): 0.05s 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: 8.13, per 1000 atoms: 0.20 Number of scatterers: 40530 At special positions: 0 Unit cell: (213.556, 152.54, 158.852, 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=2.04 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.01 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.02 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.02 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.02 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.02 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.04 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 287 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 642 " - pdb=" SG CYS C 689 " distance=2.04 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=2.01 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=2.04 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.04 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.02 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=2.04 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 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: 0.51 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: 6.241A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 Proline residue: A 982 - end of helix removed outlier: 4.023A pdb=" N TYR A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1017 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1060 through 1073 Processing helix chain 'A' and resid 1098 through 1111 Processing helix chain 'A' and resid 1119 through 1137 Processing helix chain 'A' and resid 1144 through 1157 Processing helix chain 'A' and resid 1160 through 1172 Processing helix chain 'A' and resid 1225 through 1241 Processing helix chain 'A' and resid 1251 through 1268 Processing helix chain 'A' and resid 1294 through 1297 No H-bonds generated for 'chain 'A' and resid 1294 through 1297' Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.541A pdb=" N LEU B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 666 through 673 Processing helix chain 'B' and resid 953 through 965 removed outlier: 6.830A pdb=" N SER B 957 " --> pdb=" O ASP B 953 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA B 958 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N MET B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLN B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 963 " --> pdb=" O MET B 959 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 965 " --> pdb=" O ASN B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 993 removed outlier: 3.502A pdb=" N MET B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 982 - end of helix removed outlier: 4.345A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 removed outlier: 4.061A pdb=" N TYR B1007 " --> pdb=" O LYS B1003 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B1017 " --> pdb=" O GLN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1055 removed outlier: 3.860A pdb=" N TYR B1055 " --> pdb=" O GLN B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1073 removed outlier: 4.472A pdb=" N ALA B1066 " --> pdb=" O HIS B1062 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TRP B1069 " --> pdb=" O GLN B1065 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B1070 " --> pdb=" O ALA B1066 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1111 removed outlier: 3.520A pdb=" N ILE B1107 " --> pdb=" O ALA B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1137 removed outlier: 4.088A pdb=" N PHE B1126 " --> pdb=" O ARG B1122 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B1135 " --> pdb=" O ALA B1131 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B1137 " --> pdb=" O LYS B1133 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1157 removed outlier: 3.542A pdb=" N TYR B1152 " --> pdb=" O ALA B1148 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B1153 " --> pdb=" O LEU B1149 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B1157 " --> pdb=" O ALA B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1172 removed outlier: 4.680A pdb=" N LYS B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B1165 " --> pdb=" O ASP B1161 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B1166 " --> pdb=" O LYS B1162 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B1169 " --> pdb=" O GLU B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1225 through 1241 removed outlier: 3.568A pdb=" N SER B1230 " --> pdb=" O GLU B1226 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B1235 " --> pdb=" O ALA B1231 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP B1237 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B1240 " --> pdb=" O LYS B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1251 through 1268 removed outlier: 4.422A pdb=" N LEU B1258 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS B1259 " --> pdb=" O VAL B1255 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) 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: 6.323A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 993 Proline residue: C 982 - end of helix removed outlier: 4.043A 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: 6.995A pdb=" N SER D 957 " --> pdb=" O ASP D 953 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA D 958 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET D 959 " --> pdb=" O LEU D 955 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN D 963 " --> pdb=" O MET D 959 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 965 " --> pdb=" O ASN D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 993 removed outlier: 3.696A pdb=" N MET D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 982 - end of helix removed outlier: 3.931A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 986 " --> pdb=" O PRO D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 removed outlier: 3.669A pdb=" N THR D1010 " --> pdb=" O GLY D1006 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN D1017 " --> pdb=" O GLN D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1055 removed outlier: 3.595A pdb=" N GLN D1051 " --> pdb=" O LYS D1047 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D1054 " --> pdb=" O ALA D1050 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR D1055 " --> pdb=" O GLN D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1073 removed outlier: 3.670A pdb=" N THR D1064 " --> pdb=" O GLU D1060 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TRP D1069 " --> pdb=" O GLN D1065 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D1070 " --> pdb=" O ALA D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1111 Processing helix chain 'D' and resid 1119 through 1137 removed outlier: 3.850A pdb=" N PHE D1126 " --> pdb=" O ARG D1122 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS D1127 " --> pdb=" O ASN D1123 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D1135 " --> pdb=" O ALA D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 4.007A pdb=" N LEU D1156 " --> pdb=" O TYR D1152 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA D1157 " --> pdb=" O ALA D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1172 removed outlier: 4.689A pdb=" N LYS D1164 " --> pdb=" O GLN D1160 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU D1165 " --> pdb=" O ASP D1161 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL D1166 " --> pdb=" O LYS D1162 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 3.619A pdb=" N THR D1229 " --> pdb=" O SER D1225 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D1230 " --> pdb=" O GLU D1226 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP D1237 " --> pdb=" O ASN D1233 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D1240 " --> pdb=" O LYS D1236 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D1241 " --> pdb=" O TRP D1237 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1268 removed outlier: 3.614A pdb=" N LYS D1263 " --> pdb=" O HIS D1259 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D1267 " --> pdb=" O LYS D1263 " (cutoff:3.500A) Processing helix chain 'D' and resid 1294 through 1297 No H-bonds generated for 'chain 'D' and resid 1294 through 1297' 480 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 6761 1.30 - 1.43: 10901 1.43 - 1.57: 23502 1.57 - 1.71: 3 1.71 - 1.84: 253 Bond restraints: 41420 Sorted by residual: bond pdb=" N PRO C 902 " pdb=" CA PRO C 902 " ideal model delta sigma weight residual 1.470 1.700 -0.230 1.01e-02 9.80e+03 5.18e+02 bond pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta sigma weight residual 1.469 1.710 -0.241 1.28e-02 6.10e+03 3.55e+02 bond pdb=" N PRO D 29 " pdb=" CA PRO D 29 " ideal model delta sigma weight residual 1.469 1.706 -0.237 1.28e-02 6.10e+03 3.44e+02 bond pdb=" C GLN D 168 " pdb=" N ASP D 169 " ideal model delta sigma weight residual 1.331 1.162 0.169 1.59e-02 3.96e+03 1.14e+02 bond pdb=" C GLN C 967 " pdb=" N MET C 968 " ideal model delta sigma weight residual 1.330 1.209 0.121 1.47e-02 4.63e+03 6.82e+01 ... (remaining 41415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 55145 3.84 - 7.69: 1079 7.69 - 11.53: 41 11.53 - 15.38: 2 15.38 - 19.22: 3 Bond angle restraints: 56270 Sorted by residual: angle pdb=" C LYS B 28 " pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta sigma weight residual 119.84 138.75 -18.91 1.25e+00 6.40e-01 2.29e+02 angle pdb=" C LYS D 28 " pdb=" N PRO D 29 " pdb=" CA PRO D 29 " ideal model delta sigma weight residual 119.84 138.61 -18.77 1.25e+00 6.40e-01 2.26e+02 angle pdb=" C LYS C 901 " pdb=" N PRO C 902 " pdb=" CA PRO C 902 " ideal model delta sigma weight residual 120.79 140.01 -19.22 1.30e+00 5.92e-01 2.19e+02 angle pdb=" CA PRO C 902 " pdb=" N PRO C 902 " pdb=" CD PRO C 902 " ideal model delta sigma weight residual 112.00 98.49 13.51 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA PRO B 29 " pdb=" N PRO B 29 " pdb=" CD PRO B 29 " ideal model delta sigma weight residual 112.00 100.84 11.16 1.40e+00 5.10e-01 6.36e+01 ... (remaining 56265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 21292 17.84 - 35.69: 2812 35.69 - 53.53: 489 53.53 - 71.37: 92 71.37 - 89.22: 45 Dihedral angle restraints: 24730 sinusoidal: 9816 harmonic: 14914 Sorted by residual: dihedral pdb=" C ASN B 991 " pdb=" N ASN B 991 " pdb=" CA ASN B 991 " pdb=" CB ASN B 991 " ideal model delta harmonic sigma weight residual -122.60 -144.63 22.03 0 2.50e+00 1.60e-01 7.76e+01 dihedral pdb=" CB CYS B 470 " pdb=" SG CYS B 470 " pdb=" SG CYS B 563 " pdb=" CB CYS B 563 " ideal model delta sinusoidal sigma weight residual 93.00 19.32 73.68 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS C 431 " pdb=" SG CYS C 431 " pdb=" SG CYS D 278 " pdb=" CB CYS D 278 " ideal model delta sinusoidal sigma weight residual 93.00 161.36 -68.36 1 1.00e+01 1.00e-02 6.06e+01 ... (remaining 24727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 6458 0.228 - 0.457: 48 0.457 - 0.685: 5 0.685 - 0.913: 1 0.913 - 1.142: 2 Chirality restraints: 6514 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.89e+01 chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.17e+01 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 -2.28 -0.12 2.00e-02 2.50e+03 3.71e+01 ... (remaining 6511 not shown) Planarity restraints: 7230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.351 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG E 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.314 2.00e-02 2.50e+03 2.70e-01 9.11e+02 pdb=" C7 NAG F 1 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.010 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.465 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.307 2.00e-02 2.50e+03 2.64e-01 8.72e+02 pdb=" C7 NAG L 1 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.004 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.454 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.211 2.00e-02 2.50e+03 ... (remaining 7227 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 832 2.51 - 3.11: 36462 3.11 - 3.70: 66679 3.70 - 4.30: 88971 4.30 - 4.90: 137942 Nonbonded interactions: 330886 Sorted by model distance: nonbonded pdb=" O PRO B 657 " pdb=" OG1 THR C 656 " model vdw 1.912 3.040 nonbonded pdb=" OG1 THR A 656 " pdb=" O PRO D 657 " model vdw 1.956 3.040 nonbonded pdb=" OG1 THR B 656 " pdb=" O PRO C 657 " model vdw 1.995 3.040 nonbonded pdb=" O GLN C1281 " pdb=" OG SER C1313 " model vdw 1.995 3.040 nonbonded pdb=" OG1 THR D1224 " pdb=" OD1 ASP D1227 " model vdw 2.021 3.040 ... (remaining 330881 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: 0.02 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: 1.880 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 28.970 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 : 0.013 0.241 41504 Z= 0.665 Angle : 1.348 19.221 56478 Z= 0.770 Chirality : 0.074 1.142 6514 Planarity : 0.013 0.301 7202 Dihedral : 16.348 89.217 14998 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 18.28 % Favored : 81.39 % Rotamer: Outliers : 1.07 % Allowed : 10.51 % Favored : 88.41 % Cbeta Deviations : 0.17 % 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: -5.78 (0.09), residues: 5110 helix: -3.17 (0.12), residues: 808 sheet: -3.84 (0.11), residues: 1268 loop : -4.22 (0.09), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG D 270 TYR 0.041 0.004 TYR D 166 PHE 0.039 0.004 PHE C 365 TRP 0.021 0.004 TRP B1237 HIS 0.024 0.003 HIS C 321 Details of bonding type rmsd/Z covalent geometry : bond 0.01317 / 0.66 (41420) covalent geometry : angle 1.33264 / 0.77 (56270) SS BOND : bond 0.00700 / 0.44 ( 44) SS BOND : angle 1.94802 / 1.13 ( 88) hydrogen bonds : bond 0.21865 / 15.06 ( 480) hydrogen bonds : angle 8.81432 / 5.79 ( 1440) link_BETA1-4 : bond 0.00997 / 0.81 ( 12) link_BETA1-4 : angle 3.12930 / 2.29 ( 36) link_NAG-ASN : bond 0.02003 / 1.01 ( 28) link_NAG-ASN : angle 4.83183 / 3.04 ( 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 955 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 907 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ILE cc_start: 0.8475 (mt) cc_final: 0.8273 (tt) REVERT: A 216 GLU cc_start: 0.8327 (pm20) cc_final: 0.8066 (pm20) REVERT: A 256 TYR cc_start: 0.8364 (t80) cc_final: 0.7296 (t80) REVERT: A 290 PHE cc_start: 0.7461 (m-80) cc_final: 0.7240 (m-80) REVERT: A 393 TYR cc_start: 0.9212 (t80) cc_final: 0.8933 (t80) REVERT: A 436 TRP cc_start: 0.7475 (t-100) cc_final: 0.7247 (t-100) REVERT: A 496 TYR cc_start: 0.6104 (m-80) cc_final: 0.5881 (m-10) REVERT: A 514 LEU cc_start: 0.9051 (pt) cc_final: 0.8806 (mt) REVERT: A 543 TYR cc_start: 0.7987 (p90) cc_final: 0.7782 (p90) REVERT: A 612 GLU cc_start: 0.8087 (tt0) cc_final: 0.7736 (tt0) REVERT: A 669 PHE cc_start: 0.8863 (m-80) cc_final: 0.8554 (m-80) REVERT: A 787 ARG cc_start: 0.8321 (ptp90) cc_final: 0.8029 (ptp90) REVERT: A 829 GLU cc_start: 0.8581 (tp30) cc_final: 0.7750 (mp0) REVERT: A 975 GLN cc_start: 0.8503 (mm-40) cc_final: 0.7936 (mt0) REVERT: A 976 ASN cc_start: 0.9164 (t0) cc_final: 0.8756 (t0) REVERT: A 990 LEU cc_start: 0.9012 (mt) cc_final: 0.8639 (mm) REVERT: A 1015 GLN cc_start: 0.8445 (tp40) cc_final: 0.8173 (tp40) REVERT: A 1017 ASN cc_start: 0.8884 (m110) cc_final: 0.8508 (m-40) REVERT: A 1076 ASP cc_start: 0.7796 (p0) cc_final: 0.7573 (p0) REVERT: A 1087 LEU cc_start: 0.9553 (tt) cc_final: 0.9150 (mt) REVERT: A 1146 THR cc_start: 0.8870 (p) cc_final: 0.8665 (p) REVERT: A 1208 MET cc_start: 0.9205 (ppp) cc_final: 0.8787 (ppp) REVERT: A 1217 LEU cc_start: 0.9356 (mm) cc_final: 0.9097 (mm) REVERT: B 98 GLU cc_start: 0.8631 (tt0) cc_final: 0.8264 (tm-30) REVERT: B 113 GLU cc_start: 0.6589 (pt0) cc_final: 0.6369 (pm20) REVERT: B 121 MET cc_start: 0.8297 (tpp) cc_final: 0.7696 (tpp) REVERT: B 169 ASP cc_start: 0.6657 (t0) cc_final: 0.6457 (t0) REVERT: B 256 TYR cc_start: 0.8020 (t80) cc_final: 0.7509 (t80) REVERT: B 289 LYS cc_start: 0.9089 (mttm) cc_final: 0.8775 (mmtp) REVERT: B 318 MET cc_start: 0.8216 (mtt) cc_final: 0.7801 (tpt) REVERT: B 393 TYR cc_start: 0.9038 (t80) cc_final: 0.8475 (t80) REVERT: B 533 ASP cc_start: 0.8006 (t0) cc_final: 0.7635 (t0) REVERT: B 567 LYS cc_start: 0.9196 (tppt) cc_final: 0.8924 (mmtm) REVERT: B 635 ASN cc_start: 0.8299 (p0) cc_final: 0.8004 (p0) REVERT: B 637 GLN cc_start: 0.7364 (pp30) cc_final: 0.7086 (pp30) REVERT: B 669 PHE cc_start: 0.8552 (m-80) cc_final: 0.8020 (m-80) REVERT: B 673 MET cc_start: 0.8226 (tpp) cc_final: 0.7739 (tpp) REVERT: B 741 TRP cc_start: 0.8285 (t-100) cc_final: 0.7684 (t-100) REVERT: B 766 LYS cc_start: 0.8370 (tppt) cc_final: 0.8124 (tptp) REVERT: B 792 PHE cc_start: 0.7679 (t80) cc_final: 0.7471 (t80) REVERT: B 863 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8507 (ttpt) REVERT: B 951 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6438 (pp) REVERT: B 965 LEU cc_start: 0.9163 (tt) cc_final: 0.8770 (mm) REVERT: B 975 GLN cc_start: 0.9133 (mm110) cc_final: 0.8857 (mt0) REVERT: B 976 ASN cc_start: 0.9303 (t0) cc_final: 0.9028 (t0) REVERT: B 977 MET cc_start: 0.9403 (mmm) cc_final: 0.9173 (mmm) REVERT: B 1076 ASP cc_start: 0.7806 (p0) cc_final: 0.7432 (p0) REVERT: B 1123 ASN cc_start: 0.9196 (m110) cc_final: 0.8740 (m110) REVERT: B 1125 LEU cc_start: 0.9247 (mt) cc_final: 0.8861 (mm) REVERT: B 1133 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8913 (mmtm) REVERT: B 1161 ASP cc_start: 0.9028 (p0) cc_final: 0.8730 (p0) REVERT: B 1237 TRP cc_start: 0.7443 (t60) cc_final: 0.7238 (t60) REVERT: B 1245 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8680 (tm-30) REVERT: B 1323 TYR cc_start: 0.6543 (t80) cc_final: 0.5953 (t80) REVERT: B 1325 GLN cc_start: 0.7955 (tt0) cc_final: 0.6851 (tp40) REVERT: C 76 ASP cc_start: 0.8482 (p0) cc_final: 0.8036 (m-30) REVERT: C 101 MET cc_start: 0.8322 (mtp) cc_final: 0.7883 (mmm) REVERT: C 121 MET cc_start: 0.8165 (ttt) cc_final: 0.7396 (tpt) REVERT: C 368 GLN cc_start: 0.8870 (tt0) cc_final: 0.8565 (tm-30) REVERT: C 387 ARG cc_start: 0.8268 (mmt180) cc_final: 0.7846 (mmm160) REVERT: C 635 ASN cc_start: 0.8205 (p0) cc_final: 0.7651 (p0) REVERT: C 671 GLU cc_start: 0.9055 (tt0) cc_final: 0.8510 (tt0) REVERT: C 672 ASP cc_start: 0.8884 (t0) cc_final: 0.8614 (t0) REVERT: C 688 MET cc_start: 0.7528 (ppp) cc_final: 0.6947 (ppp) REVERT: C 737 GLU cc_start: 0.8116 (mp0) cc_final: 0.7814 (mp0) REVERT: C 787 ARG cc_start: 0.8445 (ptp90) cc_final: 0.8180 (mtp180) REVERT: C 800 TYR cc_start: 0.7695 (p90) cc_final: 0.7325 (p90) REVERT: C 916 PHE cc_start: 0.8655 (m-80) cc_final: 0.8368 (m-80) REVERT: C 967 GLN cc_start: 0.9051 (mt0) cc_final: 0.8803 (mp10) REVERT: C 977 MET cc_start: 0.9159 (mmm) cc_final: 0.8933 (mmm) REVERT: C 983 ASN cc_start: 0.9141 (m-40) cc_final: 0.8938 (m-40) REVERT: C 988 ASP cc_start: 0.8304 (t0) cc_final: 0.7823 (t70) REVERT: C 1015 GLN cc_start: 0.7744 (tp40) cc_final: 0.6655 (tp40) REVERT: C 1057 PHE cc_start: 0.8012 (t80) cc_final: 0.7607 (t80) REVERT: C 1072 GLN cc_start: 0.9096 (mt0) cc_final: 0.8838 (mt0) REVERT: C 1073 ARG cc_start: 0.9111 (mmt-90) cc_final: 0.8701 (mmp80) REVERT: C 1163 ARG cc_start: 0.8646 (tmm-80) cc_final: 0.8287 (ttt180) REVERT: C 1234 ILE cc_start: 0.8225 (pt) cc_final: 0.7967 (pt) REVERT: C 1254 THR cc_start: 0.9176 (m) cc_final: 0.8861 (m) REVERT: C 1312 TYR cc_start: 0.8946 (m-80) cc_final: 0.8580 (m-80) REVERT: C 1323 TYR cc_start: 0.6384 (t80) cc_final: 0.5971 (t80) REVERT: D 98 GLU cc_start: 0.8798 (tt0) cc_final: 0.8285 (tp30) REVERT: D 121 MET cc_start: 0.7942 (mmm) cc_final: 0.7687 (mmm) REVERT: D 175 ILE cc_start: 0.8719 (tp) cc_final: 0.8440 (tp) REVERT: D 203 TYR cc_start: 0.7078 (m-80) cc_final: 0.6177 (m-80) REVERT: D 256 TYR cc_start: 0.7275 (t80) cc_final: 0.6346 (t80) REVERT: D 381 ASN cc_start: 0.9115 (m-40) cc_final: 0.8717 (p0) REVERT: D 399 THR cc_start: 0.8561 (p) cc_final: 0.8262 (p) REVERT: D 669 PHE cc_start: 0.8667 (m-80) cc_final: 0.8184 (m-80) REVERT: D 671 GLU cc_start: 0.8752 (tt0) cc_final: 0.8463 (tt0) REVERT: D 682 LYS cc_start: 0.8717 (mttt) cc_final: 0.8376 (mmtp) REVERT: D 737 GLU cc_start: 0.8108 (mp0) cc_final: 0.7793 (mp0) REVERT: D 766 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7563 (mmmt) REVERT: D 783 THR cc_start: 0.9490 (p) cc_final: 0.8727 (p) REVERT: D 976 ASN cc_start: 0.9274 (t0) cc_final: 0.8895 (t0) REVERT: D 992 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: D 1003 LYS cc_start: 0.9495 (tptt) cc_final: 0.9241 (tptp) REVERT: D 1089 ASN cc_start: 0.8828 (p0) cc_final: 0.8511 (p0) REVERT: D 1133 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8660 (mmtm) REVERT: D 1144 VAL cc_start: 0.8648 (m) cc_final: 0.7788 (m) REVERT: D 1147 LYS cc_start: 0.9306 (mttp) cc_final: 0.8874 (mttp) REVERT: D 1150 LEU cc_start: 0.9590 (mm) cc_final: 0.9385 (mm) REVERT: D 1154 PHE cc_start: 0.8721 (m-80) cc_final: 0.8456 (m-80) REVERT: D 1208 MET cc_start: 0.9467 (ppp) cc_final: 0.8995 (ppp) REVERT: D 1243 ASN cc_start: 0.9266 (t0) cc_final: 0.8980 (t0) REVERT: D 1245 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8656 (tm-30) REVERT: D 1269 PHE cc_start: 0.8709 (t80) cc_final: 0.8258 (t80) REVERT: D 1312 TYR cc_start: 0.9088 (m-80) cc_final: 0.8718 (m-80) outliers start: 48 outliers final: 26 residues processed: 946 average time/residue: 0.2127 time to fit residues: 336.0768 Evaluate side-chains 687 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 659 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1056 ILE Chi-restraints excluded: chain D residue 1214 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 494 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN A 217 HIS A 361 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 479 HIS A 511 HIS A 517 GLN A 523 HIS A 983 ASN A 995 GLN A1013 GLN A1038 ASN A1065 GLN A1072 GLN A1252 GLN B 112 GLN B 302 GLN B 325 GLN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS B 474 GLN B 483 ASN B 511 HIS B 592 GLN B 637 GLN B 790 GLN B 827 GLN B 938 ASN B 960 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 ASN B1277 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 511 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 ASN C 694 GLN C 790 GLN C 983 ASN C1171 ASN C1242 GLN C1259 HIS D 182 GLN ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN D 368 GLN D 389 ASN D 424 ASN D 460 HIS D 474 GLN ** D 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 GLN D 827 GLN ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 ASN D 938 ASN ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1035 ASN ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 GLN D1123 ASN D1233 ASN D1241 GLN D1242 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.108074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.084879 restraints weight = 144909.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.088040 restraints weight = 90887.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.090388 restraints weight = 64354.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.092086 restraints weight = 48985.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.093376 restraints weight = 39633.302| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 41504 Z= 0.226 Angle : 0.942 12.266 56478 Z= 0.470 Chirality : 0.054 0.449 6514 Planarity : 0.007 0.067 7202 Dihedral : 7.966 63.295 5516 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.96 % Favored : 88.88 % Rotamer: Outliers : 3.38 % Allowed : 16.71 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -4.79 (0.10), residues: 5110 helix: -1.55 (0.16), residues: 796 sheet: -3.33 (0.11), residues: 1516 loop : -3.68 (0.10), residues: 2798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 338 TYR 0.028 0.002 TYR B 989 PHE 0.031 0.002 PHE B 286 TRP 0.019 0.002 TRP A1132 HIS 0.013 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (41420) covalent geometry : angle 0.93105 / 0.47 (56270) SS BOND : bond 0.01113 / 0.60 ( 44) SS BOND : angle 1.76219 / 1.04 ( 88) hydrogen bonds : bond 0.06292 / 4.31 ( 480) hydrogen bonds : angle 6.07350 / 3.93 ( 1440) link_BETA1-4 : bond 0.01080 / 0.72 ( 12) link_BETA1-4 : angle 2.46013 / 1.78 ( 36) link_NAG-ASN : bond 0.00754 / 0.47 ( 28) link_NAG-ASN : angle 3.21896 / 2.10 ( 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 945 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 794 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.7744 (pp) cc_final: 0.6865 (mt) REVERT: A 209 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8650 (ttpp) REVERT: A 290 PHE cc_start: 0.7484 (m-80) cc_final: 0.7247 (m-80) REVERT: A 318 MET cc_start: 0.8929 (tpp) cc_final: 0.8568 (tpp) REVERT: A 384 ILE cc_start: 0.8549 (pt) cc_final: 0.8208 (pt) REVERT: A 514 LEU cc_start: 0.9016 (pt) cc_final: 0.8791 (mt) REVERT: A 543 TYR cc_start: 0.7550 (p90) cc_final: 0.6728 (p90) REVERT: A 566 ASN cc_start: 0.8035 (t0) cc_final: 0.7804 (m-40) REVERT: A 572 PHE cc_start: 0.7968 (p90) cc_final: 0.7632 (p90) REVERT: A 612 GLU cc_start: 0.8033 (tt0) cc_final: 0.7685 (tt0) REVERT: A 619 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: A 666 MET cc_start: 0.8251 (tpt) cc_final: 0.7803 (tpt) REVERT: A 669 PHE cc_start: 0.8756 (m-80) cc_final: 0.8476 (m-80) REVERT: A 688 MET cc_start: 0.7908 (ppp) cc_final: 0.7420 (ppp) REVERT: A 793 PHE cc_start: 0.8633 (p90) cc_final: 0.8347 (p90) REVERT: A 829 GLU cc_start: 0.8679 (tp30) cc_final: 0.7482 (mp0) REVERT: A 915 THR cc_start: 0.9173 (t) cc_final: 0.8902 (m) REVERT: A 934 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7296 (tppt) REVERT: A 975 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8090 (mt0) REVERT: A 1015 GLN cc_start: 0.8629 (tp40) cc_final: 0.8359 (tp40) REVERT: A 1017 ASN cc_start: 0.8877 (m110) cc_final: 0.8468 (m-40) REVERT: A 1034 ARG cc_start: 0.9236 (ppt170) cc_final: 0.9032 (ppt170) REVERT: A 1073 ARG cc_start: 0.9081 (mmt-90) cc_final: 0.8695 (mmp80) REVERT: A 1087 LEU cc_start: 0.9543 (tt) cc_final: 0.9203 (mt) REVERT: A 1178 ASP cc_start: 0.9362 (p0) cc_final: 0.8815 (p0) REVERT: A 1213 LEU cc_start: 0.9740 (tp) cc_final: 0.9390 (tp) REVERT: A 1216 TYR cc_start: 0.8680 (m-80) cc_final: 0.8403 (m-80) REVERT: A 1217 LEU cc_start: 0.9354 (mm) cc_final: 0.8958 (mm) REVERT: B 98 GLU cc_start: 0.8680 (tt0) cc_final: 0.8245 (tm-30) REVERT: B 121 MET cc_start: 0.8145 (tpp) cc_final: 0.7458 (tpp) REVERT: B 239 ILE cc_start: 0.8951 (tp) cc_final: 0.8667 (mp) REVERT: B 342 GLU cc_start: 0.8860 (tp30) cc_final: 0.8605 (tp30) REVERT: B 393 TYR cc_start: 0.8855 (t80) cc_final: 0.8424 (t80) REVERT: B 460 HIS cc_start: 0.8558 (t70) cc_final: 0.8297 (t-90) REVERT: B 567 LYS cc_start: 0.9134 (tppt) cc_final: 0.8863 (mmtm) REVERT: B 634 LEU cc_start: 0.9053 (pt) cc_final: 0.8742 (pp) REVERT: B 635 ASN cc_start: 0.8454 (p0) cc_final: 0.8045 (p0) REVERT: B 669 PHE cc_start: 0.8616 (m-80) cc_final: 0.7938 (m-80) REVERT: B 741 TRP cc_start: 0.8286 (t-100) cc_final: 0.8082 (t-100) REVERT: B 766 LYS cc_start: 0.8083 (tppt) cc_final: 0.7816 (tppt) REVERT: B 798 MET cc_start: 0.8728 (ptt) cc_final: 0.8501 (ptm) REVERT: B 863 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8481 (ttpt) REVERT: B 964 ASN cc_start: 0.9238 (t0) cc_final: 0.8714 (p0) REVERT: B 965 LEU cc_start: 0.9195 (tt) cc_final: 0.8548 (mt) REVERT: B 977 MET cc_start: 0.9290 (mmm) cc_final: 0.9022 (mmm) REVERT: B 988 ASP cc_start: 0.8916 (m-30) cc_final: 0.8645 (t70) REVERT: B 999 GLU cc_start: 0.8972 (mp0) cc_final: 0.8752 (mp0) REVERT: B 1003 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8698 (ttpp) REVERT: B 1076 ASP cc_start: 0.7951 (p0) cc_final: 0.7517 (p0) REVERT: B 1123 ASN cc_start: 0.9232 (m110) cc_final: 0.8895 (m110) REVERT: B 1133 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8875 (tppt) REVERT: B 1161 ASP cc_start: 0.8938 (p0) cc_final: 0.8708 (p0) REVERT: B 1183 TRP cc_start: 0.9052 (m-90) cc_final: 0.8593 (m-90) REVERT: B 1323 TYR cc_start: 0.6884 (t80) cc_final: 0.6463 (t80) REVERT: B 1325 GLN cc_start: 0.8092 (tt0) cc_final: 0.7119 (tp40) REVERT: B 1330 TYR cc_start: 0.8333 (p90) cc_final: 0.8022 (p90) REVERT: C 65 GLU cc_start: 0.7704 (mt-10) cc_final: 0.6938 (mm-30) REVERT: C 81 ASN cc_start: 0.7996 (p0) cc_final: 0.7731 (p0) REVERT: C 98 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8614 (tm-30) REVERT: C 121 MET cc_start: 0.7800 (ttt) cc_final: 0.7504 (tpp) REVERT: C 189 GLN cc_start: 0.8581 (pm20) cc_final: 0.8042 (pp30) REVERT: C 360 ARG cc_start: 0.7492 (mpt180) cc_final: 0.6894 (mmt90) REVERT: C 368 GLN cc_start: 0.8790 (tt0) cc_final: 0.8563 (tm-30) REVERT: C 458 PHE cc_start: 0.8106 (p90) cc_final: 0.7561 (p90) REVERT: C 460 HIS cc_start: 0.7931 (t-170) cc_final: 0.6994 (t-170) REVERT: C 539 ARG cc_start: 0.7757 (mtt-85) cc_final: 0.7095 (mtt90) REVERT: C 576 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6141 (pp30) REVERT: C 625 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8270 (mppt) REVERT: C 635 ASN cc_start: 0.8405 (p0) cc_final: 0.7822 (p0) REVERT: C 671 GLU cc_start: 0.9071 (tt0) cc_final: 0.8564 (tt0) REVERT: C 672 ASP cc_start: 0.8999 (t0) cc_final: 0.8657 (t0) REVERT: C 673 MET cc_start: 0.8780 (tpp) cc_final: 0.8356 (tpp) REVERT: C 678 PHE cc_start: 0.8241 (m-80) cc_final: 0.7998 (m-80) REVERT: C 688 MET cc_start: 0.8148 (ppp) cc_final: 0.7806 (ppp) REVERT: C 787 ARG cc_start: 0.8597 (ptp90) cc_final: 0.8192 (mtp180) REVERT: C 800 TYR cc_start: 0.7507 (p90) cc_final: 0.7292 (p90) REVERT: C 916 PHE cc_start: 0.8757 (m-80) cc_final: 0.8485 (m-80) REVERT: C 934 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8486 (tppt) REVERT: C 977 MET cc_start: 0.9103 (mmm) cc_final: 0.8843 (mmm) REVERT: C 988 ASP cc_start: 0.8263 (t0) cc_final: 0.7676 (t70) REVERT: C 1015 GLN cc_start: 0.7734 (tp40) cc_final: 0.6766 (tp40) REVERT: C 1073 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8682 (mmp80) REVERT: C 1104 TYR cc_start: 0.8313 (t80) cc_final: 0.7842 (t80) REVERT: C 1168 LYS cc_start: 0.9298 (mttt) cc_final: 0.8996 (mmtm) REVERT: C 1205 GLU cc_start: 0.8668 (pm20) cc_final: 0.7732 (pm20) REVERT: C 1252 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8005 (mm-40) REVERT: C 1314 MET cc_start: 0.8725 (mpp) cc_final: 0.8512 (mmt) REVERT: C 1323 TYR cc_start: 0.6303 (t80) cc_final: 0.5954 (t80) REVERT: D 98 GLU cc_start: 0.8914 (tt0) cc_final: 0.8524 (tp30) REVERT: D 108 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8723 (mmmt) REVERT: D 126 ASP cc_start: 0.9138 (p0) cc_final: 0.8822 (p0) REVERT: D 239 ILE cc_start: 0.9199 (tp) cc_final: 0.8975 (mp) REVERT: D 290 PHE cc_start: 0.8343 (m-80) cc_final: 0.8042 (m-10) REVERT: D 373 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8294 (t0) REVERT: D 557 LYS cc_start: 0.8828 (mttp) cc_final: 0.8529 (mmtp) REVERT: D 561 GLU cc_start: 0.7946 (tp30) cc_final: 0.7620 (tp30) REVERT: D 578 LEU cc_start: 0.8049 (tp) cc_final: 0.7782 (tp) REVERT: D 669 PHE cc_start: 0.8627 (m-80) cc_final: 0.8116 (m-80) REVERT: D 671 GLU cc_start: 0.8789 (tt0) cc_final: 0.8452 (tt0) REVERT: D 673 MET cc_start: 0.9023 (tpp) cc_final: 0.8695 (tpp) REVERT: D 682 LYS cc_start: 0.8615 (mttt) cc_final: 0.8322 (mmtp) REVERT: D 688 MET cc_start: 0.8162 (ppp) cc_final: 0.7814 (ppp) REVERT: D 737 GLU cc_start: 0.8007 (mp0) cc_final: 0.7530 (mp0) REVERT: D 741 TRP cc_start: 0.8092 (t-100) cc_final: 0.7732 (t60) REVERT: D 758 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7743 (p) REVERT: D 764 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: D 766 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7621 (mmtm) REVERT: D 796 LEU cc_start: 0.3467 (OUTLIER) cc_final: 0.2866 (pp) REVERT: D 827 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.8921 (pp30) REVERT: D 965 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8434 (mp) REVERT: D 976 ASN cc_start: 0.9283 (t0) cc_final: 0.9071 (t0) REVERT: D 977 MET cc_start: 0.9522 (mmm) cc_final: 0.9264 (mmm) REVERT: D 1003 LYS cc_start: 0.9412 (tptt) cc_final: 0.9103 (tppt) REVERT: D 1089 ASN cc_start: 0.8783 (p0) cc_final: 0.8286 (p0) REVERT: D 1123 ASN cc_start: 0.9164 (m-40) cc_final: 0.8928 (m110) REVERT: D 1133 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8839 (mmtm) REVERT: D 1144 VAL cc_start: 0.8088 (m) cc_final: 0.7256 (m) REVERT: D 1147 LYS cc_start: 0.9269 (mttp) cc_final: 0.8689 (mttp) REVERT: D 1154 PHE cc_start: 0.8974 (m-80) cc_final: 0.8739 (m-80) REVERT: D 1183 TRP cc_start: 0.9095 (m100) cc_final: 0.8190 (m100) REVERT: D 1209 THR cc_start: 0.9749 (p) cc_final: 0.9486 (p) REVERT: D 1243 ASN cc_start: 0.9281 (t0) cc_final: 0.8985 (t0) REVERT: D 1245 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8678 (tm-30) REVERT: D 1269 PHE cc_start: 0.8532 (t80) cc_final: 0.8021 (t80) outliers start: 151 outliers final: 82 residues processed: 887 average time/residue: 0.2062 time to fit residues: 308.5305 Evaluate side-chains 742 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 649 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1328 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 934 LYS Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 GLU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 831 SER Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1056 ILE Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 311 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 502 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 418 optimal weight: 10.0000 chunk 283 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 271 optimal weight: 1.9990 chunk 281 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 159 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN A 389 ASN A 413 ASN ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 GLN B 85 HIS B 327 GLN B 381 ASN B 389 ASN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 GLN ** B 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 173 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN C 413 ASN C 523 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 GLN C 680 ASN D 81 ASN D 85 HIS ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 GLN ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 ASN ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1233 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.103005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.079548 restraints weight = 146346.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.082591 restraints weight = 90788.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.084849 restraints weight = 64158.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.086504 restraints weight = 48986.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.087793 restraints weight = 39615.449| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 41504 Z= 0.296 Angle : 0.941 15.783 56478 Z= 0.472 Chirality : 0.053 0.397 6514 Planarity : 0.006 0.090 7202 Dihedral : 7.460 54.070 5487 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.64 % Favored : 87.24 % Rotamer: Outliers : 5.28 % Allowed : 20.04 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -4.48 (0.10), residues: 5110 helix: -1.05 (0.16), residues: 816 sheet: -3.16 (0.11), residues: 1610 loop : -3.54 (0.10), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 360 TYR 0.026 0.002 TYR C 985 PHE 0.027 0.003 PHE B 792 TRP 0.025 0.002 TRP B1237 HIS 0.012 0.002 HIS C 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.30 (41420) covalent geometry : angle 0.92802 / 0.47 (56270) SS BOND : bond 0.01522 / 1.01 ( 44) SS BOND : angle 2.12086 / 1.18 ( 88) hydrogen bonds : bond 0.05955 / 4.09 ( 480) hydrogen bonds : angle 6.15378 / 3.98 ( 1440) link_BETA1-4 : bond 0.00474 / 0.31 ( 12) link_BETA1-4 : angle 2.21085 / 1.56 ( 36) link_NAG-ASN : bond 0.00930 / 0.61 ( 28) link_NAG-ASN : angle 3.47022 / 2.16 ( 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 962 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 726 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8723 (tp) cc_final: 0.8023 (mp) REVERT: A 183 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7031 (mt) REVERT: A 290 PHE cc_start: 0.7531 (m-80) cc_final: 0.7272 (m-80) REVERT: A 505 ILE cc_start: 0.4016 (OUTLIER) cc_final: 0.3073 (tt) REVERT: A 514 LEU cc_start: 0.9024 (pt) cc_final: 0.8815 (mt) REVERT: A 539 ARG cc_start: 0.8193 (mtt-85) cc_final: 0.7543 (mtt90) REVERT: A 543 TYR cc_start: 0.7756 (p90) cc_final: 0.6966 (p90) REVERT: A 572 PHE cc_start: 0.8287 (p90) cc_final: 0.7928 (p90) REVERT: A 607 MET cc_start: 0.7510 (tpp) cc_final: 0.7224 (tmm) REVERT: A 612 GLU cc_start: 0.8121 (tt0) cc_final: 0.7884 (tt0) REVERT: A 619 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.6598 (m-80) REVERT: A 627 LEU cc_start: 0.8813 (tp) cc_final: 0.7802 (tp) REVERT: A 666 MET cc_start: 0.8316 (tpt) cc_final: 0.7994 (tpt) REVERT: A 669 PHE cc_start: 0.8764 (m-80) cc_final: 0.8316 (m-80) REVERT: A 682 LYS cc_start: 0.8736 (mttt) cc_final: 0.8348 (mmmt) REVERT: A 783 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8640 (t) REVERT: A 787 ARG cc_start: 0.8329 (ptp90) cc_final: 0.8098 (ptp90) REVERT: A 793 PHE cc_start: 0.8679 (p90) cc_final: 0.8434 (p90) REVERT: A 828 LEU cc_start: 0.7774 (tt) cc_final: 0.7319 (pp) REVERT: A 829 GLU cc_start: 0.8657 (tp30) cc_final: 0.7707 (mp0) REVERT: A 975 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8136 (mt0) REVERT: A 977 MET cc_start: 0.9454 (mmm) cc_final: 0.9117 (mmm) REVERT: A 990 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8747 (mm) REVERT: A 1003 LYS cc_start: 0.8650 (ttpp) cc_final: 0.8380 (ptmm) REVERT: A 1015 GLN cc_start: 0.8878 (tp40) cc_final: 0.8052 (tp40) REVERT: A 1017 ASN cc_start: 0.8908 (m110) cc_final: 0.8647 (m110) REVERT: A 1064 THR cc_start: 0.9357 (OUTLIER) cc_final: 0.9103 (p) REVERT: A 1065 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8760 (mm110) REVERT: A 1080 PHE cc_start: 0.8262 (m-80) cc_final: 0.7998 (m-10) REVERT: A 1087 LEU cc_start: 0.9565 (tt) cc_final: 0.9233 (mt) REVERT: A 1110 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9078 (tp) REVERT: A 1165 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8774 (pp20) REVERT: A 1178 ASP cc_start: 0.9392 (p0) cc_final: 0.9002 (p0) REVERT: A 1205 GLU cc_start: 0.8718 (pm20) cc_final: 0.8499 (pm20) REVERT: A 1213 LEU cc_start: 0.9749 (tp) cc_final: 0.9459 (tp) REVERT: A 1217 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8966 (mm) REVERT: B 98 GLU cc_start: 0.8723 (tt0) cc_final: 0.8193 (tm-30) REVERT: B 121 MET cc_start: 0.8168 (tpp) cc_final: 0.7709 (tpp) REVERT: B 138 TYR cc_start: 0.6701 (m-80) cc_final: 0.6482 (m-10) REVERT: B 327 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7852 (pp30) REVERT: B 342 GLU cc_start: 0.8942 (tp30) cc_final: 0.8715 (tp30) REVERT: B 373 ASP cc_start: 0.7504 (t0) cc_final: 0.7218 (t0) REVERT: B 393 TYR cc_start: 0.8859 (t80) cc_final: 0.8505 (t80) REVERT: B 460 HIS cc_start: 0.8844 (t70) cc_final: 0.8493 (t-90) REVERT: B 542 ILE cc_start: 0.8508 (tp) cc_final: 0.7905 (mp) REVERT: B 635 ASN cc_start: 0.8628 (p0) cc_final: 0.8317 (p0) REVERT: B 669 PHE cc_start: 0.8759 (m-80) cc_final: 0.7903 (m-80) REVERT: B 688 MET cc_start: 0.8681 (ppp) cc_final: 0.8247 (ppp) REVERT: B 741 TRP cc_start: 0.8463 (t-100) cc_final: 0.8237 (t-100) REVERT: B 762 ILE cc_start: 0.8145 (pt) cc_final: 0.7940 (pt) REVERT: B 766 LYS cc_start: 0.8193 (tppt) cc_final: 0.7932 (tppt) REVERT: B 798 MET cc_start: 0.8759 (ptt) cc_final: 0.8186 (ptt) REVERT: B 858 TRP cc_start: 0.7068 (m-90) cc_final: 0.6582 (m-90) REVERT: B 863 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8533 (ttpt) REVERT: B 964 ASN cc_start: 0.9290 (t0) cc_final: 0.8931 (p0) REVERT: B 965 LEU cc_start: 0.9313 (tt) cc_final: 0.9003 (tt) REVERT: B 988 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8787 (t70) REVERT: B 999 GLU cc_start: 0.8960 (mp0) cc_final: 0.8731 (mp0) REVERT: B 1076 ASP cc_start: 0.8153 (p0) cc_final: 0.7692 (p0) REVERT: B 1098 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7902 (tp30) REVERT: B 1123 ASN cc_start: 0.9387 (m110) cc_final: 0.9113 (m110) REVERT: B 1133 LYS cc_start: 0.9154 (ttmt) cc_final: 0.8953 (mmtm) REVERT: B 1161 ASP cc_start: 0.8875 (p0) cc_final: 0.8570 (p0) REVERT: B 1183 TRP cc_start: 0.9095 (m-90) cc_final: 0.8706 (m-90) REVERT: B 1217 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8900 (mm) REVERT: B 1325 GLN cc_start: 0.8280 (tt0) cc_final: 0.7706 (tp-100) REVERT: B 1329 LYS cc_start: 0.8117 (ptmt) cc_final: 0.7840 (pttm) REVERT: C 65 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7036 (mm-30) REVERT: C 98 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8548 (tm-30) REVERT: C 121 MET cc_start: 0.7766 (ttt) cc_final: 0.7546 (tpt) REVERT: C 189 GLN cc_start: 0.8627 (pm20) cc_final: 0.8221 (pp30) REVERT: C 229 PHE cc_start: 0.7262 (p90) cc_final: 0.6658 (p90) REVERT: C 436 TRP cc_start: 0.7850 (t-100) cc_final: 0.7578 (t-100) REVERT: C 500 MET cc_start: 0.8032 (ptm) cc_final: 0.6994 (ptm) REVERT: C 552 ILE cc_start: 0.8287 (pt) cc_final: 0.8050 (pt) REVERT: C 635 ASN cc_start: 0.8553 (p0) cc_final: 0.7906 (p0) REVERT: C 671 GLU cc_start: 0.9191 (tt0) cc_final: 0.8718 (tt0) REVERT: C 672 ASP cc_start: 0.9096 (t0) cc_final: 0.8808 (t0) REVERT: C 678 PHE cc_start: 0.8404 (m-80) cc_final: 0.8103 (m-80) REVERT: C 688 MET cc_start: 0.8204 (ppp) cc_final: 0.7873 (ppp) REVERT: C 737 GLU cc_start: 0.8166 (mp0) cc_final: 0.6998 (mp0) REVERT: C 787 ARG cc_start: 0.8653 (ptp90) cc_final: 0.8080 (mtp180) REVERT: C 916 PHE cc_start: 0.8772 (m-80) cc_final: 0.8483 (m-80) REVERT: C 977 MET cc_start: 0.9107 (mmm) cc_final: 0.8831 (mmm) REVERT: C 988 ASP cc_start: 0.8458 (t0) cc_final: 0.7977 (t70) REVERT: C 1015 GLN cc_start: 0.7909 (tp40) cc_final: 0.6928 (tp40) REVERT: C 1073 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8714 (mmp80) REVERT: C 1104 TYR cc_start: 0.8578 (t80) cc_final: 0.8143 (t80) REVERT: C 1168 LYS cc_start: 0.9386 (mttt) cc_final: 0.9105 (mmtm) REVERT: C 1232 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8825 (p) REVERT: C 1258 LEU cc_start: 0.9287 (mp) cc_final: 0.9064 (mp) REVERT: D 98 GLU cc_start: 0.8897 (tt0) cc_final: 0.8658 (tp30) REVERT: D 108 LYS cc_start: 0.9360 (mmtt) cc_final: 0.9035 (mmmt) REVERT: D 126 ASP cc_start: 0.9209 (p0) cc_final: 0.8892 (p0) REVERT: D 203 TYR cc_start: 0.7579 (m-80) cc_final: 0.6333 (m-80) REVERT: D 368 GLN cc_start: 0.8507 (pt0) cc_final: 0.8129 (mp10) REVERT: D 500 MET cc_start: 0.6243 (mtp) cc_final: 0.5725 (mtt) REVERT: D 542 ILE cc_start: 0.8590 (tt) cc_final: 0.8084 (mp) REVERT: D 557 LYS cc_start: 0.8892 (mttp) cc_final: 0.8499 (mmtm) REVERT: D 561 GLU cc_start: 0.8259 (tp30) cc_final: 0.7885 (tp30) REVERT: D 637 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7820 (pp30) REVERT: D 669 PHE cc_start: 0.8682 (m-80) cc_final: 0.8061 (m-80) REVERT: D 671 GLU cc_start: 0.8798 (tt0) cc_final: 0.8264 (mm-30) REVERT: D 673 MET cc_start: 0.9063 (tpp) cc_final: 0.8474 (tpp) REVERT: D 682 LYS cc_start: 0.8626 (mttt) cc_final: 0.8370 (mmtp) REVERT: D 737 GLU cc_start: 0.8260 (mp0) cc_final: 0.7834 (mp0) REVERT: D 758 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7783 (p) REVERT: D 764 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8263 (mp0) REVERT: D 766 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7625 (mmtm) REVERT: D 915 THR cc_start: 0.9184 (t) cc_final: 0.8888 (m) REVERT: D 965 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8547 (mp) REVERT: D 976 ASN cc_start: 0.9367 (t0) cc_final: 0.9100 (t0) REVERT: D 977 MET cc_start: 0.9452 (mmm) cc_final: 0.9249 (mmm) REVERT: D 1076 ASP cc_start: 0.7794 (p0) cc_final: 0.7364 (p0) REVERT: D 1089 ASN cc_start: 0.8860 (p0) cc_final: 0.8369 (p0) REVERT: D 1133 LYS cc_start: 0.9235 (ttmt) cc_final: 0.8874 (mmtm) REVERT: D 1154 PHE cc_start: 0.8897 (m-80) cc_final: 0.8633 (m-80) REVERT: D 1209 THR cc_start: 0.9686 (p) cc_final: 0.9392 (p) REVERT: D 1233 ASN cc_start: 0.8627 (m110) cc_final: 0.8243 (t0) REVERT: D 1241 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: D 1243 ASN cc_start: 0.9421 (t0) cc_final: 0.9132 (t0) REVERT: D 1245 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8695 (tm-30) REVERT: D 1269 PHE cc_start: 0.8575 (t80) cc_final: 0.8035 (t80) REVERT: D 1323 TYR cc_start: 0.7131 (t80) cc_final: 0.6565 (t80) outliers start: 236 outliers final: 142 residues processed: 893 average time/residue: 0.2128 time to fit residues: 323.3019 Evaluate side-chains 813 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 654 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR 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 119 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 821 CYS Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1328 LEU Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1041 LEU Chi-restraints excluded: chain C residue 1101 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 1150 LEU Chi-restraints excluded: chain C residue 1156 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1232 THR Chi-restraints excluded: chain C residue 1239 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1056 ILE Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1241 GLN 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: 6.9990 chunk 169 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 406 optimal weight: 7.9990 chunk 392 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 381 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 385 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN A 368 GLN A 466 HIS A 566 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN A1187 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 HIS ** D 880 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 = 0.3978 r_free = 0.3978 target = 0.104249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.080867 restraints weight = 142509.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.083977 restraints weight = 87952.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.086230 restraints weight = 61682.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.087937 restraints weight = 47114.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.089195 restraints weight = 37886.267| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 41504 Z= 0.203 Angle : 0.858 11.889 56478 Z= 0.423 Chirality : 0.051 0.414 6514 Planarity : 0.006 0.074 7202 Dihedral : 6.963 51.810 5485 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.65 % Favored : 89.28 % Rotamer: Outliers : 5.06 % Allowed : 22.95 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -4.12 (0.11), residues: 5110 helix: -0.66 (0.17), residues: 830 sheet: -2.88 (0.11), residues: 1628 loop : -3.38 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 387 TYR 0.025 0.002 TYR B1007 PHE 0.025 0.002 PHE D 290 TRP 0.027 0.002 TRP A 858 HIS 0.007 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (41420) covalent geometry : angle 0.84654 / 0.42 (56270) SS BOND : bond 0.00909 / 0.63 ( 44) SS BOND : angle 1.67032 / 0.95 ( 88) hydrogen bonds : bond 0.05253 / 3.61 ( 480) hydrogen bonds : angle 5.80382 / 3.72 ( 1440) link_BETA1-4 : bond 0.00476 / 0.34 ( 12) link_BETA1-4 : angle 2.14140 / 1.52 ( 36) link_NAG-ASN : bond 0.00705 / 0.44 ( 28) link_NAG-ASN : angle 3.13866 / 2.03 ( 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 956 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 730 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8013 (p) cc_final: 0.7750 (m) REVERT: A 42 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: A 183 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7007 (mt) REVERT: A 290 PHE cc_start: 0.7498 (m-80) cc_final: 0.7272 (m-80) REVERT: A 356 ASP cc_start: 0.8622 (t0) cc_final: 0.8401 (t0) REVERT: A 393 TYR cc_start: 0.8928 (t80) cc_final: 0.8689 (t80) REVERT: A 481 ILE cc_start: 0.8868 (mp) cc_final: 0.8656 (mp) REVERT: A 539 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7578 (mtt90) REVERT: A 543 TYR cc_start: 0.7715 (p90) cc_final: 0.6911 (p90) REVERT: A 561 GLU cc_start: 0.7948 (tp30) cc_final: 0.7335 (tp30) REVERT: A 572 PHE cc_start: 0.8241 (p90) cc_final: 0.7916 (p90) REVERT: A 612 GLU cc_start: 0.8142 (tt0) cc_final: 0.7856 (tt0) REVERT: A 619 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.6848 (m-80) REVERT: A 627 LEU cc_start: 0.8743 (tp) cc_final: 0.8048 (tp) REVERT: A 666 MET cc_start: 0.8374 (tpt) cc_final: 0.7954 (tpt) REVERT: A 668 SER cc_start: 0.8736 (t) cc_final: 0.8491 (p) REVERT: A 669 PHE cc_start: 0.8832 (m-80) cc_final: 0.8563 (m-80) REVERT: A 673 MET cc_start: 0.9318 (tpp) cc_final: 0.9038 (tpp) REVERT: A 682 LYS cc_start: 0.8690 (mttt) cc_final: 0.8290 (mmmt) REVERT: A 783 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8542 (t) REVERT: A 787 ARG cc_start: 0.8235 (ptp90) cc_final: 0.8000 (ptp90) REVERT: A 793 PHE cc_start: 0.8680 (p90) cc_final: 0.8419 (p90) REVERT: A 829 GLU cc_start: 0.8698 (tp30) cc_final: 0.7653 (mp0) REVERT: A 934 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7211 (tppt) REVERT: A 964 ASN cc_start: 0.8389 (t0) cc_final: 0.8130 (t0) REVERT: A 968 MET cc_start: 0.8970 (tpt) cc_final: 0.8761 (tpt) REVERT: A 975 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8060 (mt0) REVERT: A 977 MET cc_start: 0.9477 (mmm) cc_final: 0.9082 (mmm) REVERT: A 1015 GLN cc_start: 0.8846 (tp40) cc_final: 0.8036 (tp40) REVERT: A 1017 ASN cc_start: 0.8972 (m110) cc_final: 0.8537 (m110) REVERT: A 1064 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9033 (p) REVERT: A 1065 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8756 (mm110) REVERT: A 1087 LEU cc_start: 0.9563 (tt) cc_final: 0.9253 (mt) REVERT: A 1110 LEU cc_start: 0.9426 (mt) cc_final: 0.9149 (tp) REVERT: A 1123 ASN cc_start: 0.9212 (m110) cc_final: 0.8482 (p0) REVERT: A 1178 ASP cc_start: 0.9366 (p0) cc_final: 0.8963 (p0) REVERT: A 1213 LEU cc_start: 0.9721 (tp) cc_final: 0.9463 (tp) REVERT: A 1217 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8960 (mm) REVERT: B 98 GLU cc_start: 0.8728 (tt0) cc_final: 0.8140 (tm-30) REVERT: B 121 MET cc_start: 0.8132 (tpp) cc_final: 0.7799 (tpp) REVERT: B 208 GLN cc_start: 0.8298 (tt0) cc_final: 0.7661 (tp-100) REVERT: B 318 MET cc_start: 0.8329 (mtt) cc_final: 0.8028 (tpt) REVERT: B 342 GLU cc_start: 0.8880 (tp30) cc_final: 0.8626 (tp30) REVERT: B 373 ASP cc_start: 0.7509 (t0) cc_final: 0.7218 (t0) REVERT: B 386 ILE cc_start: 0.8905 (mp) cc_final: 0.8405 (pt) REVERT: B 393 TYR cc_start: 0.8751 (t80) cc_final: 0.8030 (t80) REVERT: B 460 HIS cc_start: 0.8819 (t70) cc_final: 0.8389 (t-90) REVERT: B 542 ILE cc_start: 0.8551 (tp) cc_final: 0.7871 (mp) REVERT: B 567 LYS cc_start: 0.9252 (tppt) cc_final: 0.9012 (mmtm) REVERT: B 635 ASN cc_start: 0.8643 (p0) cc_final: 0.8190 (p0) REVERT: B 669 PHE cc_start: 0.8705 (m-80) cc_final: 0.7911 (m-80) REVERT: B 688 MET cc_start: 0.8624 (ppp) cc_final: 0.8192 (ppp) REVERT: B 762 ILE cc_start: 0.7708 (pt) cc_final: 0.7458 (pt) REVERT: B 798 MET cc_start: 0.8751 (ptt) cc_final: 0.8177 (ptt) REVERT: B 863 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8531 (ttpt) REVERT: B 964 ASN cc_start: 0.9286 (t0) cc_final: 0.8926 (t0) REVERT: B 965 LEU cc_start: 0.9292 (tt) cc_final: 0.8737 (mm) REVERT: B 985 TYR cc_start: 0.9457 (m-80) cc_final: 0.9238 (m-80) REVERT: B 988 ASP cc_start: 0.8914 (m-30) cc_final: 0.8706 (t70) REVERT: B 1076 ASP cc_start: 0.8121 (p0) cc_final: 0.7644 (p0) REVERT: B 1098 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7851 (tp30) REVERT: B 1123 ASN cc_start: 0.9400 (m110) cc_final: 0.9116 (m110) REVERT: B 1133 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8896 (tppt) REVERT: B 1161 ASP cc_start: 0.8901 (p0) cc_final: 0.8650 (p0) REVERT: B 1183 TRP cc_start: 0.9043 (m-90) cc_final: 0.8731 (m-90) REVERT: B 1208 MET cc_start: 0.8960 (ptt) cc_final: 0.8712 (ppp) REVERT: B 1217 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8843 (mm) REVERT: B 1325 GLN cc_start: 0.8381 (tt0) cc_final: 0.7613 (tp40) REVERT: B 1329 LYS cc_start: 0.8159 (ptmt) cc_final: 0.7888 (pttm) REVERT: B 1330 TYR cc_start: 0.8641 (p90) cc_final: 0.8261 (p90) REVERT: C 65 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7036 (mm-30) REVERT: C 76 ASP cc_start: 0.8845 (p0) cc_final: 0.8371 (m-30) REVERT: C 98 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8421 (tm-30) REVERT: C 121 MET cc_start: 0.7809 (ttt) cc_final: 0.7323 (tpp) REVERT: C 151 MET cc_start: 0.7861 (ttm) cc_final: 0.6891 (tpp) REVERT: C 189 GLN cc_start: 0.8768 (pm20) cc_final: 0.8332 (pp30) REVERT: C 229 PHE cc_start: 0.7212 (p90) cc_final: 0.6583 (p90) REVERT: C 272 TYR cc_start: 0.4309 (OUTLIER) cc_final: 0.3703 (t80) REVERT: C 436 TRP cc_start: 0.7832 (t-100) cc_final: 0.7462 (t-100) REVERT: C 458 PHE cc_start: 0.8446 (p90) cc_final: 0.7870 (p90) REVERT: C 460 HIS cc_start: 0.8124 (t-170) cc_final: 0.7691 (t-170) REVERT: C 499 ILE cc_start: 0.7740 (mp) cc_final: 0.7515 (tp) REVERT: C 597 LEU cc_start: 0.8829 (mp) cc_final: 0.8508 (mp) REVERT: C 635 ASN cc_start: 0.8664 (p0) cc_final: 0.8030 (p0) REVERT: C 669 PHE cc_start: 0.8596 (m-80) cc_final: 0.8042 (m-80) REVERT: C 671 GLU cc_start: 0.9077 (tt0) cc_final: 0.8714 (tt0) REVERT: C 672 ASP cc_start: 0.9151 (t0) cc_final: 0.8880 (t0) REVERT: C 688 MET cc_start: 0.8296 (ppp) cc_final: 0.7891 (ppp) REVERT: C 737 GLU cc_start: 0.8192 (mp0) cc_final: 0.7079 (mp0) REVERT: C 916 PHE cc_start: 0.8807 (m-80) cc_final: 0.8486 (m-80) REVERT: C 968 MET cc_start: 0.8921 (tpt) cc_final: 0.8650 (tpp) REVERT: C 977 MET cc_start: 0.9169 (mmm) cc_final: 0.8926 (mmm) REVERT: C 988 ASP cc_start: 0.8372 (t0) cc_final: 0.7921 (t70) REVERT: C 1015 GLN cc_start: 0.7822 (tp40) cc_final: 0.6928 (tp40) REVERT: C 1079 CYS cc_start: 0.5011 (OUTLIER) cc_final: 0.4216 (p) REVERT: C 1104 TYR cc_start: 0.8663 (t80) cc_final: 0.8243 (t80) REVERT: C 1129 GLU cc_start: 0.9401 (pt0) cc_final: 0.9018 (pp20) REVERT: C 1140 HIS cc_start: 0.8751 (p-80) cc_final: 0.8482 (p90) REVERT: C 1205 GLU cc_start: 0.8763 (pm20) cc_final: 0.7998 (pm20) REVERT: C 1258 LEU cc_start: 0.9268 (mp) cc_final: 0.9007 (mp) REVERT: D 98 GLU cc_start: 0.8944 (tt0) cc_final: 0.8680 (tp30) REVERT: D 108 LYS cc_start: 0.9322 (mmtt) cc_final: 0.8790 (mmmt) REVERT: D 203 TYR cc_start: 0.7584 (m-80) cc_final: 0.6317 (m-80) REVERT: D 290 PHE cc_start: 0.8564 (m-80) cc_final: 0.8279 (m-10) REVERT: D 325 GLN cc_start: 0.8501 (mp10) cc_final: 0.8220 (mp10) REVERT: D 368 GLN cc_start: 0.8500 (pt0) cc_final: 0.8137 (mp10) REVERT: D 381 ASN cc_start: 0.9017 (m-40) cc_final: 0.8700 (p0) REVERT: D 408 SER cc_start: 0.9007 (OUTLIER) cc_final: 0.8672 (m) REVERT: D 531 LYS cc_start: 0.8917 (mttm) cc_final: 0.8505 (mtmm) REVERT: D 542 ILE cc_start: 0.8542 (tt) cc_final: 0.8099 (mp) REVERT: D 557 LYS cc_start: 0.8885 (mttp) cc_final: 0.8516 (mmtm) REVERT: D 561 GLU cc_start: 0.8121 (tp30) cc_final: 0.7758 (tp30) REVERT: D 669 PHE cc_start: 0.8718 (m-80) cc_final: 0.8126 (m-80) REVERT: D 671 GLU cc_start: 0.8720 (tt0) cc_final: 0.8118 (mm-30) REVERT: D 673 MET cc_start: 0.9009 (tpp) cc_final: 0.8450 (tpp) REVERT: D 682 LYS cc_start: 0.8576 (mttt) cc_final: 0.8328 (mmtp) REVERT: D 737 GLU cc_start: 0.8294 (mp0) cc_final: 0.7909 (mp0) REVERT: D 739 TRP cc_start: 0.7910 (t60) cc_final: 0.7608 (t60) REVERT: D 758 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7461 (p) REVERT: D 764 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8310 (mp0) REVERT: D 766 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7716 (mmtm) REVERT: D 912 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7517 (ptpp) REVERT: D 915 THR cc_start: 0.9179 (t) cc_final: 0.8797 (m) REVERT: D 957 SER cc_start: 0.8710 (t) cc_final: 0.8324 (m) REVERT: D 965 LEU cc_start: 0.8835 (tp) cc_final: 0.8572 (mp) REVERT: D 999 GLU cc_start: 0.9254 (mp0) cc_final: 0.9020 (mp0) REVERT: D 1076 ASP cc_start: 0.7886 (p0) cc_final: 0.7549 (p0) REVERT: D 1089 ASN cc_start: 0.8830 (p0) cc_final: 0.8332 (p0) REVERT: D 1123 ASN cc_start: 0.9406 (m110) cc_final: 0.8670 (p0) REVERT: D 1133 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8788 (tppt) REVERT: D 1147 LYS cc_start: 0.9318 (mttp) cc_final: 0.8876 (mttp) REVERT: D 1154 PHE cc_start: 0.9030 (m-80) cc_final: 0.8752 (m-80) REVERT: D 1209 THR cc_start: 0.9703 (p) cc_final: 0.9471 (p) REVERT: D 1233 ASN cc_start: 0.8733 (m110) cc_final: 0.8384 (t0) REVERT: D 1241 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: D 1243 ASN cc_start: 0.9422 (t0) cc_final: 0.9120 (t0) REVERT: D 1245 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8737 (tm-30) REVERT: D 1269 PHE cc_start: 0.8498 (t80) cc_final: 0.7929 (t80) REVERT: D 1323 TYR cc_start: 0.6966 (t80) cc_final: 0.6366 (t80) outliers start: 226 outliers final: 145 residues processed: 892 average time/residue: 0.2159 time to fit residues: 327.6597 Evaluate side-chains 817 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 658 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 821 CYS Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1177 LYS Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1328 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 525 SER Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1096 GLU Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1239 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 751 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1056 ILE Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1241 GLN 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: 0.3980 chunk 417 optimal weight: 10.0000 chunk 409 optimal weight: 8.9990 chunk 451 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 397 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 456 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 ASN A1072 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN B 827 GLN ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 ASN D 132 GLN ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 GLN ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 GLN D 983 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.100953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.077791 restraints weight = 146477.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.080748 restraints weight = 90547.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.082946 restraints weight = 63889.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.084556 restraints weight = 48801.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.085701 restraints weight = 39650.816| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 41504 Z= 0.265 Angle : 0.900 12.884 56478 Z= 0.446 Chirality : 0.052 0.407 6514 Planarity : 0.006 0.102 7202 Dihedral : 6.978 52.997 5481 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.35 % Favored : 87.55 % Rotamer: Outliers : 6.42 % Allowed : 23.65 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -4.11 (0.10), residues: 5110 helix: -0.75 (0.17), residues: 826 sheet: -2.84 (0.11), residues: 1606 loop : -3.36 (0.11), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 360 TYR 0.028 0.002 TYR B 138 PHE 0.022 0.002 PHE A 219 TRP 0.040 0.003 TRP A 858 HIS 0.011 0.001 HIS C 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.26 (41420) covalent geometry : angle 0.89048 / 0.44 (56270) SS BOND : bond 0.00608 / 0.37 ( 44) SS BOND : angle 1.50371 / 0.83 ( 88) hydrogen bonds : bond 0.05322 / 3.65 ( 480) hydrogen bonds : angle 6.00854 / 3.85 ( 1440) link_BETA1-4 : bond 0.00486 / 0.32 ( 12) link_BETA1-4 : angle 2.13817 / 1.50 ( 36) link_NAG-ASN : bond 0.00839 / 0.51 ( 28) link_NAG-ASN : angle 3.06126 / 2.01 ( 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 965 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 678 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: A 77 LEU cc_start: 0.8742 (tp) cc_final: 0.8071 (mp) REVERT: A 183 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.6899 (mt) REVERT: A 272 TYR cc_start: 0.4355 (OUTLIER) cc_final: 0.3004 (t80) REVERT: A 290 PHE cc_start: 0.7434 (m-80) cc_final: 0.7169 (m-80) REVERT: A 318 MET cc_start: 0.8860 (tpp) cc_final: 0.8587 (tpp) REVERT: A 356 ASP cc_start: 0.8519 (t0) cc_final: 0.8217 (t0) REVERT: A 393 TYR cc_start: 0.8947 (t80) cc_final: 0.8696 (t80) REVERT: A 505 ILE cc_start: 0.4235 (OUTLIER) cc_final: 0.3661 (mm) REVERT: A 539 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7600 (mtt90) REVERT: A 543 TYR cc_start: 0.7920 (p90) cc_final: 0.7154 (p90) REVERT: A 561 GLU cc_start: 0.8043 (tp30) cc_final: 0.7399 (tp30) REVERT: A 566 ASN cc_start: 0.8370 (t0) cc_final: 0.8009 (t0) REVERT: A 572 PHE cc_start: 0.8350 (p90) cc_final: 0.7990 (p90) REVERT: A 607 MET cc_start: 0.8235 (tmm) cc_final: 0.7946 (tpp) REVERT: A 612 GLU cc_start: 0.8147 (tt0) cc_final: 0.7712 (tt0) REVERT: A 627 LEU cc_start: 0.8753 (tp) cc_final: 0.7967 (tp) REVERT: A 668 SER cc_start: 0.8812 (t) cc_final: 0.8561 (p) REVERT: A 669 PHE cc_start: 0.8812 (m-80) cc_final: 0.8559 (m-80) REVERT: A 673 MET cc_start: 0.9303 (tpp) cc_final: 0.8793 (tpp) REVERT: A 682 LYS cc_start: 0.8691 (mttt) cc_final: 0.8282 (mmmt) REVERT: A 783 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8696 (t) REVERT: A 787 ARG cc_start: 0.8254 (ptp90) cc_final: 0.8026 (ptp90) REVERT: A 793 PHE cc_start: 0.8686 (p90) cc_final: 0.8485 (p90) REVERT: A 829 GLU cc_start: 0.8489 (tp30) cc_final: 0.7618 (mp0) REVERT: A 959 MET cc_start: 0.8067 (pmm) cc_final: 0.7857 (pmm) REVERT: A 964 ASN cc_start: 0.8475 (t0) cc_final: 0.8233 (t0) REVERT: A 975 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8125 (mt0) REVERT: A 977 MET cc_start: 0.9446 (mmm) cc_final: 0.9055 (mmm) REVERT: A 999 GLU cc_start: 0.9147 (mp0) cc_final: 0.8794 (pm20) REVERT: A 1015 GLN cc_start: 0.8938 (tp40) cc_final: 0.8143 (tp40) REVERT: A 1017 ASN cc_start: 0.9026 (m-40) cc_final: 0.8586 (m110) REVERT: A 1034 ARG cc_start: 0.9325 (ppt170) cc_final: 0.8976 (pmt-80) REVERT: A 1035 ASN cc_start: 0.8819 (t0) cc_final: 0.8566 (t0) REVERT: A 1044 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8863 (m-80) REVERT: A 1064 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9063 (p) REVERT: A 1065 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8810 (mm110) REVERT: A 1087 LEU cc_start: 0.9573 (tt) cc_final: 0.9230 (mt) REVERT: A 1110 LEU cc_start: 0.9470 (mt) cc_final: 0.9216 (tp) REVERT: A 1178 ASP cc_start: 0.9380 (p0) cc_final: 0.8990 (p0) REVERT: A 1213 LEU cc_start: 0.9717 (tp) cc_final: 0.9469 (tp) REVERT: A 1217 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8967 (mm) REVERT: B 98 GLU cc_start: 0.8704 (tt0) cc_final: 0.8222 (tm-30) REVERT: B 151 MET cc_start: 0.7152 (ttm) cc_final: 0.6526 (ttm) REVERT: B 342 GLU cc_start: 0.8871 (tp30) cc_final: 0.8640 (tp30) REVERT: B 384 ILE cc_start: 0.9361 (pt) cc_final: 0.9104 (mm) REVERT: B 386 ILE cc_start: 0.9124 (mp) cc_final: 0.8507 (pt) REVERT: B 393 TYR cc_start: 0.8803 (t80) cc_final: 0.8151 (t80) REVERT: B 421 VAL cc_start: 0.8447 (t) cc_final: 0.8210 (p) REVERT: B 460 HIS cc_start: 0.8866 (t70) cc_final: 0.8520 (t-90) REVERT: B 567 LYS cc_start: 0.9278 (tppt) cc_final: 0.8974 (mmmt) REVERT: B 669 PHE cc_start: 0.8779 (m-80) cc_final: 0.8005 (m-80) REVERT: B 688 MET cc_start: 0.8643 (ppp) cc_final: 0.8217 (ppp) REVERT: B 798 MET cc_start: 0.8813 (ptt) cc_final: 0.8160 (ptt) REVERT: B 858 TRP cc_start: 0.7312 (m-90) cc_final: 0.6906 (m-90) REVERT: B 964 ASN cc_start: 0.9263 (t0) cc_final: 0.8896 (t0) REVERT: B 965 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8820 (mm) REVERT: B 977 MET cc_start: 0.9390 (mmm) cc_final: 0.9169 (mmm) REVERT: B 1013 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8520 (mm-40) REVERT: B 1076 ASP cc_start: 0.8355 (p0) cc_final: 0.7901 (p0) REVERT: B 1098 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8028 (tp30) REVERT: B 1123 ASN cc_start: 0.9456 (m110) cc_final: 0.9179 (m110) REVERT: B 1133 LYS cc_start: 0.9184 (ttmt) cc_final: 0.8964 (tppt) REVERT: B 1161 ASP cc_start: 0.8970 (p0) cc_final: 0.8719 (p0) REVERT: B 1168 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8711 (mttp) REVERT: B 1217 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8770 (mm) REVERT: B 1325 GLN cc_start: 0.8475 (tt0) cc_final: 0.7864 (tp-100) REVERT: B 1330 TYR cc_start: 0.8674 (p90) cc_final: 0.8279 (p90) REVERT: C 65 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6994 (mm-30) REVERT: C 76 ASP cc_start: 0.8767 (p0) cc_final: 0.8280 (m-30) REVERT: C 98 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8449 (tm-30) REVERT: C 121 MET cc_start: 0.7782 (ttt) cc_final: 0.7495 (tpp) REVERT: C 151 MET cc_start: 0.8068 (ttm) cc_final: 0.7724 (tpp) REVERT: C 189 GLN cc_start: 0.8798 (pm20) cc_final: 0.8439 (pp30) REVERT: C 272 TYR cc_start: 0.4746 (OUTLIER) cc_final: 0.4056 (t80) REVERT: C 436 TRP cc_start: 0.7895 (t-100) cc_final: 0.7494 (t-100) REVERT: C 456 LYS cc_start: 0.9378 (mmtt) cc_final: 0.8898 (tptt) REVERT: C 458 PHE cc_start: 0.8472 (p90) cc_final: 0.8070 (p90) REVERT: C 462 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: C 499 ILE cc_start: 0.7464 (mp) cc_final: 0.7198 (tp) REVERT: C 635 ASN cc_start: 0.8612 (p0) cc_final: 0.7935 (p0) REVERT: C 669 PHE cc_start: 0.8763 (m-80) cc_final: 0.8107 (m-80) REVERT: C 671 GLU cc_start: 0.9163 (tt0) cc_final: 0.8726 (mt-10) REVERT: C 672 ASP cc_start: 0.9186 (t0) cc_final: 0.8896 (t0) REVERT: C 737 GLU cc_start: 0.8187 (mp0) cc_final: 0.7052 (mp0) REVERT: C 751 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7755 (p) REVERT: C 798 MET cc_start: 0.5242 (ptt) cc_final: 0.4974 (ptt) REVERT: C 800 TYR cc_start: 0.7806 (p90) cc_final: 0.7590 (p90) REVERT: C 916 PHE cc_start: 0.8771 (m-80) cc_final: 0.8513 (m-80) REVERT: C 965 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8607 (mp) REVERT: C 968 MET cc_start: 0.8924 (tpt) cc_final: 0.8615 (tpp) REVERT: C 977 MET cc_start: 0.9141 (mmm) cc_final: 0.8901 (mmm) REVERT: C 988 ASP cc_start: 0.8484 (t0) cc_final: 0.8026 (t70) REVERT: C 1015 GLN cc_start: 0.7831 (tp40) cc_final: 0.6955 (tp40) REVERT: C 1018 TYR cc_start: 0.7593 (m-10) cc_final: 0.7365 (m-10) REVERT: C 1079 CYS cc_start: 0.5001 (OUTLIER) cc_final: 0.4100 (p) REVERT: C 1104 TYR cc_start: 0.8695 (t80) cc_final: 0.8303 (t80) REVERT: C 1140 HIS cc_start: 0.8763 (p-80) cc_final: 0.8486 (p90) REVERT: C 1205 GLU cc_start: 0.8895 (pm20) cc_final: 0.8164 (pm20) REVERT: D 98 GLU cc_start: 0.8945 (tt0) cc_final: 0.8625 (tp30) REVERT: D 108 LYS cc_start: 0.9434 (mmtt) cc_final: 0.8929 (mmmt) REVERT: D 151 MET cc_start: 0.7669 (mtm) cc_final: 0.7314 (mpp) REVERT: D 203 TYR cc_start: 0.7575 (m-80) cc_final: 0.6346 (m-80) REVERT: D 290 PHE cc_start: 0.8737 (m-80) cc_final: 0.8450 (m-10) REVERT: D 325 GLN cc_start: 0.8586 (mp10) cc_final: 0.8267 (mp10) REVERT: D 368 GLN cc_start: 0.8556 (pt0) cc_final: 0.8161 (mp10) REVERT: D 381 ASN cc_start: 0.9075 (m-40) cc_final: 0.8744 (p0) REVERT: D 542 ILE cc_start: 0.8585 (tt) cc_final: 0.8089 (mp) REVERT: D 557 LYS cc_start: 0.8841 (mttp) cc_final: 0.8583 (mmtp) REVERT: D 561 GLU cc_start: 0.8291 (tp30) cc_final: 0.7930 (tp30) REVERT: D 637 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7867 (pp30) REVERT: D 669 PHE cc_start: 0.8753 (m-80) cc_final: 0.8181 (m-80) REVERT: D 671 GLU cc_start: 0.8791 (tt0) cc_final: 0.8309 (mm-30) REVERT: D 673 MET cc_start: 0.8975 (tpp) cc_final: 0.8598 (tpp) REVERT: D 682 LYS cc_start: 0.8588 (mttt) cc_final: 0.8368 (mmtp) REVERT: D 739 TRP cc_start: 0.8080 (t60) cc_final: 0.7380 (t60) REVERT: D 758 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7452 (p) REVERT: D 764 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8467 (mp0) REVERT: D 766 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7732 (mmtm) REVERT: D 915 THR cc_start: 0.9248 (t) cc_final: 0.8937 (m) REVERT: D 957 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8348 (m) REVERT: D 965 LEU cc_start: 0.8823 (tp) cc_final: 0.8538 (mp) REVERT: D 999 GLU cc_start: 0.9166 (mp0) cc_final: 0.8898 (mp0) REVERT: D 1010 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8207 (t) REVERT: D 1076 ASP cc_start: 0.7933 (p0) cc_final: 0.7597 (p0) REVERT: D 1089 ASN cc_start: 0.8886 (p0) cc_final: 0.8343 (p0) REVERT: D 1105 ILE cc_start: 0.8958 (mt) cc_final: 0.8574 (mt) REVERT: D 1133 LYS cc_start: 0.9265 (ttmt) cc_final: 0.8850 (tppt) REVERT: D 1209 THR cc_start: 0.9684 (p) cc_final: 0.9394 (p) REVERT: D 1233 ASN cc_start: 0.8937 (m110) cc_final: 0.8511 (t0) REVERT: D 1243 ASN cc_start: 0.9429 (t0) cc_final: 0.9124 (t0) REVERT: D 1245 GLN cc_start: 0.9227 (tm-30) cc_final: 0.8799 (tm-30) REVERT: D 1269 PHE cc_start: 0.8603 (t80) cc_final: 0.8005 (t80) REVERT: D 1323 TYR cc_start: 0.6961 (t80) cc_final: 0.6371 (t80) outliers start: 287 outliers final: 200 residues processed: 886 average time/residue: 0.2025 time to fit residues: 308.2281 Evaluate side-chains 852 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 632 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 525 SER Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 751 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 792 PHE Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1041 LEU Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1096 GLU Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1239 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1316 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 751 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 983 ASN Chi-restraints excluded: chain D residue 1010 THR Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1056 ILE Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1270 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: 0.9980 chunk 445 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 384 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 289 optimal weight: 7.9990 chunk 419 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS A 637 GLN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN B 441 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 GLN ** D 880 GLN ** 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 = 0.3959 r_free = 0.3959 target = 0.102954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.079462 restraints weight = 143862.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.082543 restraints weight = 88241.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.084773 restraints weight = 61756.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.086445 restraints weight = 47191.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087529 restraints weight = 38093.345| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4646 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= 0.181 Angle : 0.840 14.364 56478 Z= 0.409 Chirality : 0.051 0.422 6514 Planarity : 0.005 0.083 7202 Dihedral : 6.628 50.043 5481 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.61 % Favored : 89.30 % Rotamer: Outliers : 5.48 % Allowed : 25.73 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -3.90 (0.11), residues: 5110 helix: -0.46 (0.17), residues: 828 sheet: -2.73 (0.11), residues: 1634 loop : -3.26 (0.11), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 360 TYR 0.034 0.002 TYR D 256 PHE 0.027 0.002 PHE C 359 TRP 0.037 0.002 TRP B 741 HIS 0.007 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (41420) covalent geometry : angle 0.83059 / 0.41 (56270) SS BOND : bond 0.00507 / 0.33 ( 44) SS BOND : angle 1.28382 / 0.72 ( 88) hydrogen bonds : bond 0.05038 / 3.45 ( 480) hydrogen bonds : angle 5.68837 / 3.64 ( 1440) link_BETA1-4 : bond 0.00456 / 0.30 ( 12) link_BETA1-4 : angle 2.08267 / 1.49 ( 36) link_NAG-ASN : bond 0.00703 / 0.41 ( 28) link_NAG-ASN : angle 2.93134 / 1.93 ( 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 927 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 682 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8089 (p) cc_final: 0.7823 (m) REVERT: A 42 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: A 125 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8103 (pp20) REVERT: A 151 MET cc_start: 0.5897 (tpp) cc_final: 0.5626 (tpp) REVERT: A 183 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.6895 (mt) REVERT: A 272 TYR cc_start: 0.4349 (OUTLIER) cc_final: 0.2987 (t80) REVERT: A 290 PHE cc_start: 0.7484 (m-80) cc_final: 0.7096 (m-80) REVERT: A 318 MET cc_start: 0.8887 (tpp) cc_final: 0.8324 (tpp) REVERT: A 356 ASP cc_start: 0.8453 (t0) cc_final: 0.8187 (t0) REVERT: A 393 TYR cc_start: 0.8873 (t80) cc_final: 0.8619 (t80) REVERT: A 460 HIS cc_start: 0.8470 (t-90) cc_final: 0.8207 (t-90) REVERT: A 539 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7705 (mtt90) REVERT: A 543 TYR cc_start: 0.7777 (p90) cc_final: 0.6988 (p90) REVERT: A 561 GLU cc_start: 0.8047 (tp30) cc_final: 0.7452 (tp30) REVERT: A 572 PHE cc_start: 0.8331 (p90) cc_final: 0.7982 (p90) REVERT: A 607 MET cc_start: 0.8339 (tmm) cc_final: 0.8020 (tpp) REVERT: A 612 GLU cc_start: 0.8155 (tt0) cc_final: 0.7685 (tt0) REVERT: A 619 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7160 (m-10) REVERT: A 627 LEU cc_start: 0.8720 (tp) cc_final: 0.8236 (tp) REVERT: A 669 PHE cc_start: 0.8826 (m-80) cc_final: 0.8517 (m-80) REVERT: A 682 LYS cc_start: 0.8669 (mttt) cc_final: 0.8269 (mmmt) REVERT: A 783 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8634 (t) REVERT: A 787 ARG cc_start: 0.8183 (ptp90) cc_final: 0.7906 (ptp90) REVERT: A 793 PHE cc_start: 0.8764 (p90) cc_final: 0.8524 (p90) REVERT: A 829 GLU cc_start: 0.8572 (tp30) cc_final: 0.7729 (mp0) REVERT: A 959 MET cc_start: 0.8122 (pmm) cc_final: 0.7871 (pmm) REVERT: A 964 ASN cc_start: 0.8397 (t0) cc_final: 0.8167 (t0) REVERT: A 975 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8097 (mt0) REVERT: A 977 MET cc_start: 0.9448 (mmm) cc_final: 0.9089 (mmm) REVERT: A 1015 GLN cc_start: 0.8898 (tp40) cc_final: 0.8182 (tp40) REVERT: A 1017 ASN cc_start: 0.9039 (m-40) cc_final: 0.8600 (m110) REVERT: A 1034 ARG cc_start: 0.9336 (ppt170) cc_final: 0.9006 (pmt-80) REVERT: A 1035 ASN cc_start: 0.8829 (t0) cc_final: 0.8586 (t0) REVERT: A 1064 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.9096 (p) REVERT: A 1065 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8740 (mm110) REVERT: A 1076 ASP cc_start: 0.8355 (m-30) cc_final: 0.7910 (m-30) REVERT: A 1080 PHE cc_start: 0.8255 (m-80) cc_final: 0.7973 (m-10) REVERT: A 1087 LEU cc_start: 0.9585 (tt) cc_final: 0.9310 (mt) REVERT: A 1110 LEU cc_start: 0.9463 (mt) cc_final: 0.9150 (tp) REVERT: A 1111 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8218 (mm-30) REVERT: A 1123 ASN cc_start: 0.9236 (m110) cc_final: 0.8515 (p0) REVERT: A 1178 ASP cc_start: 0.9365 (p0) cc_final: 0.8973 (p0) REVERT: A 1208 MET cc_start: 0.9336 (ppp) cc_final: 0.9016 (ppp) REVERT: A 1213 LEU cc_start: 0.9699 (tp) cc_final: 0.9407 (tp) REVERT: A 1217 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8982 (mm) REVERT: A 1330 TYR cc_start: 0.8239 (p90) cc_final: 0.7294 (p90) REVERT: B 98 GLU cc_start: 0.8609 (tt0) cc_final: 0.8112 (tm-30) REVERT: B 208 GLN cc_start: 0.8488 (tt0) cc_final: 0.7796 (tp-100) REVERT: B 342 GLU cc_start: 0.8785 (tp30) cc_final: 0.8534 (tp30) REVERT: B 393 TYR cc_start: 0.8715 (t80) cc_final: 0.8332 (t80) REVERT: B 460 HIS cc_start: 0.8823 (t70) cc_final: 0.8450 (t-90) REVERT: B 542 ILE cc_start: 0.8502 (tp) cc_final: 0.7849 (mp) REVERT: B 567 LYS cc_start: 0.9257 (tppt) cc_final: 0.9028 (mmtm) REVERT: B 669 PHE cc_start: 0.8678 (m-80) cc_final: 0.7979 (m-80) REVERT: B 688 MET cc_start: 0.8612 (ppp) cc_final: 0.8122 (ppp) REVERT: B 798 MET cc_start: 0.8805 (ptt) cc_final: 0.8125 (ptt) REVERT: B 858 TRP cc_start: 0.7235 (m-90) cc_final: 0.6792 (m-90) REVERT: B 964 ASN cc_start: 0.9268 (t0) cc_final: 0.8944 (t0) REVERT: B 965 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8792 (mm) REVERT: B 1013 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8638 (mm-40) REVERT: B 1076 ASP cc_start: 0.8306 (p0) cc_final: 0.7854 (p0) REVERT: B 1098 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8080 (tp30) REVERT: B 1123 ASN cc_start: 0.9410 (m110) cc_final: 0.9126 (m110) REVERT: B 1133 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8892 (tppt) REVERT: B 1161 ASP cc_start: 0.8933 (p0) cc_final: 0.8695 (p0) REVERT: B 1168 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8625 (mttp) REVERT: B 1183 TRP cc_start: 0.9180 (m-90) cc_final: 0.8775 (m-90) REVERT: B 1184 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8710 (mt-10) REVERT: B 1217 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 1325 GLN cc_start: 0.8364 (tt0) cc_final: 0.7841 (tp-100) REVERT: B 1330 TYR cc_start: 0.8662 (p90) cc_final: 0.8255 (p90) REVERT: C 65 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7197 (mm-30) REVERT: C 76 ASP cc_start: 0.8850 (p0) cc_final: 0.8415 (m-30) REVERT: C 98 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 121 MET cc_start: 0.7800 (ttt) cc_final: 0.7325 (tpp) REVERT: C 151 MET cc_start: 0.8042 (ttm) cc_final: 0.7701 (tpp) REVERT: C 189 GLN cc_start: 0.8836 (pm20) cc_final: 0.8445 (pp30) REVERT: C 207 VAL cc_start: 0.9175 (m) cc_final: 0.8385 (p) REVERT: C 215 THR cc_start: 0.9200 (m) cc_final: 0.8721 (p) REVERT: C 272 TYR cc_start: 0.4406 (OUTLIER) cc_final: 0.3761 (t80) REVERT: C 393 TYR cc_start: 0.8876 (t80) cc_final: 0.8638 (t80) REVERT: C 436 TRP cc_start: 0.7939 (t-100) cc_final: 0.7544 (t-100) REVERT: C 458 PHE cc_start: 0.8422 (p90) cc_final: 0.7814 (p90) REVERT: C 462 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: C 539 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7241 (mtt90) REVERT: C 635 ASN cc_start: 0.8678 (p0) cc_final: 0.8028 (p0) REVERT: C 669 PHE cc_start: 0.8752 (m-80) cc_final: 0.8132 (m-80) REVERT: C 671 GLU cc_start: 0.9051 (tt0) cc_final: 0.8685 (mt-10) REVERT: C 672 ASP cc_start: 0.9194 (t0) cc_final: 0.8678 (t0) REVERT: C 673 MET cc_start: 0.9127 (tpp) cc_final: 0.8596 (tpp) REVERT: C 737 GLU cc_start: 0.8068 (mp0) cc_final: 0.7162 (mp0) REVERT: C 916 PHE cc_start: 0.8788 (m-80) cc_final: 0.8497 (m-80) REVERT: C 965 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8622 (mp) REVERT: C 988 ASP cc_start: 0.8326 (t0) cc_final: 0.7942 (t70) REVERT: C 1015 GLN cc_start: 0.7930 (tp40) cc_final: 0.7185 (tp40) REVERT: C 1079 CYS cc_start: 0.4883 (OUTLIER) cc_final: 0.4034 (p) REVERT: C 1104 TYR cc_start: 0.8753 (t80) cc_final: 0.8358 (t80) REVERT: C 1129 GLU cc_start: 0.9461 (pt0) cc_final: 0.9142 (pp20) REVERT: C 1140 HIS cc_start: 0.8780 (p-80) cc_final: 0.8500 (p90) REVERT: C 1205 GLU cc_start: 0.8879 (pm20) cc_final: 0.8154 (pm20) REVERT: C 1258 LEU cc_start: 0.9260 (mp) cc_final: 0.8981 (mp) REVERT: D 32 MET cc_start: 0.8602 (mtp) cc_final: 0.8225 (tpp) REVERT: D 98 GLU cc_start: 0.8984 (tt0) cc_final: 0.8698 (tp30) REVERT: D 108 LYS cc_start: 0.9407 (mmtt) cc_final: 0.8892 (mmmt) REVERT: D 151 MET cc_start: 0.7827 (mtm) cc_final: 0.7255 (mpp) REVERT: D 203 TYR cc_start: 0.7512 (m-80) cc_final: 0.6317 (m-80) REVERT: D 290 PHE cc_start: 0.8751 (m-80) cc_final: 0.8435 (m-10) REVERT: D 325 GLN cc_start: 0.8612 (mp10) cc_final: 0.8309 (mp10) REVERT: D 381 ASN cc_start: 0.9081 (m-40) cc_final: 0.8753 (p0) REVERT: D 542 ILE cc_start: 0.8489 (tt) cc_final: 0.8068 (mp) REVERT: D 557 LYS cc_start: 0.8870 (mttp) cc_final: 0.8470 (mmtp) REVERT: D 561 GLU cc_start: 0.8178 (tp30) cc_final: 0.7825 (tp30) REVERT: D 634 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8076 (pp) REVERT: D 637 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7961 (pp30) REVERT: D 669 PHE cc_start: 0.8731 (m-80) cc_final: 0.8159 (m-80) REVERT: D 671 GLU cc_start: 0.8650 (tt0) cc_final: 0.8120 (mm-30) REVERT: D 673 MET cc_start: 0.8983 (tpp) cc_final: 0.8290 (tpp) REVERT: D 682 LYS cc_start: 0.8522 (mttt) cc_final: 0.8300 (mmtp) REVERT: D 739 TRP cc_start: 0.8089 (t60) cc_final: 0.7738 (t60) REVERT: D 758 VAL cc_start: 0.7957 (OUTLIER) cc_final: 0.7436 (p) REVERT: D 764 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: D 766 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7747 (mmtm) REVERT: D 915 THR cc_start: 0.9240 (t) cc_final: 0.8911 (m) REVERT: D 957 SER cc_start: 0.8703 (t) cc_final: 0.8331 (m) REVERT: D 965 LEU cc_start: 0.8922 (tp) cc_final: 0.8651 (mt) REVERT: D 999 GLU cc_start: 0.9167 (mp0) cc_final: 0.8921 (mp0) REVERT: D 1076 ASP cc_start: 0.7871 (p0) cc_final: 0.7521 (p0) REVERT: D 1089 ASN cc_start: 0.8836 (p0) cc_final: 0.8275 (p0) REVERT: D 1123 ASN cc_start: 0.9436 (m-40) cc_final: 0.8776 (p0) REVERT: D 1133 LYS cc_start: 0.9226 (ttmt) cc_final: 0.8840 (tppt) REVERT: D 1150 LEU cc_start: 0.9637 (mm) cc_final: 0.9356 (mm) REVERT: D 1154 PHE cc_start: 0.8923 (m-80) cc_final: 0.8307 (m-80) REVERT: D 1183 TRP cc_start: 0.8965 (OUTLIER) cc_final: 0.8504 (m100) REVERT: D 1209 THR cc_start: 0.9654 (p) cc_final: 0.9386 (p) REVERT: D 1233 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8499 (t0) REVERT: D 1243 ASN cc_start: 0.9429 (t0) cc_final: 0.9128 (t0) REVERT: D 1245 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8764 (tm-30) REVERT: D 1269 PHE cc_start: 0.8594 (t80) cc_final: 0.7775 (t80) REVERT: D 1323 TYR cc_start: 0.6851 (t80) cc_final: 0.6283 (t80) outliers start: 245 outliers final: 166 residues processed: 859 average time/residue: 0.2230 time to fit residues: 328.9043 Evaluate side-chains 818 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 631 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1096 GLU Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1239 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 751 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 GLU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 983 ASN Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1056 ILE Chi-restraints excluded: chain D residue 1116 VAL Chi-restraints excluded: chain D residue 1183 TRP Chi-restraints excluded: chain D residue 1233 ASN Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 503 optimal weight: 0.7980 chunk 121 optimal weight: 20.0000 chunk 116 optimal weight: 0.7980 chunk 448 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 422 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 353 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN A1072 GLN A1242 GLN ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 GLN D 827 GLN ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 ASN D1233 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.105297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.081593 restraints weight = 139826.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.084778 restraints weight = 85371.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.087098 restraints weight = 59465.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.088813 restraints weight = 45132.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.090121 restraints weight = 36293.018| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41504 Z= 0.141 Angle : 0.820 14.263 56478 Z= 0.391 Chirality : 0.050 0.421 6514 Planarity : 0.005 0.064 7202 Dihedral : 6.199 50.226 5480 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.06 % Favored : 89.88 % Rotamer: Outliers : 4.63 % Allowed : 27.27 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -3.64 (0.11), residues: 5110 helix: -0.21 (0.17), residues: 836 sheet: -2.50 (0.12), residues: 1598 loop : -3.16 (0.11), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 360 TYR 0.032 0.001 TYR D 256 PHE 0.029 0.002 PHE B1028 TRP 0.025 0.002 TRP B 741 HIS 0.034 0.001 HIS B 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (41420) covalent geometry : angle 0.81141 / 0.39 (56270) SS BOND : bond 0.00673 / 0.38 ( 44) SS BOND : angle 1.04152 / 0.59 ( 88) hydrogen bonds : bond 0.04841 / 3.29 ( 480) hydrogen bonds : angle 5.47272 / 3.52 ( 1440) link_BETA1-4 : bond 0.00727 / 0.48 ( 12) link_BETA1-4 : angle 2.08997 / 1.48 ( 36) link_NAG-ASN : bond 0.00666 / 0.38 ( 28) link_NAG-ASN : angle 2.84288 / 1.87 ( 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 909 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 702 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8029 (p) cc_final: 0.7768 (m) REVERT: A 42 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: A 125 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: A 151 MET cc_start: 0.5859 (tpp) cc_final: 0.5487 (tpp) REVERT: A 183 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.6804 (mt) REVERT: A 272 TYR cc_start: 0.4262 (OUTLIER) cc_final: 0.3041 (t80) REVERT: A 318 MET cc_start: 0.8859 (tpp) cc_final: 0.8303 (tpp) REVERT: A 356 ASP cc_start: 0.8433 (t0) cc_final: 0.8158 (t0) REVERT: A 360 ARG cc_start: 0.8153 (tpt170) cc_final: 0.7914 (tpt170) REVERT: A 393 TYR cc_start: 0.8839 (t80) cc_final: 0.8585 (t80) REVERT: A 436 TRP cc_start: 0.6908 (t-100) cc_final: 0.6622 (t-100) REVERT: A 460 HIS cc_start: 0.8423 (t-90) cc_final: 0.8128 (t-90) REVERT: A 543 TYR cc_start: 0.7494 (p90) cc_final: 0.6560 (p90) REVERT: A 561 GLU cc_start: 0.8048 (tp30) cc_final: 0.7477 (tp30) REVERT: A 572 PHE cc_start: 0.8182 (p90) cc_final: 0.7865 (p90) REVERT: A 607 MET cc_start: 0.8346 (tmm) cc_final: 0.7952 (tmm) REVERT: A 612 GLU cc_start: 0.8097 (tt0) cc_final: 0.7850 (tt0) REVERT: A 619 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7092 (m-10) REVERT: A 627 LEU cc_start: 0.8755 (tp) cc_final: 0.8313 (tt) REVERT: A 666 MET cc_start: 0.8277 (tpt) cc_final: 0.7780 (tpt) REVERT: A 669 PHE cc_start: 0.8734 (m-80) cc_final: 0.8427 (m-80) REVERT: A 682 LYS cc_start: 0.8659 (mttt) cc_final: 0.8226 (mmmt) REVERT: A 783 THR cc_start: 0.8776 (p) cc_final: 0.8555 (t) REVERT: A 787 ARG cc_start: 0.8138 (ptp90) cc_final: 0.7857 (ptp90) REVERT: A 829 GLU cc_start: 0.8534 (tp30) cc_final: 0.7791 (mp0) REVERT: A 870 PHE cc_start: 0.5666 (m-80) cc_final: 0.4921 (m-80) REVERT: A 964 ASN cc_start: 0.8392 (t0) cc_final: 0.8153 (t0) REVERT: A 975 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8062 (mt0) REVERT: A 977 MET cc_start: 0.9393 (mmm) cc_final: 0.9059 (mmm) REVERT: A 1015 GLN cc_start: 0.8876 (tp40) cc_final: 0.8201 (tp40) REVERT: A 1017 ASN cc_start: 0.9025 (m-40) cc_final: 0.8604 (m110) REVERT: A 1034 ARG cc_start: 0.9258 (ppt170) cc_final: 0.8962 (pmt-80) REVERT: A 1035 ASN cc_start: 0.8801 (t0) cc_final: 0.8597 (t0) REVERT: A 1065 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8791 (mm110) REVERT: A 1076 ASP cc_start: 0.8330 (m-30) cc_final: 0.7848 (m-30) REVERT: A 1080 PHE cc_start: 0.8366 (m-80) cc_final: 0.7864 (m-10) REVERT: A 1087 LEU cc_start: 0.9551 (tt) cc_final: 0.9288 (mt) REVERT: A 1098 GLU cc_start: 0.8545 (pm20) cc_final: 0.8177 (mm-30) REVERT: A 1110 LEU cc_start: 0.9429 (mt) cc_final: 0.9096 (tp) REVERT: A 1111 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 1123 ASN cc_start: 0.9148 (m110) cc_final: 0.8426 (p0) REVERT: A 1208 MET cc_start: 0.9327 (ppp) cc_final: 0.9009 (ppp) REVERT: A 1217 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9111 (mm) REVERT: A 1330 TYR cc_start: 0.8172 (p90) cc_final: 0.7212 (p90) REVERT: B 126 ASP cc_start: 0.9083 (p0) cc_final: 0.8789 (p0) REVERT: B 208 GLN cc_start: 0.8406 (tt0) cc_final: 0.7816 (tp-100) REVERT: B 310 GLN cc_start: 0.8785 (mp10) cc_final: 0.8547 (mp10) REVERT: B 318 MET cc_start: 0.8409 (mtt) cc_final: 0.8124 (tpt) REVERT: B 342 GLU cc_start: 0.8673 (tp30) cc_final: 0.8416 (tp30) REVERT: B 393 TYR cc_start: 0.8645 (t80) cc_final: 0.8248 (t80) REVERT: B 460 HIS cc_start: 0.8725 (t70) cc_final: 0.8371 (t-90) REVERT: B 542 ILE cc_start: 0.8478 (tp) cc_final: 0.7958 (mp) REVERT: B 562 ASN cc_start: 0.7760 (m-40) cc_final: 0.7290 (m-40) REVERT: B 567 LYS cc_start: 0.9214 (tppt) cc_final: 0.8913 (mmmt) REVERT: B 669 PHE cc_start: 0.8659 (m-80) cc_final: 0.7947 (m-80) REVERT: B 688 MET cc_start: 0.8570 (ppp) cc_final: 0.8073 (ppp) REVERT: B 798 MET cc_start: 0.8752 (ptt) cc_final: 0.8058 (ptt) REVERT: B 858 TRP cc_start: 0.7257 (m-90) cc_final: 0.6809 (m-90) REVERT: B 863 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8449 (ttpt) REVERT: B 964 ASN cc_start: 0.9235 (t0) cc_final: 0.8932 (t0) REVERT: B 965 LEU cc_start: 0.9266 (tt) cc_final: 0.8750 (mm) REVERT: B 1013 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8785 (mm-40) REVERT: B 1015 GLN cc_start: 0.8660 (tp40) cc_final: 0.8034 (tp40) REVERT: B 1076 ASP cc_start: 0.8198 (p0) cc_final: 0.7744 (p0) REVERT: B 1098 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7821 (tp30) REVERT: B 1123 ASN cc_start: 0.9398 (m110) cc_final: 0.9111 (m110) REVERT: B 1161 ASP cc_start: 0.8818 (p0) cc_final: 0.8528 (p0) REVERT: B 1168 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8569 (mttp) REVERT: B 1183 TRP cc_start: 0.9201 (m-90) cc_final: 0.8682 (m-90) REVERT: B 1217 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8746 (mm) REVERT: B 1325 GLN cc_start: 0.8304 (tt0) cc_final: 0.7797 (tp40) REVERT: B 1330 TYR cc_start: 0.8603 (p90) cc_final: 0.8160 (p90) REVERT: C 65 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6764 (mm-30) REVERT: C 76 ASP cc_start: 0.8849 (p0) cc_final: 0.8481 (m-30) REVERT: C 121 MET cc_start: 0.7807 (ttt) cc_final: 0.7275 (tmm) REVERT: C 151 MET cc_start: 0.8076 (ttm) cc_final: 0.7717 (tpp) REVERT: C 189 GLN cc_start: 0.8835 (pm20) cc_final: 0.8396 (pp30) REVERT: C 207 VAL cc_start: 0.9101 (m) cc_final: 0.8799 (t) REVERT: C 215 THR cc_start: 0.9156 (m) cc_final: 0.8869 (p) REVERT: C 272 TYR cc_start: 0.4250 (OUTLIER) cc_final: 0.3531 (t80) REVERT: C 436 TRP cc_start: 0.7950 (t-100) cc_final: 0.7545 (t-100) REVERT: C 456 LYS cc_start: 0.9296 (mmtt) cc_final: 0.9057 (mmtt) REVERT: C 461 LEU cc_start: 0.9347 (mt) cc_final: 0.9138 (mm) REVERT: C 462 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: C 499 ILE cc_start: 0.7603 (mp) cc_final: 0.7386 (tp) REVERT: C 539 ARG cc_start: 0.7861 (mtt-85) cc_final: 0.7297 (mtt90) REVERT: C 540 LEU cc_start: 0.8480 (tt) cc_final: 0.8221 (tt) REVERT: C 551 VAL cc_start: 0.8476 (p) cc_final: 0.8254 (p) REVERT: C 635 ASN cc_start: 0.8639 (p0) cc_final: 0.8043 (p0) REVERT: C 666 MET cc_start: 0.8375 (mmm) cc_final: 0.7902 (mmm) REVERT: C 669 PHE cc_start: 0.8676 (m-80) cc_final: 0.8038 (m-80) REVERT: C 671 GLU cc_start: 0.8969 (tt0) cc_final: 0.8554 (mt-10) REVERT: C 672 ASP cc_start: 0.9154 (t0) cc_final: 0.8637 (t0) REVERT: C 673 MET cc_start: 0.9056 (tpp) cc_final: 0.8564 (tpp) REVERT: C 737 GLU cc_start: 0.7969 (mp0) cc_final: 0.7087 (mp0) REVERT: C 798 MET cc_start: 0.5169 (ptt) cc_final: 0.4913 (ptt) REVERT: C 916 PHE cc_start: 0.8800 (m-80) cc_final: 0.8458 (m-80) REVERT: C 988 ASP cc_start: 0.8263 (t0) cc_final: 0.7903 (t70) REVERT: C 1015 GLN cc_start: 0.7859 (tp40) cc_final: 0.7654 (tp40) REVERT: C 1079 CYS cc_start: 0.5222 (OUTLIER) cc_final: 0.4386 (p) REVERT: C 1089 ASN cc_start: 0.9105 (m-40) cc_final: 0.8296 (p0) REVERT: C 1104 TYR cc_start: 0.8744 (t80) cc_final: 0.8377 (t80) REVERT: C 1129 GLU cc_start: 0.9440 (pt0) cc_final: 0.9115 (pp20) REVERT: C 1140 HIS cc_start: 0.8667 (p-80) cc_final: 0.8383 (p90) REVERT: C 1205 GLU cc_start: 0.8862 (pm20) cc_final: 0.8133 (pm20) REVERT: C 1258 LEU cc_start: 0.9217 (mp) cc_final: 0.8959 (mp) REVERT: D 32 MET cc_start: 0.8439 (mtp) cc_final: 0.8118 (tpp) REVERT: D 98 GLU cc_start: 0.8944 (tt0) cc_final: 0.8602 (tp30) REVERT: D 108 LYS cc_start: 0.9325 (mmtt) cc_final: 0.8787 (mmmt) REVERT: D 203 TYR cc_start: 0.7435 (m-80) cc_final: 0.6212 (m-80) REVERT: D 290 PHE cc_start: 0.8723 (m-80) cc_final: 0.8415 (m-10) REVERT: D 325 GLN cc_start: 0.8587 (mp10) cc_final: 0.8286 (mp10) REVERT: D 381 ASN cc_start: 0.9114 (m-40) cc_final: 0.8746 (p0) REVERT: D 432 TYR cc_start: 0.7711 (p90) cc_final: 0.6811 (p90) REVERT: D 542 ILE cc_start: 0.8454 (tt) cc_final: 0.8103 (mp) REVERT: D 557 LYS cc_start: 0.8870 (mttp) cc_final: 0.8448 (mmtp) REVERT: D 637 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7923 (pp30) REVERT: D 669 PHE cc_start: 0.8653 (m-80) cc_final: 0.8104 (m-80) REVERT: D 671 GLU cc_start: 0.8566 (tt0) cc_final: 0.8041 (mm-30) REVERT: D 673 MET cc_start: 0.8956 (tpp) cc_final: 0.8173 (tpp) REVERT: D 739 TRP cc_start: 0.8035 (t60) cc_final: 0.7820 (t60) REVERT: D 758 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7396 (p) REVERT: D 764 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: D 766 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7702 (mmtm) REVERT: D 861 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8178 (m) REVERT: D 915 THR cc_start: 0.9202 (t) cc_final: 0.8878 (m) REVERT: D 957 SER cc_start: 0.8776 (t) cc_final: 0.8439 (m) REVERT: D 965 LEU cc_start: 0.8860 (tp) cc_final: 0.8602 (mp) REVERT: D 968 MET cc_start: 0.9072 (tpt) cc_final: 0.8804 (tpp) REVERT: D 999 GLU cc_start: 0.9137 (mp0) cc_final: 0.8795 (mp0) REVERT: D 1007 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: D 1015 GLN cc_start: 0.8789 (tp40) cc_final: 0.8069 (tp40) REVERT: D 1076 ASP cc_start: 0.7782 (p0) cc_final: 0.7459 (p0) REVERT: D 1089 ASN cc_start: 0.8894 (p0) cc_final: 0.8330 (p0) REVERT: D 1133 LYS cc_start: 0.9223 (ttmt) cc_final: 0.8889 (mmtm) REVERT: D 1150 LEU cc_start: 0.9621 (mm) cc_final: 0.9295 (mm) REVERT: D 1154 PHE cc_start: 0.8933 (m-80) cc_final: 0.8185 (m-80) REVERT: D 1209 THR cc_start: 0.9638 (p) cc_final: 0.9299 (p) REVERT: D 1233 ASN cc_start: 0.8923 (m-40) cc_final: 0.8475 (t0) REVERT: D 1243 ASN cc_start: 0.9395 (t0) cc_final: 0.9083 (t0) REVERT: D 1245 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8722 (tm-30) REVERT: D 1269 PHE cc_start: 0.8501 (t80) cc_final: 0.7705 (t80) REVERT: D 1323 TYR cc_start: 0.7022 (t80) cc_final: 0.6411 (t80) outliers start: 207 outliers final: 142 residues processed: 853 average time/residue: 0.2193 time to fit residues: 320.8257 Evaluate side-chains 809 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 651 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 595 CYS Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 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 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 525 SER Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 751 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 GLU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 917 ASN Chi-restraints excluded: chain D residue 1007 TYR Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1183 TRP Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 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: 6.9990 chunk 205 optimal weight: 3.9990 chunk 465 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 351 optimal weight: 0.5980 chunk 438 optimal weight: 9.9990 chunk 490 optimal weight: 0.9990 chunk 464 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 ASN ** C1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 GLN ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.103246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.079792 restraints weight = 141352.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.082898 restraints weight = 86528.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.085146 restraints weight = 60369.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.086791 restraints weight = 45909.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.087928 restraints weight = 37096.443| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5135 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= 0.173 Angle : 0.827 17.831 56478 Z= 0.397 Chirality : 0.051 0.402 6514 Planarity : 0.005 0.063 7202 Dihedral : 6.132 49.301 5477 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.25 % Favored : 89.69 % Rotamer: Outliers : 4.56 % Allowed : 28.21 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -3.57 (0.11), residues: 5110 helix: -0.17 (0.17), residues: 838 sheet: -2.44 (0.12), residues: 1542 loop : -3.12 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1163 TYR 0.035 0.002 TYR D 256 PHE 0.027 0.002 PHE C 458 TRP 0.030 0.002 TRP B1237 HIS 0.008 0.001 HIS D 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (41420) covalent geometry : angle 0.81834 / 0.39 (56270) SS BOND : bond 0.00484 / 0.31 ( 44) SS BOND : angle 1.19042 / 0.68 ( 88) hydrogen bonds : bond 0.04798 / 3.29 ( 480) hydrogen bonds : angle 5.62425 / 3.61 ( 1440) link_BETA1-4 : bond 0.00519 / 0.32 ( 12) link_BETA1-4 : angle 2.02768 / 1.43 ( 36) link_NAG-ASN : bond 0.00723 / 0.41 ( 28) link_NAG-ASN : angle 2.80738 / 1.84 ( 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 880 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 676 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8113 (p) cc_final: 0.7837 (m) REVERT: A 42 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: A 77 LEU cc_start: 0.8868 (tp) cc_final: 0.8149 (mp) REVERT: A 125 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8221 (pm20) REVERT: A 128 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6875 (pt) REVERT: A 151 MET cc_start: 0.6095 (tpp) cc_final: 0.5884 (tpp) REVERT: A 183 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.6821 (mt) REVERT: A 318 MET cc_start: 0.8904 (tpp) cc_final: 0.8439 (tpp) REVERT: A 353 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.7482 (m) REVERT: A 356 ASP cc_start: 0.8497 (t0) cc_final: 0.8263 (t0) REVERT: A 368 GLN cc_start: 0.8264 (tt0) cc_final: 0.7702 (tm-30) REVERT: A 370 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7310 (ttt180) REVERT: A 373 ASP cc_start: 0.7865 (t0) cc_final: 0.7542 (m-30) REVERT: A 393 TYR cc_start: 0.8831 (t80) cc_final: 0.8575 (t80) REVERT: A 436 TRP cc_start: 0.7081 (t-100) cc_final: 0.6733 (t-100) REVERT: A 539 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7590 (mtt90) REVERT: A 543 TYR cc_start: 0.7755 (p90) cc_final: 0.6762 (p90) REVERT: A 561 GLU cc_start: 0.8059 (tp30) cc_final: 0.7478 (tp30) REVERT: A 572 PHE cc_start: 0.8362 (p90) cc_final: 0.8014 (p90) REVERT: A 595 CYS cc_start: 0.4040 (m) cc_final: 0.3672 (m) REVERT: A 607 MET cc_start: 0.8236 (tmm) cc_final: 0.7813 (tmm) REVERT: A 612 GLU cc_start: 0.8091 (tt0) cc_final: 0.7854 (tt0) REVERT: A 627 LEU cc_start: 0.8752 (tp) cc_final: 0.8069 (tp) REVERT: A 669 PHE cc_start: 0.8773 (m-80) cc_final: 0.8459 (m-80) REVERT: A 682 LYS cc_start: 0.8699 (mttt) cc_final: 0.8264 (mmmt) REVERT: A 783 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8592 (t) REVERT: A 787 ARG cc_start: 0.8175 (ptp90) cc_final: 0.7861 (ptp90) REVERT: A 829 GLU cc_start: 0.8599 (tp30) cc_final: 0.7826 (mp0) REVERT: A 975 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8104 (mt0) REVERT: A 977 MET cc_start: 0.9412 (mmm) cc_final: 0.9072 (mmm) REVERT: A 985 TYR cc_start: 0.6964 (m-10) cc_final: 0.6698 (m-10) REVERT: A 1015 GLN cc_start: 0.8897 (tp40) cc_final: 0.8210 (tp40) REVERT: A 1017 ASN cc_start: 0.9062 (m-40) cc_final: 0.8651 (m110) REVERT: A 1065 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8822 (mm110) REVERT: A 1076 ASP cc_start: 0.8333 (m-30) cc_final: 0.7841 (m-30) REVERT: A 1080 PHE cc_start: 0.8345 (m-80) cc_final: 0.8131 (m-10) REVERT: A 1087 LEU cc_start: 0.9570 (tt) cc_final: 0.9304 (mt) REVERT: A 1110 LEU cc_start: 0.9480 (mt) cc_final: 0.9125 (tp) REVERT: A 1111 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 1123 ASN cc_start: 0.9239 (m110) cc_final: 0.8523 (p0) REVERT: A 1208 MET cc_start: 0.9389 (ppp) cc_final: 0.9055 (ppp) REVERT: A 1217 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9155 (mm) REVERT: A 1330 TYR cc_start: 0.8130 (p90) cc_final: 0.7169 (p90) REVERT: B 33 VAL cc_start: 0.8871 (p) cc_final: 0.8537 (m) REVERT: B 98 GLU cc_start: 0.8632 (tt0) cc_final: 0.7801 (tm-30) REVERT: B 126 ASP cc_start: 0.9211 (p0) cc_final: 0.8918 (p0) REVERT: B 208 GLN cc_start: 0.8473 (tt0) cc_final: 0.7810 (tp-100) REVERT: B 303 GLN cc_start: 0.7886 (mp10) cc_final: 0.7651 (mp10) REVERT: B 310 GLN cc_start: 0.8853 (mp10) cc_final: 0.8609 (mp10) REVERT: B 318 MET cc_start: 0.8486 (mtt) cc_final: 0.8184 (tpt) REVERT: B 342 GLU cc_start: 0.8644 (tp30) cc_final: 0.8394 (tp30) REVERT: B 386 ILE cc_start: 0.9046 (mp) cc_final: 0.8531 (pt) REVERT: B 393 TYR cc_start: 0.8699 (t80) cc_final: 0.7946 (t80) REVERT: B 460 HIS cc_start: 0.8876 (t70) cc_final: 0.8512 (t-90) REVERT: B 542 ILE cc_start: 0.8445 (tp) cc_final: 0.7840 (mp) REVERT: B 567 LYS cc_start: 0.9239 (tppt) cc_final: 0.8985 (mmpt) REVERT: B 666 MET cc_start: 0.9024 (ppp) cc_final: 0.8782 (ppp) REVERT: B 669 PHE cc_start: 0.8768 (m-80) cc_final: 0.8048 (m-80) REVERT: B 688 MET cc_start: 0.8539 (ppp) cc_final: 0.8076 (ppp) REVERT: B 797 THR cc_start: 0.6709 (OUTLIER) cc_final: 0.6480 (m) REVERT: B 798 MET cc_start: 0.8784 (ptt) cc_final: 0.7656 (ptm) REVERT: B 858 TRP cc_start: 0.7259 (m-90) cc_final: 0.6808 (m-90) REVERT: B 964 ASN cc_start: 0.9239 (t0) cc_final: 0.8928 (t0) REVERT: B 965 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8752 (mm) REVERT: B 1013 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8795 (mm-40) REVERT: B 1076 ASP cc_start: 0.8309 (p0) cc_final: 0.7861 (p0) REVERT: B 1098 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7852 (tp30) REVERT: B 1123 ASN cc_start: 0.9419 (m110) cc_final: 0.9126 (m110) REVERT: B 1161 ASP cc_start: 0.8884 (p0) cc_final: 0.8599 (p0) REVERT: B 1168 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8616 (mttp) REVERT: B 1183 TRP cc_start: 0.9213 (m-90) cc_final: 0.8874 (m-90) REVERT: B 1217 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8779 (mm) REVERT: B 1325 GLN cc_start: 0.8496 (tt0) cc_final: 0.8019 (tp40) REVERT: B 1330 TYR cc_start: 0.8607 (p90) cc_final: 0.8151 (p90) REVERT: C 65 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7039 (mm-30) REVERT: C 76 ASP cc_start: 0.8867 (p0) cc_final: 0.8487 (m-30) REVERT: C 121 MET cc_start: 0.7864 (ttt) cc_final: 0.7328 (tmm) REVERT: C 151 MET cc_start: 0.8122 (ttm) cc_final: 0.7625 (tpp) REVERT: C 189 GLN cc_start: 0.8863 (pm20) cc_final: 0.8453 (pp30) REVERT: C 207 VAL cc_start: 0.9171 (m) cc_final: 0.8872 (t) REVERT: C 215 THR cc_start: 0.9197 (m) cc_final: 0.8903 (p) REVERT: C 272 TYR cc_start: 0.4346 (OUTLIER) cc_final: 0.3619 (t80) REVERT: C 436 TRP cc_start: 0.7945 (t-100) cc_final: 0.7532 (t-100) REVERT: C 456 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8934 (tptt) REVERT: C 462 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: C 499 ILE cc_start: 0.7675 (mp) cc_final: 0.7419 (tp) REVERT: C 539 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7291 (mtt90) REVERT: C 561 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7679 (tm-30) REVERT: C 635 ASN cc_start: 0.8691 (p0) cc_final: 0.8079 (p0) REVERT: C 669 PHE cc_start: 0.8774 (m-80) cc_final: 0.8158 (m-80) REVERT: C 671 GLU cc_start: 0.9003 (tt0) cc_final: 0.8622 (mt-10) REVERT: C 672 ASP cc_start: 0.9211 (t0) cc_final: 0.8677 (t0) REVERT: C 673 MET cc_start: 0.9092 (tpp) cc_final: 0.8558 (tpp) REVERT: C 737 GLU cc_start: 0.8122 (mp0) cc_final: 0.7250 (mp0) REVERT: C 787 ARG cc_start: 0.8611 (ptp90) cc_final: 0.7905 (mtp180) REVERT: C 798 MET cc_start: 0.5125 (ptt) cc_final: 0.4789 (ptt) REVERT: C 916 PHE cc_start: 0.8785 (m-80) cc_final: 0.8491 (m-80) REVERT: C 988 ASP cc_start: 0.8385 (t0) cc_final: 0.8102 (t70) REVERT: C 1079 CYS cc_start: 0.5130 (OUTLIER) cc_final: 0.4139 (p) REVERT: C 1089 ASN cc_start: 0.9145 (m-40) cc_final: 0.8338 (p0) REVERT: C 1104 TYR cc_start: 0.8785 (t80) cc_final: 0.8460 (t80) REVERT: C 1129 GLU cc_start: 0.9443 (pt0) cc_final: 0.9143 (pp20) REVERT: C 1140 HIS cc_start: 0.8635 (p-80) cc_final: 0.8345 (p90) REVERT: C 1168 LYS cc_start: 0.9432 (mttt) cc_final: 0.9224 (mttt) REVERT: C 1205 GLU cc_start: 0.8878 (pm20) cc_final: 0.8265 (pm20) REVERT: C 1258 LEU cc_start: 0.9221 (mp) cc_final: 0.8920 (mp) REVERT: D 32 MET cc_start: 0.8492 (mtp) cc_final: 0.8170 (tpp) REVERT: D 78 GLU cc_start: 0.8197 (pp20) cc_final: 0.7973 (tm-30) REVERT: D 98 GLU cc_start: 0.8976 (tt0) cc_final: 0.8615 (tp30) REVERT: D 108 LYS cc_start: 0.9393 (mmtt) cc_final: 0.8869 (mmmt) REVERT: D 203 TYR cc_start: 0.7609 (m-80) cc_final: 0.6244 (m-80) REVERT: D 290 PHE cc_start: 0.8787 (m-80) cc_final: 0.8458 (m-10) REVERT: D 325 GLN cc_start: 0.8597 (mp10) cc_final: 0.8286 (mp10) REVERT: D 381 ASN cc_start: 0.9138 (m-40) cc_final: 0.8817 (p0) REVERT: D 432 TYR cc_start: 0.7695 (p90) cc_final: 0.6799 (p90) REVERT: D 500 MET cc_start: 0.5052 (mtt) cc_final: 0.4850 (mtt) REVERT: D 542 ILE cc_start: 0.8468 (tt) cc_final: 0.8087 (mp) REVERT: D 557 LYS cc_start: 0.8871 (mttp) cc_final: 0.8420 (mmtm) REVERT: D 561 GLU cc_start: 0.8175 (tp30) cc_final: 0.7832 (tp30) REVERT: D 637 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7918 (pp30) REVERT: D 669 PHE cc_start: 0.8733 (m-80) cc_final: 0.8158 (m-80) REVERT: D 671 GLU cc_start: 0.8568 (tt0) cc_final: 0.8099 (mm-30) REVERT: D 673 MET cc_start: 0.8996 (tpp) cc_final: 0.8356 (tpp) REVERT: D 739 TRP cc_start: 0.8124 (t60) cc_final: 0.7720 (t60) REVERT: D 758 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7371 (p) REVERT: D 764 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: D 766 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7680 (mmtm) REVERT: D 798 MET cc_start: 0.7177 (pmm) cc_final: 0.6673 (pmm) REVERT: D 915 THR cc_start: 0.9247 (t) cc_final: 0.8920 (m) REVERT: D 957 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8449 (m) REVERT: D 965 LEU cc_start: 0.8928 (tp) cc_final: 0.8666 (mt) REVERT: D 977 MET cc_start: 0.9627 (mmm) cc_final: 0.9278 (mmm) REVERT: D 999 GLU cc_start: 0.9166 (mp0) cc_final: 0.8847 (mp0) REVERT: D 1015 GLN cc_start: 0.8801 (tp40) cc_final: 0.8015 (tp40) REVERT: D 1076 ASP cc_start: 0.7920 (p0) cc_final: 0.7571 (p0) REVERT: D 1089 ASN cc_start: 0.8908 (p0) cc_final: 0.8349 (p0) REVERT: D 1123 ASN cc_start: 0.9392 (m-40) cc_final: 0.8679 (p0) REVERT: D 1133 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8826 (mmtm) REVERT: D 1183 TRP cc_start: 0.8876 (OUTLIER) cc_final: 0.8387 (m100) REVERT: D 1209 THR cc_start: 0.9637 (p) cc_final: 0.9312 (p) REVERT: D 1233 ASN cc_start: 0.8939 (m-40) cc_final: 0.8406 (t0) REVERT: D 1243 ASN cc_start: 0.9443 (t0) cc_final: 0.9168 (t0) REVERT: D 1269 PHE cc_start: 0.8548 (t80) cc_final: 0.7760 (t80) REVERT: D 1323 TYR cc_start: 0.7019 (t80) cc_final: 0.6402 (t80) outliers start: 204 outliers final: 160 residues processed: 825 average time/residue: 0.2042 time to fit residues: 288.7239 Evaluate side-chains 828 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 649 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL 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 1101 LEU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 525 SER Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 792 PHE Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1316 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 764 GLU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 955 LEU Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 983 ASN Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1183 TRP Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 412 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 415 optimal weight: 0.0670 chunk 179 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 283 optimal weight: 0.0470 chunk 394 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN A 938 ASN A1072 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN B 441 HIS ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 ASN D 637 GLN ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 ASN D1072 GLN D1143 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.105991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.082158 restraints weight = 139017.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.085402 restraints weight = 84372.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.087782 restraints weight = 58518.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.089475 restraints weight = 44090.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.090679 restraints weight = 35523.057| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 41504 Z= 0.137 Angle : 0.836 16.929 56478 Z= 0.395 Chirality : 0.051 0.431 6514 Planarity : 0.005 0.062 7202 Dihedral : 5.893 49.950 5477 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.61 % Favored : 90.33 % Rotamer: Outliers : 3.80 % Allowed : 29.26 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.11), residues: 5110 helix: -0.01 (0.17), residues: 822 sheet: -2.25 (0.12), residues: 1624 loop : -3.07 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1163 TYR 0.030 0.001 TYR D 256 PHE 0.028 0.001 PHE A1269 TRP 0.025 0.001 TRP B1237 HIS 0.007 0.001 HIS C1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (41420) covalent geometry : angle 0.82733 / 0.39 (56270) SS BOND : bond 0.00463 / 0.31 ( 44) SS BOND : angle 1.00147 / 0.57 ( 88) hydrogen bonds : bond 0.04681 / 3.17 ( 480) hydrogen bonds : angle 5.53399 / 3.57 ( 1440) link_BETA1-4 : bond 0.00537 / 0.36 ( 12) link_BETA1-4 : angle 2.06244 / 1.48 ( 36) link_NAG-ASN : bond 0.00638 / 0.36 ( 28) link_NAG-ASN : angle 2.95722 / 1.89 ( 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 868 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 698 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7988 (p) cc_final: 0.7708 (m) REVERT: A 151 MET cc_start: 0.5976 (tpp) cc_final: 0.5744 (tpp) REVERT: A 183 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6541 (mt) REVERT: A 318 MET cc_start: 0.8955 (tpp) cc_final: 0.8448 (tpp) REVERT: A 353 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.7354 (m) REVERT: A 356 ASP cc_start: 0.8490 (t0) cc_final: 0.8190 (t0) REVERT: A 368 GLN cc_start: 0.8204 (tt0) cc_final: 0.7615 (tm-30) REVERT: A 373 ASP cc_start: 0.7834 (t0) cc_final: 0.7469 (m-30) REVERT: A 393 TYR cc_start: 0.8784 (t80) cc_final: 0.8554 (t80) REVERT: A 436 TRP cc_start: 0.6853 (t-100) cc_final: 0.6517 (t-100) REVERT: A 543 TYR cc_start: 0.7356 (p90) cc_final: 0.6276 (p90) REVERT: A 561 GLU cc_start: 0.8034 (tp30) cc_final: 0.7487 (tp30) REVERT: A 572 PHE cc_start: 0.8225 (p90) cc_final: 0.7944 (p90) REVERT: A 607 MET cc_start: 0.8282 (tmm) cc_final: 0.7912 (tmm) REVERT: A 612 GLU cc_start: 0.8027 (tt0) cc_final: 0.7780 (tt0) REVERT: A 619 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.6882 (m-10) REVERT: A 627 LEU cc_start: 0.8729 (tp) cc_final: 0.8473 (tp) REVERT: A 666 MET cc_start: 0.8141 (tpt) cc_final: 0.7597 (tpt) REVERT: A 669 PHE cc_start: 0.8713 (m-80) cc_final: 0.8409 (m-80) REVERT: A 682 LYS cc_start: 0.8680 (mttt) cc_final: 0.8230 (mmmt) REVERT: A 783 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8567 (t) REVERT: A 787 ARG cc_start: 0.8113 (ptp90) cc_final: 0.7804 (ptp90) REVERT: A 793 PHE cc_start: 0.8800 (p90) cc_final: 0.8431 (p90) REVERT: A 829 GLU cc_start: 0.8571 (tp30) cc_final: 0.7793 (mp0) REVERT: A 965 LEU cc_start: 0.8439 (mt) cc_final: 0.8126 (mt) REVERT: A 975 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8064 (mt0) REVERT: A 977 MET cc_start: 0.9367 (mmm) cc_final: 0.8934 (mmm) REVERT: A 1017 ASN cc_start: 0.9070 (m-40) cc_final: 0.8660 (m110) REVERT: A 1065 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8766 (mm110) REVERT: A 1076 ASP cc_start: 0.8172 (m-30) cc_final: 0.7633 (m-30) REVERT: A 1087 LEU cc_start: 0.9561 (tt) cc_final: 0.9298 (mt) REVERT: A 1110 LEU cc_start: 0.9445 (mt) cc_final: 0.9082 (tp) REVERT: A 1111 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8209 (mm-30) REVERT: A 1123 ASN cc_start: 0.9207 (m110) cc_final: 0.8492 (p0) REVERT: A 1217 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9165 (mm) REVERT: A 1226 GLU cc_start: 0.8580 (pm20) cc_final: 0.7326 (tm-30) REVERT: A 1330 TYR cc_start: 0.8097 (p90) cc_final: 0.7094 (p90) REVERT: B 98 GLU cc_start: 0.8629 (tt0) cc_final: 0.7753 (tm-30) REVERT: B 126 ASP cc_start: 0.9116 (p0) cc_final: 0.8834 (p0) REVERT: B 151 MET cc_start: 0.6131 (tpp) cc_final: 0.5813 (tpp) REVERT: B 208 GLN cc_start: 0.8408 (tt0) cc_final: 0.7884 (tp-100) REVERT: B 303 GLN cc_start: 0.7930 (mp10) cc_final: 0.7722 (mp10) REVERT: B 310 GLN cc_start: 0.8794 (mp10) cc_final: 0.8539 (mp10) REVERT: B 318 MET cc_start: 0.8431 (mtt) cc_final: 0.8158 (tpt) REVERT: B 342 GLU cc_start: 0.8529 (tp30) cc_final: 0.8279 (tp30) REVERT: B 393 TYR cc_start: 0.8689 (t80) cc_final: 0.8278 (t80) REVERT: B 460 HIS cc_start: 0.8789 (t70) cc_final: 0.8417 (t-90) REVERT: B 542 ILE cc_start: 0.8406 (tp) cc_final: 0.7904 (mp) REVERT: B 567 LYS cc_start: 0.9203 (tppt) cc_final: 0.8939 (mmpt) REVERT: B 666 MET cc_start: 0.8980 (ppp) cc_final: 0.8705 (ppp) REVERT: B 669 PHE cc_start: 0.8653 (m-80) cc_final: 0.7955 (m-80) REVERT: B 688 MET cc_start: 0.8536 (ppp) cc_final: 0.8050 (ppp) REVERT: B 798 MET cc_start: 0.8799 (ptt) cc_final: 0.7635 (ptm) REVERT: B 858 TRP cc_start: 0.7378 (m-90) cc_final: 0.7029 (m-90) REVERT: B 965 LEU cc_start: 0.9252 (tt) cc_final: 0.9049 (tt) REVERT: B 977 MET cc_start: 0.9391 (mmm) cc_final: 0.9061 (mmm) REVERT: B 1013 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8782 (mm-40) REVERT: B 1076 ASP cc_start: 0.8217 (p0) cc_final: 0.7762 (p0) REVERT: B 1098 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7986 (tp30) REVERT: B 1123 ASN cc_start: 0.9398 (m110) cc_final: 0.9092 (m110) REVERT: B 1161 ASP cc_start: 0.8783 (p0) cc_final: 0.8494 (p0) REVERT: B 1183 TRP cc_start: 0.9214 (m-90) cc_final: 0.8999 (m-90) REVERT: B 1217 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8789 (mm) REVERT: B 1325 GLN cc_start: 0.8462 (tt0) cc_final: 0.8067 (tp-100) REVERT: B 1330 TYR cc_start: 0.8577 (p90) cc_final: 0.8090 (p90) REVERT: C 76 ASP cc_start: 0.8894 (p0) cc_final: 0.8566 (m-30) REVERT: C 98 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8579 (tm-30) REVERT: C 121 MET cc_start: 0.7891 (ttt) cc_final: 0.7170 (tmm) REVERT: C 151 MET cc_start: 0.8090 (ttm) cc_final: 0.6567 (mmt) REVERT: C 189 GLN cc_start: 0.8839 (pm20) cc_final: 0.8390 (pp30) REVERT: C 207 VAL cc_start: 0.9132 (m) cc_final: 0.8803 (t) REVERT: C 215 THR cc_start: 0.9162 (m) cc_final: 0.8881 (p) REVERT: C 256 TYR cc_start: 0.8059 (t80) cc_final: 0.7697 (t80) REVERT: C 272 TYR cc_start: 0.4251 (OUTLIER) cc_final: 0.3484 (t80) REVERT: C 436 TRP cc_start: 0.7819 (t-100) cc_final: 0.7476 (t-100) REVERT: C 456 LYS cc_start: 0.9266 (mmtt) cc_final: 0.8976 (tptt) REVERT: C 462 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: C 499 ILE cc_start: 0.7669 (mp) cc_final: 0.7423 (tp) REVERT: C 551 VAL cc_start: 0.8393 (p) cc_final: 0.8188 (p) REVERT: C 635 ASN cc_start: 0.8646 (p0) cc_final: 0.8074 (p0) REVERT: C 669 PHE cc_start: 0.8672 (m-80) cc_final: 0.8080 (m-80) REVERT: C 671 GLU cc_start: 0.8958 (tt0) cc_final: 0.8571 (mt-10) REVERT: C 672 ASP cc_start: 0.9180 (t0) cc_final: 0.8917 (t0) REVERT: C 737 GLU cc_start: 0.8045 (mp0) cc_final: 0.7290 (mp0) REVERT: C 787 ARG cc_start: 0.8574 (ptp90) cc_final: 0.8005 (ptt-90) REVERT: C 916 PHE cc_start: 0.8790 (m-80) cc_final: 0.8467 (m-80) REVERT: C 988 ASP cc_start: 0.8403 (t0) cc_final: 0.7927 (t0) REVERT: C 1079 CYS cc_start: 0.4891 (OUTLIER) cc_final: 0.3902 (p) REVERT: C 1089 ASN cc_start: 0.9134 (m-40) cc_final: 0.8314 (p0) REVERT: C 1104 TYR cc_start: 0.8784 (t80) cc_final: 0.8399 (t80) REVERT: C 1129 GLU cc_start: 0.9431 (pt0) cc_final: 0.9111 (pp20) REVERT: C 1140 HIS cc_start: 0.8593 (p-80) cc_final: 0.8299 (p90) REVERT: C 1205 GLU cc_start: 0.8891 (pm20) cc_final: 0.8268 (pm20) REVERT: C 1258 LEU cc_start: 0.9187 (mp) cc_final: 0.8929 (mp) REVERT: D 32 MET cc_start: 0.8489 (mtp) cc_final: 0.8163 (tpp) REVERT: D 78 GLU cc_start: 0.8206 (pp20) cc_final: 0.7972 (tm-30) REVERT: D 98 GLU cc_start: 0.8961 (tt0) cc_final: 0.8733 (tp30) REVERT: D 108 LYS cc_start: 0.9302 (mmtt) cc_final: 0.8759 (mmmt) REVERT: D 177 GLN cc_start: 0.9126 (tt0) cc_final: 0.8695 (tm-30) REVERT: D 203 TYR cc_start: 0.7561 (m-80) cc_final: 0.6306 (m-80) REVERT: D 208 GLN cc_start: 0.8369 (tt0) cc_final: 0.7478 (tp40) REVERT: D 290 PHE cc_start: 0.8730 (m-80) cc_final: 0.8410 (m-10) REVERT: D 325 GLN cc_start: 0.8602 (mp10) cc_final: 0.8310 (mp10) REVERT: D 381 ASN cc_start: 0.9141 (m-40) cc_final: 0.8802 (p0) REVERT: D 432 TYR cc_start: 0.7748 (p90) cc_final: 0.6802 (p90) REVERT: D 542 ILE cc_start: 0.8435 (tt) cc_final: 0.8101 (mp) REVERT: D 557 LYS cc_start: 0.8901 (mttp) cc_final: 0.8476 (mmtp) REVERT: D 637 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7888 (pp30) REVERT: D 669 PHE cc_start: 0.8696 (m-80) cc_final: 0.8179 (m-80) REVERT: D 671 GLU cc_start: 0.8588 (tt0) cc_final: 0.8118 (mm-30) REVERT: D 739 TRP cc_start: 0.8112 (t60) cc_final: 0.7887 (t60) REVERT: D 758 VAL cc_start: 0.7778 (OUTLIER) cc_final: 0.7292 (p) REVERT: D 764 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: D 766 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7564 (mmtm) REVERT: D 798 MET cc_start: 0.7266 (pmm) cc_final: 0.6822 (pmm) REVERT: D 915 THR cc_start: 0.9197 (t) cc_final: 0.8869 (m) REVERT: D 957 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8503 (m) REVERT: D 965 LEU cc_start: 0.8899 (tp) cc_final: 0.8642 (mp) REVERT: D 977 MET cc_start: 0.9646 (mmm) cc_final: 0.9315 (mmm) REVERT: D 999 GLU cc_start: 0.9128 (mp0) cc_final: 0.8872 (mp0) REVERT: D 1015 GLN cc_start: 0.8834 (tp40) cc_final: 0.8122 (tp40) REVERT: D 1076 ASP cc_start: 0.7776 (p0) cc_final: 0.7435 (p0) REVERT: D 1089 ASN cc_start: 0.8889 (p0) cc_final: 0.8341 (p0) REVERT: D 1123 ASN cc_start: 0.9328 (m-40) cc_final: 0.8627 (p0) REVERT: D 1133 LYS cc_start: 0.9271 (ttmt) cc_final: 0.8867 (mmtm) REVERT: D 1147 LYS cc_start: 0.9273 (mttp) cc_final: 0.8750 (mttp) REVERT: D 1154 PHE cc_start: 0.8870 (m-80) cc_final: 0.8097 (m-80) REVERT: D 1233 ASN cc_start: 0.8909 (m-40) cc_final: 0.8426 (t0) REVERT: D 1243 ASN cc_start: 0.9423 (t0) cc_final: 0.9146 (t0) REVERT: D 1269 PHE cc_start: 0.8478 (t80) cc_final: 0.7682 (t80) REVERT: D 1323 TYR cc_start: 0.7047 (t80) cc_final: 0.6465 (t80) outliers start: 170 outliers final: 125 residues processed: 817 average time/residue: 0.2070 time to fit residues: 289.6930 Evaluate side-chains 808 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 669 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 119 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1316 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 764 GLU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 301 optimal weight: 0.0870 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 0.0060 chunk 425 optimal weight: 7.9990 chunk 332 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 135 optimal weight: 0.4980 chunk 432 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 overall best weight: 0.9178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.105860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.082100 restraints weight = 139033.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.085304 restraints weight = 84763.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.087620 restraints weight = 59058.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.089327 restraints weight = 44853.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.090650 restraints weight = 36174.917| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.292 41504 Z= 0.249 Angle : 0.944 59.187 56478 Z= 0.462 Chirality : 0.054 0.885 6514 Planarity : 0.005 0.106 7202 Dihedral : 5.860 49.948 5474 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.69 % Favored : 90.25 % Rotamer: Outliers : 3.49 % Allowed : 29.80 % Favored : 66.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.11), residues: 5110 helix: -0.05 (0.17), residues: 834 sheet: -2.23 (0.12), residues: 1624 loop : -3.06 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1034 TYR 0.037 0.002 TYR A1007 PHE 0.100 0.002 PHE D 181 TRP 0.059 0.002 TRP D1183 HIS 0.006 0.001 HIS C1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.25 (41420) covalent geometry : angle 0.92357 / 0.46 (56270) SS BOND : bond 0.01011 / 0.98 ( 44) SS BOND : angle 3.83490 / 2.04 ( 88) hydrogen bonds : bond 0.04683 / 3.17 ( 480) hydrogen bonds : angle 5.56608 / 3.59 ( 1440) link_BETA1-4 : bond 0.00499 / 0.37 ( 12) link_BETA1-4 : angle 2.07123 / 1.49 ( 36) link_NAG-ASN : bond 0.00894 / 0.47 ( 28) link_NAG-ASN : angle 3.21155 / 2.03 ( 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 825 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 669 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7952 (p) cc_final: 0.7686 (m) REVERT: A 151 MET cc_start: 0.5922 (tpp) cc_final: 0.5693 (tpp) REVERT: A 183 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6542 (mt) REVERT: A 318 MET cc_start: 0.8953 (tpp) cc_final: 0.8443 (tpp) REVERT: A 353 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7449 (m) REVERT: A 356 ASP cc_start: 0.8468 (t0) cc_final: 0.8189 (t0) REVERT: A 368 GLN cc_start: 0.8195 (tt0) cc_final: 0.7607 (tm-30) REVERT: A 373 ASP cc_start: 0.7811 (t0) cc_final: 0.7470 (m-30) REVERT: A 393 TYR cc_start: 0.8776 (t80) cc_final: 0.8551 (t80) REVERT: A 436 TRP cc_start: 0.6847 (t-100) cc_final: 0.6505 (t-100) REVERT: A 539 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.7390 (mtt90) REVERT: A 543 TYR cc_start: 0.7340 (p90) cc_final: 0.6291 (p90) REVERT: A 561 GLU cc_start: 0.8037 (tp30) cc_final: 0.7489 (tp30) REVERT: A 572 PHE cc_start: 0.8220 (p90) cc_final: 0.7936 (p90) REVERT: A 607 MET cc_start: 0.8292 (tmm) cc_final: 0.7918 (tmm) REVERT: A 612 GLU cc_start: 0.8026 (tt0) cc_final: 0.7781 (tt0) REVERT: A 619 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.6875 (m-10) REVERT: A 627 LEU cc_start: 0.8728 (tp) cc_final: 0.8175 (tp) REVERT: A 666 MET cc_start: 0.8134 (tpt) cc_final: 0.7587 (tpt) REVERT: A 669 PHE cc_start: 0.8706 (m-80) cc_final: 0.8407 (m-80) REVERT: A 682 LYS cc_start: 0.8685 (mttt) cc_final: 0.8237 (mmmt) REVERT: A 783 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8579 (t) REVERT: A 787 ARG cc_start: 0.8118 (ptp90) cc_final: 0.7813 (ptp90) REVERT: A 793 PHE cc_start: 0.8788 (p90) cc_final: 0.8411 (p90) REVERT: A 829 GLU cc_start: 0.8570 (tp30) cc_final: 0.7798 (mp0) REVERT: A 965 LEU cc_start: 0.8434 (mt) cc_final: 0.8171 (mt) REVERT: A 975 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8073 (mt0) REVERT: A 977 MET cc_start: 0.9336 (mmm) cc_final: 0.8970 (mmm) REVERT: A 1017 ASN cc_start: 0.9076 (m-40) cc_final: 0.8672 (m110) REVERT: A 1065 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8769 (mm110) REVERT: A 1076 ASP cc_start: 0.8180 (m-30) cc_final: 0.7640 (m-30) REVERT: A 1080 PHE cc_start: 0.8231 (m-10) cc_final: 0.7841 (m-10) REVERT: A 1087 LEU cc_start: 0.9557 (tt) cc_final: 0.9296 (mt) REVERT: A 1098 GLU cc_start: 0.8521 (pm20) cc_final: 0.8015 (mm-30) REVERT: A 1110 LEU cc_start: 0.9451 (mt) cc_final: 0.9088 (tp) REVERT: A 1111 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8213 (mm-30) REVERT: A 1123 ASN cc_start: 0.9208 (m110) cc_final: 0.8495 (p0) REVERT: A 1217 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9159 (mm) REVERT: A 1226 GLU cc_start: 0.8591 (pm20) cc_final: 0.7339 (tm-30) REVERT: A 1330 TYR cc_start: 0.8082 (p90) cc_final: 0.7083 (p90) REVERT: B 98 GLU cc_start: 0.8622 (tt0) cc_final: 0.7752 (tm-30) REVERT: B 126 ASP cc_start: 0.9099 (p0) cc_final: 0.8822 (p0) REVERT: B 151 MET cc_start: 0.6144 (tpp) cc_final: 0.5772 (tpp) REVERT: B 208 GLN cc_start: 0.8472 (tt0) cc_final: 0.7892 (tp-100) REVERT: B 303 GLN cc_start: 0.7932 (mp10) cc_final: 0.7728 (mp10) REVERT: B 310 GLN cc_start: 0.8790 (mp10) cc_final: 0.8538 (mp10) REVERT: B 318 MET cc_start: 0.8428 (mtt) cc_final: 0.8161 (tpt) REVERT: B 342 GLU cc_start: 0.8516 (tp30) cc_final: 0.8261 (tp30) REVERT: B 393 TYR cc_start: 0.8691 (t80) cc_final: 0.8280 (t80) REVERT: B 460 HIS cc_start: 0.8797 (t70) cc_final: 0.8419 (t-90) REVERT: B 542 ILE cc_start: 0.8417 (tp) cc_final: 0.7898 (mp) REVERT: B 567 LYS cc_start: 0.9197 (tppt) cc_final: 0.8936 (mmpt) REVERT: B 666 MET cc_start: 0.9006 (ppp) cc_final: 0.8772 (ppp) REVERT: B 669 PHE cc_start: 0.8663 (m-80) cc_final: 0.7974 (m-80) REVERT: B 688 MET cc_start: 0.8535 (ppp) cc_final: 0.8053 (ppp) REVERT: B 798 MET cc_start: 0.8714 (ptt) cc_final: 0.7643 (ptm) REVERT: B 858 TRP cc_start: 0.7370 (m-90) cc_final: 0.7023 (m-90) REVERT: B 977 MET cc_start: 0.9390 (mmm) cc_final: 0.9009 (mmm) REVERT: B 1013 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8777 (mm-40) REVERT: B 1076 ASP cc_start: 0.8190 (p0) cc_final: 0.7732 (p0) REVERT: B 1098 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7857 (tp30) REVERT: B 1123 ASN cc_start: 0.9403 (m110) cc_final: 0.9100 (m110) REVERT: B 1161 ASP cc_start: 0.8774 (p0) cc_final: 0.8483 (p0) REVERT: B 1183 TRP cc_start: 0.9213 (m-90) cc_final: 0.8996 (m-90) REVERT: B 1217 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8778 (mm) REVERT: B 1325 GLN cc_start: 0.8419 (tt0) cc_final: 0.8063 (tp-100) REVERT: B 1330 TYR cc_start: 0.8561 (p90) cc_final: 0.8075 (p90) REVERT: C 76 ASP cc_start: 0.8885 (p0) cc_final: 0.8566 (m-30) REVERT: C 98 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8586 (tm-30) REVERT: C 121 MET cc_start: 0.7898 (ttt) cc_final: 0.7181 (tmm) REVERT: C 151 MET cc_start: 0.8094 (ttm) cc_final: 0.6581 (mmt) REVERT: C 189 GLN cc_start: 0.8823 (pm20) cc_final: 0.8388 (pp30) REVERT: C 207 VAL cc_start: 0.9139 (m) cc_final: 0.8809 (t) REVERT: C 215 THR cc_start: 0.9167 (m) cc_final: 0.8887 (p) REVERT: C 256 TYR cc_start: 0.8036 (t80) cc_final: 0.7671 (t80) REVERT: C 272 TYR cc_start: 0.4271 (OUTLIER) cc_final: 0.3497 (t80) REVERT: C 436 TRP cc_start: 0.7812 (t-100) cc_final: 0.7486 (t-100) REVERT: C 456 LYS cc_start: 0.9256 (mmtt) cc_final: 0.8972 (tptt) REVERT: C 462 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: C 539 ARG cc_start: 0.7864 (mtt-85) cc_final: 0.7273 (mtt90) REVERT: C 551 VAL cc_start: 0.8392 (p) cc_final: 0.8077 (p) REVERT: C 635 ASN cc_start: 0.8659 (p0) cc_final: 0.8088 (p0) REVERT: C 669 PHE cc_start: 0.8660 (m-80) cc_final: 0.8119 (m-80) REVERT: C 671 GLU cc_start: 0.8981 (tt0) cc_final: 0.8616 (mt-10) REVERT: C 672 ASP cc_start: 0.9199 (t0) cc_final: 0.8638 (t0) REVERT: C 737 GLU cc_start: 0.8060 (mp0) cc_final: 0.7296 (mp0) REVERT: C 787 ARG cc_start: 0.8588 (ptp90) cc_final: 0.8021 (ptt-90) REVERT: C 916 PHE cc_start: 0.8777 (m-80) cc_final: 0.8454 (m-80) REVERT: C 988 ASP cc_start: 0.8403 (t0) cc_final: 0.7925 (t0) REVERT: C 1079 CYS cc_start: 0.4819 (OUTLIER) cc_final: 0.3933 (p) REVERT: C 1089 ASN cc_start: 0.9126 (m-40) cc_final: 0.8318 (p0) REVERT: C 1104 TYR cc_start: 0.8772 (t80) cc_final: 0.8381 (t80) REVERT: C 1129 GLU cc_start: 0.9430 (pt0) cc_final: 0.9114 (pp20) REVERT: C 1140 HIS cc_start: 0.8553 (p-80) cc_final: 0.8264 (p90) REVERT: C 1205 GLU cc_start: 0.8851 (pm20) cc_final: 0.8266 (pm20) REVERT: C 1258 LEU cc_start: 0.9195 (mp) cc_final: 0.8926 (mp) REVERT: D 32 MET cc_start: 0.8485 (mtp) cc_final: 0.8158 (tpp) REVERT: D 78 GLU cc_start: 0.8177 (pp20) cc_final: 0.7947 (tm-30) REVERT: D 98 GLU cc_start: 0.8956 (tt0) cc_final: 0.8734 (tp30) REVERT: D 108 LYS cc_start: 0.9305 (mmtt) cc_final: 0.8758 (mmmt) REVERT: D 177 GLN cc_start: 0.9127 (tt0) cc_final: 0.8702 (tm-30) REVERT: D 203 TYR cc_start: 0.7553 (m-80) cc_final: 0.6308 (m-80) REVERT: D 208 GLN cc_start: 0.8367 (tt0) cc_final: 0.7504 (tp40) REVERT: D 290 PHE cc_start: 0.8726 (m-80) cc_final: 0.8405 (m-10) REVERT: D 325 GLN cc_start: 0.8598 (mp10) cc_final: 0.8303 (mp10) REVERT: D 381 ASN cc_start: 0.9137 (m-40) cc_final: 0.8792 (p0) REVERT: D 432 TYR cc_start: 0.7726 (p90) cc_final: 0.6783 (p90) REVERT: D 542 ILE cc_start: 0.8423 (tt) cc_final: 0.8106 (mp) REVERT: D 557 LYS cc_start: 0.8901 (mttp) cc_final: 0.8480 (mmtp) REVERT: D 637 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7862 (pp30) REVERT: D 669 PHE cc_start: 0.8730 (m-80) cc_final: 0.8170 (m-80) REVERT: D 671 GLU cc_start: 0.8600 (tt0) cc_final: 0.8129 (mm-30) REVERT: D 739 TRP cc_start: 0.8096 (t60) cc_final: 0.7884 (t60) REVERT: D 758 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7295 (p) REVERT: D 764 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: D 766 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7562 (mmtm) REVERT: D 798 MET cc_start: 0.7244 (pmm) cc_final: 0.6763 (pmm) REVERT: D 915 THR cc_start: 0.9190 (t) cc_final: 0.8867 (m) REVERT: D 957 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8472 (m) REVERT: D 965 LEU cc_start: 0.8884 (tp) cc_final: 0.8638 (mp) REVERT: D 977 MET cc_start: 0.9643 (mmm) cc_final: 0.9335 (mmm) REVERT: D 999 GLU cc_start: 0.9123 (mp0) cc_final: 0.8866 (mp0) REVERT: D 1015 GLN cc_start: 0.8835 (tp40) cc_final: 0.8127 (tp40) REVERT: D 1076 ASP cc_start: 0.7764 (p0) cc_final: 0.7421 (p0) REVERT: D 1089 ASN cc_start: 0.8890 (p0) cc_final: 0.8346 (p0) REVERT: D 1123 ASN cc_start: 0.9353 (m-40) cc_final: 0.8646 (p0) REVERT: D 1133 LYS cc_start: 0.9274 (ttmt) cc_final: 0.8870 (mmtm) REVERT: D 1147 LYS cc_start: 0.9269 (mttp) cc_final: 0.8751 (mttp) REVERT: D 1154 PHE cc_start: 0.8871 (m-80) cc_final: 0.8092 (m-80) REVERT: D 1233 ASN cc_start: 0.8906 (m-40) cc_final: 0.8413 (t0) REVERT: D 1243 ASN cc_start: 0.9410 (t0) cc_final: 0.9135 (t0) REVERT: D 1269 PHE cc_start: 0.8470 (t80) cc_final: 0.7672 (t80) REVERT: D 1323 TYR cc_start: 0.7065 (t80) cc_final: 0.6478 (t80) outliers start: 156 outliers final: 133 residues processed: 781 average time/residue: 0.2066 time to fit residues: 277.1102 Evaluate side-chains 799 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 652 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 107 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1238 ILE Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1316 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 764 GLU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 500 optimal weight: 0.9990 chunk 480 optimal weight: 9.9990 chunk 393 optimal weight: 5.9990 chunk 180 optimal weight: 0.0000 chunk 20 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 chunk 395 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 299 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.105680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.082005 restraints weight = 140842.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.085167 restraints weight = 86412.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.087490 restraints weight = 60460.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.089155 restraints weight = 45898.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.090493 restraints weight = 36997.807| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.280 41504 Z= 0.398 Angle : 0.962 58.840 56478 Z= 0.471 Chirality : 0.054 0.882 6514 Planarity : 0.005 0.106 7202 Dihedral : 5.860 49.948 5474 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.71 % Favored : 90.23 % Rotamer: Outliers : 3.42 % Allowed : 30.18 % Favored : 66.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.11), residues: 5110 helix: -0.05 (0.17), residues: 834 sheet: -2.23 (0.12), residues: 1624 loop : -3.06 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1034 TYR 0.037 0.002 TYR A1007 PHE 0.099 0.002 PHE D 181 TRP 0.062 0.002 TRP D1183 HIS 0.006 0.001 HIS C1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.24 (41420) covalent geometry : angle 0.92156 / 0.45 (56270) SS BOND : bond 0.19324 / 9.24 ( 44) SS BOND : angle 6.31738 / 3.99 ( 88) hydrogen bonds : bond 0.04683 / 3.17 ( 480) hydrogen bonds : angle 5.56598 / 3.59 ( 1440) link_BETA1-4 : bond 0.00477 / 0.31 ( 12) link_BETA1-4 : angle 2.06596 / 1.48 ( 36) link_NAG-ASN : bond 0.00887 / 0.47 ( 28) link_NAG-ASN : angle 3.21138 / 2.03 ( 84) =============================================================================== Job complete usr+sys time: 8522.25 seconds wall clock time: 148 minutes 12.30 seconds (8892.30 seconds total)