Starting phenix.real_space_refine on Thu Feb 5 13:44:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9j_52961/02_2026/9q9j_52961.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9j_52961/02_2026/9q9j_52961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q9j_52961/02_2026/9q9j_52961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9j_52961/02_2026/9q9j_52961.map" model { file = "/net/cci-nas-00/data/ceres_data/9q9j_52961/02_2026/9q9j_52961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9j_52961/02_2026/9q9j_52961.cif" } resolution = 2.71 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.093 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: 9 Type Number sf(0) Gaussians Mn 4 7.51 5 P 56 5.49 5 Mg 2 5.21 5 S 81 5.16 5 Be 2 3.05 5 C 10862 2.51 5 N 3049 2.21 5 O 3403 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17465 Number of models: 1 Model: "" Number of chains: 16 Chain: "J" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 154 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "P" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "T" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "F" Number of atoms: 731 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 87, 723 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 87, 723 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain breaks: 1 bond proxies already assigned to first conformer: 729 Chain: "A" Number of atoms: 3791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 468, 3783 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 459} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 468, 3783 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 459} Chain breaks: 1 bond proxies already assigned to first conformer: 3824 Chain: "B" Number of atoms: 3823 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 472, 3815 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 463} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 472, 3815 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 463} Chain breaks: 1 bond proxies already assigned to first conformer: 3857 Chain: "D" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3909 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 20, 'TRANS': 458} Chain breaks: 1 Chain: "E" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3917 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 20, 'TRANS': 459} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.88, per 1000 atoms: 0.34 Number of scatterers: 17465 At special positions: 0 Unit cell: (105.415, 114.139, 183.931, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Mn 4 24.99 S 81 16.00 P 56 15.00 Mg 2 11.99 F 6 9.00 O 3403 8.00 N 3049 7.00 C 10862 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 1.0 seconds 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 16 sheets defined 44.2% alpha, 18.4% beta 25 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'J' and resid 467 through 472 Processing helix chain 'F' and resid 716 through 746 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.776A pdb=" N ILE A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 132 through 145 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 182 through 236 removed outlier: 3.802A pdb=" N LYS A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1092 removed outlier: 3.821A pdb=" N LYS A1090 " --> pdb=" O ILE A1086 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A1091 " --> pdb=" O HIS A1087 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A1092 " --> pdb=" O PHE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1099 Processing helix chain 'A' and resid 1100 through 1155 removed outlier: 4.258A pdb=" N GLU A1142 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A1149 " --> pdb=" O LYS A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1222 Processing helix chain 'A' and resid 1238 through 1258 removed outlier: 3.907A pdb=" N GLN A1258 " --> pdb=" O LYS A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1278 removed outlier: 3.577A pdb=" N VAL A1274 " --> pdb=" O ASP A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1281 No H-bonds generated for 'chain 'A' and resid 1279 through 1281' Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.623A pdb=" N LYS B 22 " --> pdb=" O ASP B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 55 removed outlier: 3.711A pdb=" N ILE B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.716A pdb=" N SER B 162 " --> pdb=" O GLN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 182 through 237 removed outlier: 3.821A pdb=" N LYS B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1092 Processing helix chain 'B' and resid 1094 through 1099 removed outlier: 4.284A pdb=" N ASP B1099 " --> pdb=" O PRO B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1155 removed outlier: 4.322A pdb=" N GLU B1142 " --> pdb=" O MET B1138 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B1143 " --> pdb=" O LYS B1139 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE B1146 " --> pdb=" O GLU B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1222 Processing helix chain 'B' and resid 1238 through 1257 Processing helix chain 'B' and resid 1270 through 1281 removed outlier: 3.591A pdb=" N VAL B1274 " --> pdb=" O ASP B1270 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER B1280 " --> pdb=" O LEU B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1305 through 1310 removed outlier: 4.495A pdb=" N GLY B1308 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 50 Processing helix chain 'D' and resid 68 through 83 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 139 through 148 Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'D' and resid 206 through 210 removed outlier: 4.066A pdb=" N TRP D 210 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 317 No H-bonds generated for 'chain 'D' and resid 315 through 317' Processing helix chain 'D' and resid 327 through 352 removed outlier: 3.645A pdb=" N ALA D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 428 through 444 Processing helix chain 'D' and resid 452 through 464 removed outlier: 3.844A pdb=" N GLU D 456 " --> pdb=" O ARG D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 488 Processing helix chain 'D' and resid 493 through 508 Processing helix chain 'E' and resid 34 through 50 Processing helix chain 'E' and resid 68 through 83 Processing helix chain 'E' and resid 96 through 101 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'E' and resid 185 through 195 Processing helix chain 'E' and resid 275 through 280 removed outlier: 3.878A pdb=" N VAL E 280 " --> pdb=" O GLY E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 352 removed outlier: 3.564A pdb=" N ALA E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 384 removed outlier: 3.522A pdb=" N GLN E 383 " --> pdb=" O LEU E 379 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 444 Processing helix chain 'E' and resid 453 through 465 Processing helix chain 'E' and resid 468 through 488 Processing helix chain 'E' and resid 493 through 508 removed outlier: 3.776A pdb=" N ARG E 508 " --> pdb=" O PHE E 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 460 through 462 removed outlier: 6.529A pdb=" N ILE B 33 " --> pdb=" O TYR B1287 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE B1289 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 35 " --> pdb=" O ILE B1289 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N LYS B1291 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B1230 " --> pdb=" O ILE B1267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 656 through 660 Processing sheet with id=AA3, first strand: chain 'F' and resid 708 through 711 removed outlier: 4.328A pdb=" N MET E 200 " --> pdb=" O HIS F 711 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR E 199 " --> pdb=" O ILE E 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.233A pdb=" N ILE A 4 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG A 87 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.233A pdb=" N ILE A 4 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG A 87 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 93 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR A 121 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1227 through 1231 removed outlier: 6.280A pdb=" N THR A 32 " --> pdb=" O VAL A1266 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU A 31 " --> pdb=" O LYS A1285 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N TYR A1287 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 33 " --> pdb=" O TYR A1287 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A1289 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 35 " --> pdb=" O ILE A1289 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N LYS A1291 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1163 through 1168 removed outlier: 4.030A pdb=" N ASN A1183 " --> pdb=" O ASP A1168 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A1193 " --> pdb=" O LYS A1190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 23 through 26 removed outlier: 6.604A pdb=" N GLN B 85 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET B 7 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 83 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE B 9 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN B 81 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 93 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B 121 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 113 removed outlier: 6.835A pdb=" N LEU B 93 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B 121 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1163 through 1168 removed outlier: 3.981A pdb=" N ASN B1183 " --> pdb=" O ASP B1168 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B1193 " --> pdb=" O LYS B1190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 151 through 152 removed outlier: 6.488A pdb=" N VAL D 122 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE D 55 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N PHE D 54 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS D 14 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU D 56 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU D 16 " --> pdb=" O LEU D 56 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.939A pdb=" N LYS D 175 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU D 213 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA D 177 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL D 215 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR D 179 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN D 212 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE D 242 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE D 214 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL D 241 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE D 263 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA D 252 " --> pdb=" O ILE D 263 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 307 through 313 removed outlier: 3.595A pdb=" N GLU D 310 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 151 through 152 removed outlier: 6.834A pdb=" N VAL E 122 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE E 55 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE E 54 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.856A pdb=" N HIS E 217 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE E 214 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLY E 244 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE E 216 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL E 241 " --> pdb=" O SER E 264 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 307 through 313 removed outlier: 3.538A pdb=" N GLU E 310 " --> pdb=" O ARG E 364 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2402 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2884 1.31 - 1.44: 4700 1.44 - 1.56: 10050 1.56 - 1.69: 108 1.69 - 1.81: 128 Bond restraints: 17870 Sorted by residual: bond pdb=" C MET B1107 " pdb=" N MET B1108 " ideal model delta sigma weight residual 1.334 1.437 -0.103 1.27e-02 6.20e+03 6.58e+01 bond pdb=" C MET B1108 " pdb=" N ILE B1109 " ideal model delta sigma weight residual 1.335 1.237 0.098 1.23e-02 6.61e+03 6.30e+01 bond pdb=" C GLY D 453 " pdb=" N MET D 454 " ideal model delta sigma weight residual 1.335 1.241 0.094 1.38e-02 5.25e+03 4.68e+01 bond pdb=" C LYS D 384 " pdb=" N PHE D 385 " ideal model delta sigma weight residual 1.333 1.428 -0.095 1.42e-02 4.96e+03 4.50e+01 bond pdb=" C ILE E 312 " pdb=" N VAL E 313 " ideal model delta sigma weight residual 1.330 1.408 -0.078 1.25e-02 6.40e+03 3.92e+01 ... (remaining 17865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 23743 2.54 - 5.08: 410 5.08 - 7.62: 100 7.62 - 10.17: 7 10.17 - 12.71: 5 Bond angle restraints: 24265 Sorted by residual: angle pdb=" C MET B1107 " pdb=" N MET B1108 " pdb=" CA MET B1108 " ideal model delta sigma weight residual 120.44 112.34 8.10 1.30e+00 5.92e-01 3.88e+01 angle pdb=" N PRO A1095 " pdb=" CA PRO A1095 " pdb=" C PRO A1095 " ideal model delta sigma weight residual 113.65 105.51 8.14 1.35e+00 5.49e-01 3.63e+01 angle pdb=" N LYS A1090 " pdb=" CA LYS A1090 " pdb=" C LYS A1090 " ideal model delta sigma weight residual 113.88 106.70 7.18 1.23e+00 6.61e-01 3.41e+01 angle pdb=" N LYS B1079 " pdb=" CA LYS B1079 " pdb=" C LYS B1079 " ideal model delta sigma weight residual 111.82 105.30 6.52 1.16e+00 7.43e-01 3.16e+01 angle pdb=" O GLY D 453 " pdb=" C GLY D 453 " pdb=" N MET D 454 " ideal model delta sigma weight residual 122.70 115.88 6.82 1.30e+00 5.92e-01 2.75e+01 ... (remaining 24260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8854 17.97 - 35.95: 1289 35.95 - 53.92: 552 53.92 - 71.90: 150 71.90 - 89.87: 23 Dihedral angle restraints: 10868 sinusoidal: 5004 harmonic: 5864 Sorted by residual: dihedral pdb=" CD ARG D 488 " pdb=" NE ARG D 488 " pdb=" CZ ARG D 488 " pdb=" NH1 ARG D 488 " ideal model delta sinusoidal sigma weight residual 0.00 83.09 -83.09 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CA ASP A 177 " pdb=" C ASP A 177 " pdb=" N GLU A 178 " pdb=" CA GLU A 178 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CD ARG B1093 " pdb=" NE ARG B1093 " pdb=" CZ ARG B1093 " pdb=" NH1 ARG B1093 " ideal model delta sinusoidal sigma weight residual 0.00 -32.49 32.49 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 10865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2592 0.117 - 0.235: 56 0.235 - 0.352: 7 0.352 - 0.470: 4 0.470 - 0.587: 20 Chirality restraints: 2679 Sorted by residual: chirality pdb=" P DT P 5 " pdb=" OP1 DT P 5 " pdb=" OP2 DT P 5 " pdb=" O5' DT P 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.61e+00 chirality pdb=" P DT P 27 " pdb=" OP1 DT P 27 " pdb=" OP2 DT P 27 " pdb=" O5' DT P 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" P DA T 32 " pdb=" OP1 DA T 32 " pdb=" OP2 DA T 32 " pdb=" O5' DA T 32 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.06e+00 ... (remaining 2676 not shown) Planarity restraints: 2950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 488 " -1.072 9.50e-02 1.11e+02 4.80e-01 1.39e+02 pdb=" NE ARG D 488 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG D 488 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 488 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 488 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1093 " 0.575 9.50e-02 1.11e+02 2.58e-01 4.06e+01 pdb=" NE ARG B1093 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG B1093 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B1093 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B1093 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1260 " -0.504 9.50e-02 1.11e+02 2.26e-01 3.13e+01 pdb=" NE ARG A1260 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A1260 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A1260 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1260 " -0.016 2.00e-02 2.50e+03 ... (remaining 2947 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 39 2.51 - 3.11: 12132 3.11 - 3.71: 27136 3.71 - 4.30: 40854 4.30 - 4.90: 66411 Nonbonded interactions: 146572 Sorted by model distance: nonbonded pdb=" F3 BEF A1403 " pdb="MG MG B1401 " model vdw 1.917 2.120 nonbonded pdb="MG MG A1401 " pdb=" F3 BEF A1404 " model vdw 1.929 2.120 nonbonded pdb=" OG1 THR B 43 " pdb="MG MG B1401 " model vdw 2.000 2.170 nonbonded pdb="MG MG A1401 " pdb=" O HOH A1501 " model vdw 2.020 2.170 nonbonded pdb=" OG1 THR A 43 " pdb="MG MG A1401 " model vdw 2.022 2.170 ... (remaining 146567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 2 or resid 4 through 78 or resid 80 through 1309 \ )) selection = (chain 'B' and (resid 1 through 2 or resid 4 through 78 or resid 80 through 236 \ or resid 1078 through 1309)) } ncs_group { reference = (chain 'D' and (resid 8 through 402 or resid 426 through 802)) selection = (chain 'E' and (resid 8 through 508 or resid 801 through 802)) } 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=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.370 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:9.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.005 0.103 17870 Z= 0.321 Angle : 0.821 12.708 24265 Z= 0.485 Chirality : 0.068 0.587 2679 Planarity : 0.013 0.480 2950 Dihedral : 20.380 89.869 7052 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.65 % Allowed : 23.61 % Favored : 74.74 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.39 % 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: 0.53 (0.18), residues: 1985 helix: 1.78 (0.18), residues: 819 sheet: 0.46 (0.27), residues: 343 loop : -1.19 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 483 TYR 0.010 0.001 TYR A 216 PHE 0.026 0.001 PHE E 484 TRP 0.010 0.001 TRP A 164 HIS 0.003 0.001 HIS E 283 Details of bonding type rmsd covalent geometry : bond 0.00508 (17870) covalent geometry : angle 0.82084 (24265) hydrogen bonds : bond 0.15370 ( 865) hydrogen bonds : angle 6.63357 ( 2502) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 652 LYS cc_start: 0.6395 (tttp) cc_final: 0.5529 (OUTLIER) REVERT: A 1 MET cc_start: 0.7432 (ttm) cc_final: 0.6777 (ttm) REVERT: A 19 ASP cc_start: 0.7729 (t70) cc_final: 0.7463 (m-30) REVERT: A 69 ASP cc_start: 0.8310 (t70) cc_final: 0.8080 (t0) REVERT: A 71 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8294 (mtpm) REVERT: A 75 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6772 (mm-30) REVERT: A 92 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 129 LEU cc_start: 0.7937 (mp) cc_final: 0.7455 (tp) REVERT: A 135 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7505 (mm-30) REVERT: A 138 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7495 (mtm110) REVERT: A 190 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7139 (mt-10) REVERT: A 201 GLN cc_start: 0.7927 (tp40) cc_final: 0.7259 (mt0) REVERT: A 204 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6819 (mppt) REVERT: A 211 LYS cc_start: 0.7641 (mttm) cc_final: 0.7182 (pttp) REVERT: A 1111 MET cc_start: 0.7475 (tmm) cc_final: 0.6942 (tmm) REVERT: A 1115 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7050 (mt-10) REVERT: A 1126 LYS cc_start: 0.7759 (ttpt) cc_final: 0.7063 (tptt) REVERT: A 1142 GLU cc_start: 0.7467 (tp30) cc_final: 0.7095 (tp30) REVERT: A 1168 ASP cc_start: 0.7389 (m-30) cc_final: 0.7003 (m-30) REVERT: A 1243 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 1254 LYS cc_start: 0.7940 (mtmt) cc_final: 0.7503 (mttt) REVERT: A 1261 ASN cc_start: 0.7998 (m110) cc_final: 0.7618 (m110) REVERT: A 1290 LYS cc_start: 0.8515 (ptpt) cc_final: 0.7998 (ptmt) REVERT: B 1 MET cc_start: 0.6248 (mmm) cc_final: 0.5878 (mmm) REVERT: B 79 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8347 (ttp-110) REVERT: B 148 LYS cc_start: 0.7996 (tttt) cc_final: 0.7596 (ttmm) REVERT: B 160 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8482 (mm-30) REVERT: B 177 ASP cc_start: 0.8204 (p0) cc_final: 0.7998 (p0) REVERT: B 194 GLN cc_start: 0.7871 (tp40) cc_final: 0.6759 (tt0) REVERT: B 1223 LEU cc_start: 0.8643 (mm) cc_final: 0.8094 (mm) REVERT: B 1251 GLU cc_start: 0.8016 (tp30) cc_final: 0.7622 (mm-30) REVERT: B 1260 ARG cc_start: 0.7613 (mmt180) cc_final: 0.6295 (tmm160) REVERT: B 1294 ASP cc_start: 0.7817 (m-30) cc_final: 0.7343 (m-30) REVERT: D 105 LYS cc_start: 0.7762 (mttp) cc_final: 0.7465 (mtmm) REVERT: D 310 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6508 (mp0) REVERT: D 327 LYS cc_start: 0.7532 (mttt) cc_final: 0.7275 (ptmt) REVERT: D 341 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6521 (tm-30) REVERT: D 442 LYS cc_start: 0.7469 (mtmt) cc_final: 0.6816 (ttpp) REVERT: D 451 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7706 (mt-10) REVERT: D 452 ARG cc_start: 0.8128 (mtp-110) cc_final: 0.7682 (mtm-85) REVERT: D 467 LYS cc_start: 0.6640 (tttt) cc_final: 0.6346 (mppt) REVERT: D 480 LYS cc_start: 0.7544 (ttmm) cc_final: 0.7117 (ttmt) REVERT: D 503 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7049 (mmm160) REVERT: E 64 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7495 (mp0) REVERT: E 157 MET cc_start: 0.7910 (mtt) cc_final: 0.6553 (pmm) REVERT: E 227 ASN cc_start: 0.6832 (p0) cc_final: 0.5949 (m-40) REVERT: E 281 LYS cc_start: 0.7811 (mttt) cc_final: 0.7300 (mtpt) REVERT: E 290 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8479 (tttt) REVERT: E 327 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6794 (mtpt) REVERT: E 341 GLU cc_start: 0.7781 (mm-30) cc_final: 0.6830 (tt0) REVERT: E 345 GLU cc_start: 0.6826 (tt0) cc_final: 0.6414 (mt-10) REVERT: E 387 ASP cc_start: 0.8035 (m-30) cc_final: 0.7783 (p0) REVERT: E 430 GLU cc_start: 0.7652 (mp0) cc_final: 0.7380 (mp0) REVERT: E 431 ASP cc_start: 0.7923 (m-30) cc_final: 0.7476 (t0) REVERT: E 452 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7119 (ptm160) REVERT: E 459 GLN cc_start: 0.7018 (mm-40) cc_final: 0.6386 (mt0) REVERT: E 479 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7315 (pp20) outliers start: 30 outliers final: 11 residues processed: 312 average time/residue: 0.7229 time to fit residues: 247.9513 Evaluate side-chains 241 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 227 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 342 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1181 ASN D 256 ASN D 317 HIS D 401 HIS E 218 GLN E 256 ASN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 ASN E 317 HIS E 330 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115849 restraints weight = 37898.526| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.63 r_work: 0.3174 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17870 Z= 0.152 Angle : 0.568 9.137 24265 Z= 0.301 Chirality : 0.042 0.155 2679 Planarity : 0.004 0.044 2950 Dihedral : 17.301 72.439 2846 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.51 % Allowed : 23.23 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.79 (0.18), residues: 1985 helix: 2.05 (0.18), residues: 826 sheet: 0.50 (0.26), residues: 367 loop : -1.15 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1260 TYR 0.014 0.001 TYR B1282 PHE 0.015 0.001 PHE A 15 TRP 0.007 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00348 (17870) covalent geometry : angle 0.56830 (24265) hydrogen bonds : bond 0.04294 ( 865) hydrogen bonds : angle 4.72368 ( 2502) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 0.733 Fit side-chains REVERT: J 461 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7178 (pp20) REVERT: A 1 MET cc_start: 0.7538 (ttm) cc_final: 0.6714 (ttm) REVERT: A 71 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8498 (mtpm) REVERT: A 92 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7289 (mt-10) REVERT: A 138 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7815 (ttm-80) REVERT: A 190 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 201 GLN cc_start: 0.8014 (tp40) cc_final: 0.7410 (mt0) REVERT: A 204 LYS cc_start: 0.7461 (mttp) cc_final: 0.6963 (mppt) REVERT: A 211 LYS cc_start: 0.7665 (mttm) cc_final: 0.7162 (pttp) REVERT: A 215 GLN cc_start: 0.7440 (tt0) cc_final: 0.7006 (pt0) REVERT: A 218 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 1115 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 1126 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7311 (tptt) REVERT: A 1168 ASP cc_start: 0.7532 (m-30) cc_final: 0.7226 (m-30) REVERT: A 1254 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7659 (mttt) REVERT: A 1261 ASN cc_start: 0.7680 (m110) cc_final: 0.7344 (m110) REVERT: A 1290 LYS cc_start: 0.8451 (ptpt) cc_final: 0.8047 (ptmt) REVERT: B 1 MET cc_start: 0.6406 (mmm) cc_final: 0.6154 (mmm) REVERT: B 138 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7664 (ptp-170) REVERT: B 148 LYS cc_start: 0.8353 (tttt) cc_final: 0.8047 (ttmm) REVERT: B 194 GLN cc_start: 0.8214 (tp40) cc_final: 0.7185 (tt0) REVERT: B 1260 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6605 (tmm160) REVERT: B 1294 ASP cc_start: 0.8215 (m-30) cc_final: 0.7817 (m-30) REVERT: D 105 LYS cc_start: 0.7685 (mttp) cc_final: 0.7413 (mtmm) REVERT: D 274 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7764 (mt) REVERT: D 310 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6437 (mm-30) REVERT: D 327 LYS cc_start: 0.7787 (mttt) cc_final: 0.7354 (ptmt) REVERT: D 338 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6867 (pt0) REVERT: D 341 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6410 (tm-30) REVERT: D 348 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: D 442 LYS cc_start: 0.7470 (mtmt) cc_final: 0.6790 (ttpp) REVERT: D 451 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7576 (mt-10) REVERT: D 452 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7705 (mtm-85) REVERT: D 467 LYS cc_start: 0.6595 (tttt) cc_final: 0.6310 (mppt) REVERT: D 479 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7103 (mt-10) REVERT: D 480 LYS cc_start: 0.7430 (ttmm) cc_final: 0.6973 (ttmt) REVERT: D 503 ARG cc_start: 0.7599 (mtt180) cc_final: 0.7125 (mmm160) REVERT: E 64 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7371 (mp0) REVERT: E 227 ASN cc_start: 0.6950 (p0) cc_final: 0.6105 (m-40) REVERT: E 229 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8470 (mp) REVERT: E 281 LYS cc_start: 0.7606 (mttt) cc_final: 0.7062 (mtpt) REVERT: E 290 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8079 (tttp) REVERT: E 341 GLU cc_start: 0.7698 (mm-30) cc_final: 0.6850 (tt0) REVERT: E 345 GLU cc_start: 0.6731 (tt0) cc_final: 0.6309 (mt-10) REVERT: E 387 ASP cc_start: 0.7985 (m-30) cc_final: 0.7758 (p0) REVERT: E 430 GLU cc_start: 0.7770 (mp0) cc_final: 0.7499 (mp0) REVERT: E 431 ASP cc_start: 0.7998 (m-30) cc_final: 0.7719 (t0) REVERT: E 435 GLN cc_start: 0.7585 (mt0) cc_final: 0.6705 (mt0) REVERT: E 452 ARG cc_start: 0.7937 (ptp90) cc_final: 0.7309 (ptm160) REVERT: E 459 GLN cc_start: 0.6994 (mm-40) cc_final: 0.6472 (mt0) REVERT: E 479 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7303 (pp20) outliers start: 64 outliers final: 26 residues processed: 271 average time/residue: 0.6608 time to fit residues: 198.8746 Evaluate side-chains 245 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1260 ARG Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 355 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 192 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 ASN D 317 HIS D 401 HIS D 477 GLN E 297 HIS E 317 HIS E 330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.153050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113106 restraints weight = 32172.359| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.33 r_work: 0.3156 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17870 Z= 0.209 Angle : 0.589 7.241 24265 Z= 0.313 Chirality : 0.044 0.163 2679 Planarity : 0.004 0.051 2950 Dihedral : 17.067 61.511 2818 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.50 % Allowed : 22.90 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.80 (0.18), residues: 1985 helix: 2.08 (0.18), residues: 821 sheet: 0.52 (0.26), residues: 362 loop : -1.15 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 87 TYR 0.017 0.001 TYR B1282 PHE 0.015 0.002 PHE E 54 TRP 0.008 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00496 (17870) covalent geometry : angle 0.58936 (24265) hydrogen bonds : bond 0.04607 ( 865) hydrogen bonds : angle 4.53147 ( 2502) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 218 time to evaluate : 0.498 Fit side-chains REVERT: J 461 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7194 (pp20) REVERT: A 1 MET cc_start: 0.7561 (ttm) cc_final: 0.6672 (ttm) REVERT: A 92 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 138 ARG cc_start: 0.8257 (ttp-170) cc_final: 0.7787 (ttm-80) REVERT: A 190 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7224 (mm-30) REVERT: A 201 GLN cc_start: 0.7937 (tp40) cc_final: 0.7333 (mt0) REVERT: A 204 LYS cc_start: 0.7349 (mttp) cc_final: 0.6837 (mppt) REVERT: A 211 LYS cc_start: 0.7611 (mttm) cc_final: 0.7107 (pttp) REVERT: A 215 GLN cc_start: 0.7478 (tt0) cc_final: 0.7083 (pt0) REVERT: A 1115 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 1126 LYS cc_start: 0.7910 (ttpt) cc_final: 0.7193 (tptt) REVERT: A 1145 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7803 (mtpt) REVERT: A 1168 ASP cc_start: 0.7627 (m-30) cc_final: 0.7341 (m-30) REVERT: A 1178 LYS cc_start: 0.8905 (mttm) cc_final: 0.8427 (mttp) REVERT: A 1254 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7614 (mttt) REVERT: A 1261 ASN cc_start: 0.7787 (m110) cc_final: 0.7480 (m110) REVERT: A 1290 LYS cc_start: 0.8391 (ptpt) cc_final: 0.7948 (ptmt) REVERT: B 1 MET cc_start: 0.6381 (mmm) cc_final: 0.6164 (mmm) REVERT: B 148 LYS cc_start: 0.8310 (tttt) cc_final: 0.8058 (ttmm) REVERT: B 194 GLN cc_start: 0.8113 (tp40) cc_final: 0.7057 (tt0) REVERT: B 1260 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.6529 (ttm110) REVERT: B 1294 ASP cc_start: 0.8261 (m-30) cc_final: 0.7855 (m-30) REVERT: D 274 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7708 (mt) REVERT: D 310 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6484 (mm-30) REVERT: D 327 LYS cc_start: 0.7840 (mttt) cc_final: 0.7441 (ptmt) REVERT: D 341 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6460 (tm-30) REVERT: D 348 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: D 438 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: D 442 LYS cc_start: 0.7512 (mtmt) cc_final: 0.6826 (ttpp) REVERT: D 451 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7647 (tt0) REVERT: D 452 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7687 (mtm-85) REVERT: D 467 LYS cc_start: 0.6653 (tttt) cc_final: 0.6378 (mppt) REVERT: D 473 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6975 (tp) REVERT: D 480 LYS cc_start: 0.7474 (ttmm) cc_final: 0.7063 (ttmt) REVERT: D 503 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7090 (mmm160) REVERT: E 64 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7396 (mp0) REVERT: E 227 ASN cc_start: 0.6937 (p0) cc_final: 0.6087 (m-40) REVERT: E 229 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8417 (mp) REVERT: E 281 LYS cc_start: 0.7606 (mttt) cc_final: 0.7070 (mtpt) REVERT: E 290 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8063 (tttp) REVERT: E 341 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6901 (tt0) REVERT: E 430 GLU cc_start: 0.7757 (mp0) cc_final: 0.7448 (mp0) REVERT: E 431 ASP cc_start: 0.7965 (m-30) cc_final: 0.7701 (t0) REVERT: E 435 GLN cc_start: 0.7478 (mt0) cc_final: 0.6533 (mt0) REVERT: E 452 ARG cc_start: 0.7980 (ptp90) cc_final: 0.7376 (ptm160) REVERT: E 459 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6539 (tt0) REVERT: E 479 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7361 (pp20) REVERT: E 487 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6247 (mt-10) outliers start: 82 outliers final: 39 residues processed: 272 average time/residue: 0.6171 time to fit residues: 187.1371 Evaluate side-chains 249 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 460 GLU Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1145 LYS Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1260 ARG Chi-restraints excluded: chain B residue 1284 GLU Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 355 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 138 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 725 GLN B 123 HIS D 256 ASN D 317 HIS D 401 HIS E 317 HIS E 330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108304 restraints weight = 36095.758| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.49 r_work: 0.3151 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17870 Z= 0.241 Angle : 0.620 7.373 24265 Z= 0.329 Chirality : 0.045 0.165 2679 Planarity : 0.004 0.041 2950 Dihedral : 17.052 62.002 2818 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.72 % Allowed : 23.34 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.66 (0.18), residues: 1985 helix: 1.93 (0.17), residues: 827 sheet: 0.39 (0.26), residues: 363 loop : -1.18 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 87 TYR 0.018 0.002 TYR B1282 PHE 0.016 0.002 PHE E 54 TRP 0.009 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00579 (17870) covalent geometry : angle 0.61995 (24265) hydrogen bonds : bond 0.04720 ( 865) hydrogen bonds : angle 4.48790 ( 2502) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 214 time to evaluate : 0.648 Fit side-chains REVERT: J 461 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: A 1 MET cc_start: 0.7751 (ttm) cc_final: 0.6734 (ttm) REVERT: A 92 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7430 (mt-10) REVERT: A 138 ARG cc_start: 0.8448 (ttp-170) cc_final: 0.8206 (tmm160) REVERT: A 190 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7537 (mm-30) REVERT: A 201 GLN cc_start: 0.8123 (tp40) cc_final: 0.7445 (mt0) REVERT: A 204 LYS cc_start: 0.7447 (mttp) cc_final: 0.6931 (mppt) REVERT: A 211 LYS cc_start: 0.7720 (mttm) cc_final: 0.7193 (pttp) REVERT: A 215 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: A 218 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: A 1115 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 1126 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7475 (tptt) REVERT: A 1145 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7960 (mtpt) REVERT: A 1168 ASP cc_start: 0.7868 (m-30) cc_final: 0.7582 (m-30) REVERT: A 1178 LYS cc_start: 0.9004 (mttm) cc_final: 0.8515 (mttp) REVERT: A 1254 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7731 (mttt) REVERT: A 1261 ASN cc_start: 0.7918 (m110) cc_final: 0.7610 (m110) REVERT: A 1290 LYS cc_start: 0.8511 (ptpt) cc_final: 0.7778 (mttm) REVERT: B 92 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: B 106 SER cc_start: 0.7858 (OUTLIER) cc_final: 0.7442 (t) REVERT: B 148 LYS cc_start: 0.8413 (tttt) cc_final: 0.8129 (ttmm) REVERT: B 194 GLN cc_start: 0.8373 (tp40) cc_final: 0.7326 (tt0) REVERT: B 1197 MET cc_start: 0.9105 (ttt) cc_final: 0.8770 (ttt) REVERT: B 1294 ASP cc_start: 0.8474 (m-30) cc_final: 0.8055 (m-30) REVERT: D 186 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: D 274 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7783 (mt) REVERT: D 310 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6699 (mm-30) REVERT: D 327 LYS cc_start: 0.7962 (mttt) cc_final: 0.7574 (ptmt) REVERT: D 348 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: D 442 LYS cc_start: 0.7607 (mtmt) cc_final: 0.6867 (ttpp) REVERT: D 451 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7680 (tt0) REVERT: D 452 ARG cc_start: 0.8233 (mtp-110) cc_final: 0.7724 (mtm-85) REVERT: D 467 LYS cc_start: 0.6749 (tttt) cc_final: 0.6485 (mppt) REVERT: D 473 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7204 (tp) REVERT: D 480 LYS cc_start: 0.7716 (ttmm) cc_final: 0.7299 (ttmt) REVERT: D 503 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7124 (mmm160) REVERT: E 64 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7621 (mp0) REVERT: E 227 ASN cc_start: 0.6916 (p0) cc_final: 0.6070 (m-40) REVERT: E 229 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8554 (mp) REVERT: E 281 LYS cc_start: 0.7586 (mttt) cc_final: 0.7045 (mtpt) REVERT: E 290 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8274 (tttm) REVERT: E 341 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7090 (tt0) REVERT: E 430 GLU cc_start: 0.7799 (mp0) cc_final: 0.7475 (mp0) REVERT: E 431 ASP cc_start: 0.8163 (m-30) cc_final: 0.7866 (t0) REVERT: E 435 GLN cc_start: 0.7616 (mt0) cc_final: 0.6840 (mt0) REVERT: E 452 ARG cc_start: 0.8045 (ptp90) cc_final: 0.7432 (ptm160) outliers start: 86 outliers final: 41 residues processed: 270 average time/residue: 0.6485 time to fit residues: 194.1008 Evaluate side-chains 254 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1145 LYS Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 363 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 53 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 ASN D 317 HIS D 401 HIS E 317 HIS E 330 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.155684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115735 restraints weight = 33564.570| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.41 r_work: 0.3183 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17870 Z= 0.130 Angle : 0.535 6.884 24265 Z= 0.286 Chirality : 0.041 0.153 2679 Planarity : 0.003 0.036 2950 Dihedral : 16.746 63.043 2818 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.40 % Allowed : 24.49 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.96 (0.18), residues: 1985 helix: 2.27 (0.17), residues: 818 sheet: 0.52 (0.26), residues: 361 loop : -1.08 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 488 TYR 0.014 0.001 TYR B1282 PHE 0.014 0.001 PHE E 461 TRP 0.010 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00296 (17870) covalent geometry : angle 0.53512 (24265) hydrogen bonds : bond 0.03805 ( 865) hydrogen bonds : angle 4.21036 ( 2502) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 219 time to evaluate : 0.538 Fit side-chains REVERT: J 461 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7158 (pp20) REVERT: A 1 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6629 (ttm) REVERT: A 19 ASP cc_start: 0.7376 (t0) cc_final: 0.7141 (m-30) REVERT: A 92 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 138 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.8130 (tmm160) REVERT: A 190 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7319 (mm-30) REVERT: A 201 GLN cc_start: 0.7983 (tp40) cc_final: 0.7396 (mt0) REVERT: A 204 LYS cc_start: 0.7327 (mttp) cc_final: 0.6845 (mppt) REVERT: A 211 LYS cc_start: 0.7676 (mttm) cc_final: 0.7200 (pttp) REVERT: A 215 GLN cc_start: 0.7565 (tt0) cc_final: 0.7165 (pt0) REVERT: A 1115 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7460 (mt-10) REVERT: A 1126 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7328 (tptt) REVERT: A 1168 ASP cc_start: 0.7642 (m-30) cc_final: 0.7363 (m-30) REVERT: A 1178 LYS cc_start: 0.8929 (mttm) cc_final: 0.8464 (mttp) REVERT: A 1254 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7690 (mttt) REVERT: A 1261 ASN cc_start: 0.7677 (m110) cc_final: 0.7387 (m110) REVERT: A 1290 LYS cc_start: 0.8401 (ptpt) cc_final: 0.7819 (mmtp) REVERT: B 106 SER cc_start: 0.7820 (OUTLIER) cc_final: 0.7460 (t) REVERT: B 138 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7753 (ptp-170) REVERT: B 148 LYS cc_start: 0.8308 (tttt) cc_final: 0.8074 (ttmm) REVERT: B 194 GLN cc_start: 0.8206 (tp40) cc_final: 0.7243 (tt0) REVERT: B 215 GLN cc_start: 0.7638 (tt0) cc_final: 0.7196 (mt0) REVERT: B 1294 ASP cc_start: 0.8289 (m-30) cc_final: 0.7910 (m-30) REVERT: D 274 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7681 (mt) REVERT: D 310 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6640 (mm-30) REVERT: D 327 LYS cc_start: 0.7924 (mttt) cc_final: 0.7573 (ptmt) REVERT: D 348 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: D 442 LYS cc_start: 0.7657 (mtmt) cc_final: 0.6910 (ttpp) REVERT: D 451 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7525 (tt0) REVERT: D 452 ARG cc_start: 0.8171 (mtp-110) cc_final: 0.7750 (mtm-85) REVERT: D 467 LYS cc_start: 0.6629 (tttt) cc_final: 0.6396 (mppt) REVERT: D 473 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7077 (tp) REVERT: D 480 LYS cc_start: 0.7603 (ttmm) cc_final: 0.7156 (ttmt) REVERT: D 503 ARG cc_start: 0.7574 (mtt180) cc_final: 0.7266 (mmm160) REVERT: D 505 ARG cc_start: 0.6425 (OUTLIER) cc_final: 0.6073 (ttt-90) REVERT: E 64 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7440 (mp0) REVERT: E 204 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8001 (mtpp) REVERT: E 227 ASN cc_start: 0.6922 (p0) cc_final: 0.6124 (m-40) REVERT: E 281 LYS cc_start: 0.7600 (mttt) cc_final: 0.7098 (mtpt) REVERT: E 290 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8263 (tttm) REVERT: E 341 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7007 (tt0) REVERT: E 430 GLU cc_start: 0.7751 (mp0) cc_final: 0.7519 (mp0) REVERT: E 435 GLN cc_start: 0.7503 (mt0) cc_final: 0.6618 (mt0) REVERT: E 452 ARG cc_start: 0.8073 (ptp90) cc_final: 0.7455 (ptm160) REVERT: E 479 GLU cc_start: 0.7655 (pp20) cc_final: 0.7403 (pp20) outliers start: 62 outliers final: 34 residues processed: 263 average time/residue: 0.6031 time to fit residues: 176.9997 Evaluate side-chains 238 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 505 ARG Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 355 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 126 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 179 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 ASN D 317 HIS D 401 HIS ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS E 330 GLN E 459 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109989 restraints weight = 44800.970| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.81 r_work: 0.3164 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17870 Z= 0.167 Angle : 0.561 7.357 24265 Z= 0.298 Chirality : 0.042 0.158 2679 Planarity : 0.003 0.037 2950 Dihedral : 16.736 62.784 2818 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.68 % Allowed : 24.55 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.96 (0.18), residues: 1985 helix: 2.28 (0.17), residues: 817 sheet: 0.53 (0.26), residues: 361 loop : -1.08 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 87 TYR 0.014 0.001 TYR B1104 PHE 0.016 0.001 PHE E 103 TRP 0.008 0.001 TRP A 164 HIS 0.006 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00394 (17870) covalent geometry : angle 0.56125 (24265) hydrogen bonds : bond 0.04092 ( 865) hydrogen bonds : angle 4.22114 ( 2502) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 0.458 Fit side-chains REVERT: J 461 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7109 (pp20) REVERT: A 1 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.6509 (ttm) REVERT: A 19 ASP cc_start: 0.7388 (t0) cc_final: 0.7131 (m-30) REVERT: A 92 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 138 ARG cc_start: 0.8337 (ttp-170) cc_final: 0.8101 (tmm160) REVERT: A 190 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7273 (mm-30) REVERT: A 201 GLN cc_start: 0.8007 (tp40) cc_final: 0.7393 (mt0) REVERT: A 204 LYS cc_start: 0.7318 (mttp) cc_final: 0.6814 (mppt) REVERT: A 211 LYS cc_start: 0.7692 (mttm) cc_final: 0.7208 (pttp) REVERT: A 215 GLN cc_start: 0.7570 (tt0) cc_final: 0.7153 (pt0) REVERT: A 1115 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 1126 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7225 (tptt) REVERT: A 1145 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7690 (mtpt) REVERT: A 1168 ASP cc_start: 0.7635 (m-30) cc_final: 0.7355 (m-30) REVERT: A 1178 LYS cc_start: 0.8921 (mttm) cc_final: 0.8440 (mttp) REVERT: A 1254 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7639 (mttt) REVERT: A 1261 ASN cc_start: 0.7689 (m110) cc_final: 0.7362 (m110) REVERT: A 1290 LYS cc_start: 0.8395 (ptpt) cc_final: 0.7786 (mmtp) REVERT: B 106 SER cc_start: 0.7853 (OUTLIER) cc_final: 0.7475 (t) REVERT: B 138 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7719 (ptp-170) REVERT: B 148 LYS cc_start: 0.8254 (tttt) cc_final: 0.7993 (ttmm) REVERT: B 194 GLN cc_start: 0.8160 (tp40) cc_final: 0.7168 (tt0) REVERT: B 215 GLN cc_start: 0.7660 (tt0) cc_final: 0.7225 (mt0) REVERT: B 1260 ARG cc_start: 0.7841 (mmt180) cc_final: 0.6611 (ttm110) REVERT: B 1294 ASP cc_start: 0.8274 (m-30) cc_final: 0.7874 (m-30) REVERT: B 1310 ASN cc_start: 0.7784 (m-40) cc_final: 0.7549 (m110) REVERT: D 51 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: D 274 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7664 (mt) REVERT: D 310 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6622 (mm-30) REVERT: D 327 LYS cc_start: 0.7939 (mttt) cc_final: 0.7556 (ptmt) REVERT: D 348 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: D 442 LYS cc_start: 0.7655 (mtmt) cc_final: 0.6842 (ttpp) REVERT: D 451 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7455 (tt0) REVERT: D 452 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7733 (mtm-85) REVERT: D 467 LYS cc_start: 0.6673 (tttt) cc_final: 0.6438 (mppt) REVERT: D 473 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7061 (tp) REVERT: D 480 LYS cc_start: 0.7650 (ttmm) cc_final: 0.7199 (ttmt) REVERT: D 503 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7189 (mmm160) REVERT: D 505 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.6074 (ttt-90) REVERT: E 64 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7434 (mp0) REVERT: E 192 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.6817 (mmt) REVERT: E 204 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7946 (mtpp) REVERT: E 227 ASN cc_start: 0.6849 (p0) cc_final: 0.6093 (m-40) REVERT: E 281 LYS cc_start: 0.7584 (mttt) cc_final: 0.7061 (mtpt) REVERT: E 290 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8046 (tttp) REVERT: E 341 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6918 (tt0) REVERT: E 452 ARG cc_start: 0.8078 (ptp90) cc_final: 0.7457 (ptm160) REVERT: E 459 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6393 (tt0) REVERT: E 479 GLU cc_start: 0.7589 (pp20) cc_final: 0.7327 (pp20) REVERT: E 487 GLU cc_start: 0.6570 (mm-30) cc_final: 0.6285 (mt-10) outliers start: 67 outliers final: 43 residues processed: 255 average time/residue: 0.5812 time to fit residues: 164.6723 Evaluate side-chains 252 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1145 LYS Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 505 ARG Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 459 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 168 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 140 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 ASN D 317 HIS D 401 HIS E 232 GLN E 259 GLN E 317 HIS E 330 GLN E 435 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.152995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112397 restraints weight = 32245.956| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.46 r_work: 0.3133 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17870 Z= 0.212 Angle : 0.597 8.676 24265 Z= 0.316 Chirality : 0.044 0.173 2679 Planarity : 0.004 0.050 2950 Dihedral : 16.784 62.687 2818 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.90 % Allowed : 24.33 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.84 (0.18), residues: 1985 helix: 2.12 (0.17), residues: 823 sheet: 0.48 (0.26), residues: 362 loop : -1.11 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1105 TYR 0.015 0.002 TYR B1282 PHE 0.017 0.002 PHE E 103 TRP 0.008 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00506 (17870) covalent geometry : angle 0.59663 (24265) hydrogen bonds : bond 0.04402 ( 865) hydrogen bonds : angle 4.28513 ( 2502) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 212 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: J 461 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7162 (pp20) REVERT: A 1 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.6563 (ttm) REVERT: A 19 ASP cc_start: 0.7534 (t0) cc_final: 0.7239 (m-30) REVERT: A 92 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 110 GLU cc_start: 0.8058 (tt0) cc_final: 0.7829 (tt0) REVERT: A 138 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.8146 (tmm160) REVERT: A 190 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7308 (mm-30) REVERT: A 201 GLN cc_start: 0.8024 (tp40) cc_final: 0.7403 (mt0) REVERT: A 204 LYS cc_start: 0.7305 (mttp) cc_final: 0.6791 (mppt) REVERT: A 211 LYS cc_start: 0.7707 (mttm) cc_final: 0.7208 (pttp) REVERT: A 215 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: A 216 TYR cc_start: 0.7859 (m-10) cc_final: 0.7654 (m-10) REVERT: A 1115 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 1126 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7301 (tptt) REVERT: A 1145 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7810 (mtpt) REVERT: A 1168 ASP cc_start: 0.7698 (m-30) cc_final: 0.7425 (m-30) REVERT: A 1178 LYS cc_start: 0.8933 (mttm) cc_final: 0.8464 (mttp) REVERT: A 1254 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7706 (mttt) REVERT: A 1261 ASN cc_start: 0.7790 (m110) cc_final: 0.7477 (m110) REVERT: A 1290 LYS cc_start: 0.8401 (ptpt) cc_final: 0.7817 (mmtp) REVERT: B 92 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: B 106 SER cc_start: 0.7852 (OUTLIER) cc_final: 0.7477 (t) REVERT: B 138 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7637 (ptp-170) REVERT: B 148 LYS cc_start: 0.8330 (tttt) cc_final: 0.8091 (ttmm) REVERT: B 194 GLN cc_start: 0.8221 (tp40) cc_final: 0.7204 (tt0) REVERT: B 1260 ARG cc_start: 0.7828 (mmt180) cc_final: 0.6615 (ttm110) REVERT: B 1294 ASP cc_start: 0.8373 (m-30) cc_final: 0.7971 (m-30) REVERT: B 1310 ASN cc_start: 0.7880 (m-40) cc_final: 0.7609 (m110) REVERT: D 51 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: D 274 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7686 (mt) REVERT: D 310 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6664 (mm-30) REVERT: D 327 LYS cc_start: 0.7950 (mttt) cc_final: 0.7608 (ptmt) REVERT: D 348 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7184 (tt0) REVERT: D 442 LYS cc_start: 0.7651 (mtmt) cc_final: 0.6921 (tmtm) REVERT: D 451 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7478 (tt0) REVERT: D 452 ARG cc_start: 0.8182 (mtp-110) cc_final: 0.7739 (mtm-85) REVERT: D 467 LYS cc_start: 0.6698 (tttt) cc_final: 0.6437 (mppt) REVERT: D 473 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7077 (tp) REVERT: D 480 LYS cc_start: 0.7665 (ttmm) cc_final: 0.7212 (ttmt) REVERT: D 503 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7178 (mmm160) REVERT: D 505 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6015 (ttt-90) REVERT: E 64 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7494 (mp0) REVERT: E 192 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.6846 (mmt) REVERT: E 204 LYS cc_start: 0.8307 (ttmm) cc_final: 0.7961 (mtpp) REVERT: E 227 ASN cc_start: 0.6892 (p0) cc_final: 0.6112 (m-40) REVERT: E 232 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7871 (mm-40) REVERT: E 281 LYS cc_start: 0.7630 (mttt) cc_final: 0.7122 (mtpt) REVERT: E 290 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8104 (tttp) REVERT: E 341 GLU cc_start: 0.7669 (mm-30) cc_final: 0.6983 (tt0) REVERT: E 452 ARG cc_start: 0.8070 (ptp90) cc_final: 0.7427 (ptm160) REVERT: E 459 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6564 (tt0) REVERT: E 479 GLU cc_start: 0.7571 (pp20) cc_final: 0.7314 (pp20) REVERT: E 487 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6288 (mt-10) outliers start: 71 outliers final: 43 residues processed: 261 average time/residue: 0.6436 time to fit residues: 186.6774 Evaluate side-chains 257 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1145 LYS Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 505 ARG Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 459 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 67 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 ASN D 317 HIS D 401 HIS E 232 GLN E 317 HIS E 330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114716 restraints weight = 36104.181| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.59 r_work: 0.3152 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17870 Z= 0.148 Angle : 0.556 9.102 24265 Z= 0.295 Chirality : 0.042 0.153 2679 Planarity : 0.003 0.058 2950 Dihedral : 16.678 63.078 2818 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.51 % Allowed : 24.77 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.98 (0.18), residues: 1985 helix: 2.27 (0.17), residues: 818 sheet: 0.55 (0.26), residues: 361 loop : -1.06 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1105 TYR 0.014 0.001 TYR B1282 PHE 0.026 0.001 PHE E 233 TRP 0.009 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00345 (17870) covalent geometry : angle 0.55637 (24265) hydrogen bonds : bond 0.03979 ( 865) hydrogen bonds : angle 4.19610 ( 2502) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 211 time to evaluate : 0.726 Fit side-chains REVERT: J 461 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: A 1 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.6552 (ttm) REVERT: A 19 ASP cc_start: 0.7551 (t0) cc_final: 0.7237 (m-30) REVERT: A 92 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7398 (mt-10) REVERT: A 110 GLU cc_start: 0.8072 (tt0) cc_final: 0.7846 (tt0) REVERT: A 138 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.8130 (tmm160) REVERT: A 190 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 201 GLN cc_start: 0.8012 (tp40) cc_final: 0.7397 (mt0) REVERT: A 204 LYS cc_start: 0.7276 (mttp) cc_final: 0.6763 (mppt) REVERT: A 211 LYS cc_start: 0.7710 (mttm) cc_final: 0.7211 (pttp) REVERT: A 215 GLN cc_start: 0.7528 (tt0) cc_final: 0.7098 (pt0) REVERT: A 216 TYR cc_start: 0.7876 (m-10) cc_final: 0.7662 (m-10) REVERT: A 1115 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7458 (mt-10) REVERT: A 1126 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7274 (tptt) REVERT: A 1168 ASP cc_start: 0.7663 (m-30) cc_final: 0.7396 (m-30) REVERT: A 1254 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7700 (mttt) REVERT: A 1261 ASN cc_start: 0.7696 (m110) cc_final: 0.7390 (m110) REVERT: A 1290 LYS cc_start: 0.8404 (ptpt) cc_final: 0.7819 (mmtp) REVERT: B 92 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: B 106 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7490 (t) REVERT: B 138 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7748 (ptp90) REVERT: B 148 LYS cc_start: 0.8294 (tttt) cc_final: 0.8049 (ttmm) REVERT: B 194 GLN cc_start: 0.8184 (tp40) cc_final: 0.7191 (tt0) REVERT: B 215 GLN cc_start: 0.7593 (tt0) cc_final: 0.7162 (mt0) REVERT: B 1105 ARG cc_start: 0.7583 (mmm160) cc_final: 0.6923 (mmp-170) REVERT: B 1260 ARG cc_start: 0.7753 (mmt180) cc_final: 0.6526 (ttm110) REVERT: B 1294 ASP cc_start: 0.8321 (m-30) cc_final: 0.7925 (m-30) REVERT: B 1310 ASN cc_start: 0.7847 (m-40) cc_final: 0.7588 (m110) REVERT: D 51 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: D 274 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7640 (mt) REVERT: D 310 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6657 (mm-30) REVERT: D 327 LYS cc_start: 0.7975 (mttt) cc_final: 0.7611 (ptmt) REVERT: D 348 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: D 354 ASN cc_start: 0.7562 (t0) cc_final: 0.7328 (t0) REVERT: D 442 LYS cc_start: 0.7637 (mtmt) cc_final: 0.6882 (tmtm) REVERT: D 451 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7454 (tt0) REVERT: D 452 ARG cc_start: 0.8170 (mtp-110) cc_final: 0.7718 (mtm-85) REVERT: D 467 LYS cc_start: 0.6638 (tttt) cc_final: 0.6413 (mppt) REVERT: D 473 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7026 (tp) REVERT: D 479 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7212 (mt-10) REVERT: D 480 LYS cc_start: 0.7651 (ttmm) cc_final: 0.7195 (ttmt) REVERT: D 503 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7175 (mmm160) REVERT: D 505 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.6042 (ttt-90) REVERT: E 64 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7499 (mp0) REVERT: E 204 LYS cc_start: 0.8296 (ttmm) cc_final: 0.8053 (mtpt) REVERT: E 227 ASN cc_start: 0.6864 (p0) cc_final: 0.6130 (m-40) REVERT: E 232 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7896 (mm-40) REVERT: E 281 LYS cc_start: 0.7575 (mttt) cc_final: 0.7053 (mtpt) REVERT: E 290 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8087 (tttp) REVERT: E 341 GLU cc_start: 0.7670 (mm-30) cc_final: 0.6960 (tt0) REVERT: E 452 ARG cc_start: 0.8049 (ptp90) cc_final: 0.7400 (ptm160) REVERT: E 459 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6348 (tt0) REVERT: E 479 GLU cc_start: 0.7545 (pp20) cc_final: 0.7291 (pp20) REVERT: E 487 GLU cc_start: 0.6563 (mm-30) cc_final: 0.6301 (mt-10) outliers start: 64 outliers final: 43 residues processed: 256 average time/residue: 0.6245 time to fit residues: 179.0937 Evaluate side-chains 258 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 505 ARG Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 459 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 115 optimal weight: 0.0270 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 ASN D 317 HIS D 401 HIS E 232 GLN E 317 HIS E 330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.155672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115722 restraints weight = 37264.343| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.63 r_work: 0.3168 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17870 Z= 0.130 Angle : 0.545 9.814 24265 Z= 0.289 Chirality : 0.041 0.152 2679 Planarity : 0.003 0.056 2950 Dihedral : 16.533 63.190 2818 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.29 % Allowed : 25.15 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.08 (0.18), residues: 1985 helix: 2.36 (0.17), residues: 818 sheet: 0.61 (0.26), residues: 362 loop : -1.01 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1105 TYR 0.017 0.001 TYR D 262 PHE 0.037 0.001 PHE E 233 TRP 0.010 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00298 (17870) covalent geometry : angle 0.54489 (24265) hydrogen bonds : bond 0.03799 ( 865) hydrogen bonds : angle 4.13776 ( 2502) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 0.596 Fit side-chains REVERT: J 461 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: J 462 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8041 (mmtm) REVERT: F 687 LYS cc_start: 0.7564 (mttt) cc_final: 0.6706 (ptmt) REVERT: A 1 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.6525 (ttm) REVERT: A 19 ASP cc_start: 0.7520 (t0) cc_final: 0.7217 (m-30) REVERT: A 92 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7410 (mt-10) REVERT: A 110 GLU cc_start: 0.8067 (tt0) cc_final: 0.7808 (tm-30) REVERT: A 138 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.8135 (tmm160) REVERT: A 190 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7303 (mm-30) REVERT: A 201 GLN cc_start: 0.8006 (tp40) cc_final: 0.7404 (mt0) REVERT: A 204 LYS cc_start: 0.7292 (mttp) cc_final: 0.6778 (mppt) REVERT: A 211 LYS cc_start: 0.7704 (mttm) cc_final: 0.7202 (pttp) REVERT: A 215 GLN cc_start: 0.7535 (tt0) cc_final: 0.7089 (pt0) REVERT: A 216 TYR cc_start: 0.7873 (m-10) cc_final: 0.7645 (m-10) REVERT: A 1096 GLN cc_start: 0.6059 (pm20) cc_final: 0.5797 (pm20) REVERT: A 1115 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7452 (mt-10) REVERT: A 1126 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7301 (tptt) REVERT: A 1168 ASP cc_start: 0.7657 (m-30) cc_final: 0.7388 (m-30) REVERT: A 1254 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7659 (mttt) REVERT: A 1261 ASN cc_start: 0.7628 (m110) cc_final: 0.7308 (m110) REVERT: A 1290 LYS cc_start: 0.8398 (ptpt) cc_final: 0.7820 (mmtp) REVERT: B 92 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: B 106 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7463 (t) REVERT: B 138 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7739 (ptp90) REVERT: B 148 LYS cc_start: 0.8299 (tttt) cc_final: 0.8060 (ttmm) REVERT: B 194 GLN cc_start: 0.8172 (tp40) cc_final: 0.7080 (pt0) REVERT: B 215 GLN cc_start: 0.7567 (tt0) cc_final: 0.7160 (mt0) REVERT: B 1105 ARG cc_start: 0.7560 (mmm160) cc_final: 0.7018 (mmp-170) REVERT: B 1294 ASP cc_start: 0.8244 (m-30) cc_final: 0.7840 (m-30) REVERT: B 1310 ASN cc_start: 0.7802 (m-40) cc_final: 0.7539 (m110) REVERT: D 51 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: D 274 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7520 (mt) REVERT: D 309 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7504 (tpt) REVERT: D 310 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6613 (mm-30) REVERT: D 327 LYS cc_start: 0.7968 (mttt) cc_final: 0.7636 (ptmt) REVERT: D 348 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: D 442 LYS cc_start: 0.7644 (mtmt) cc_final: 0.6869 (ttpp) REVERT: D 451 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7436 (tt0) REVERT: D 452 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7711 (mtm-85) REVERT: D 467 LYS cc_start: 0.6597 (tttt) cc_final: 0.6394 (mppt) REVERT: D 473 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7031 (tp) REVERT: D 480 LYS cc_start: 0.7662 (ttmm) cc_final: 0.7200 (ttmt) REVERT: D 503 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7150 (mmm160) REVERT: D 505 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.6010 (ttt-90) REVERT: E 64 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7502 (mp0) REVERT: E 204 LYS cc_start: 0.8323 (ttmm) cc_final: 0.8090 (mtpt) REVERT: E 208 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7252 (m110) REVERT: E 227 ASN cc_start: 0.6879 (p0) cc_final: 0.6143 (m-40) REVERT: E 281 LYS cc_start: 0.7550 (mttt) cc_final: 0.7027 (mtpt) REVERT: E 290 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8091 (tttp) REVERT: E 341 GLU cc_start: 0.7687 (mm-30) cc_final: 0.6973 (tt0) REVERT: E 452 ARG cc_start: 0.8066 (ptp90) cc_final: 0.7424 (ptm160) REVERT: E 479 GLU cc_start: 0.7570 (pp20) cc_final: 0.7301 (pp20) REVERT: E 487 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6319 (mt-10) outliers start: 60 outliers final: 37 residues processed: 252 average time/residue: 0.6408 time to fit residues: 180.2624 Evaluate side-chains 253 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 505 ARG Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 355 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 140 optimal weight: 0.0060 chunk 88 optimal weight: 2.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 ASN D 317 HIS D 401 HIS E 232 GLN E 317 HIS E 330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116726 restraints weight = 33534.609| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.49 r_work: 0.3198 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17870 Z= 0.121 Angle : 0.538 9.550 24265 Z= 0.284 Chirality : 0.041 0.153 2679 Planarity : 0.003 0.060 2950 Dihedral : 16.342 62.981 2817 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.53 % Allowed : 25.86 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.16 (0.18), residues: 1985 helix: 2.45 (0.17), residues: 817 sheet: 0.65 (0.26), residues: 362 loop : -0.99 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1105 TYR 0.013 0.001 TYR B1282 PHE 0.018 0.001 PHE E 103 TRP 0.011 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00274 (17870) covalent geometry : angle 0.53806 (24265) hydrogen bonds : bond 0.03625 ( 865) hydrogen bonds : angle 4.05185 ( 2502) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.665 Fit side-chains REVERT: J 461 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7012 (pp20) REVERT: J 462 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8007 (mmtm) REVERT: F 687 LYS cc_start: 0.7560 (mttt) cc_final: 0.6781 (ptmt) REVERT: A 1 MET cc_start: 0.7553 (ttm) cc_final: 0.6478 (ttm) REVERT: A 19 ASP cc_start: 0.7458 (t0) cc_final: 0.7179 (m-30) REVERT: A 92 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7432 (mt-10) REVERT: A 110 GLU cc_start: 0.8050 (tt0) cc_final: 0.7800 (tm-30) REVERT: A 138 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.8134 (tmm160) REVERT: A 190 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 201 GLN cc_start: 0.7976 (tp40) cc_final: 0.7377 (mt0) REVERT: A 204 LYS cc_start: 0.7268 (mttp) cc_final: 0.6758 (mppt) REVERT: A 211 LYS cc_start: 0.7631 (mttm) cc_final: 0.7129 (pttp) REVERT: A 215 GLN cc_start: 0.7506 (tt0) cc_final: 0.7063 (pt0) REVERT: A 216 TYR cc_start: 0.7854 (m-10) cc_final: 0.7625 (m-10) REVERT: A 1096 GLN cc_start: 0.6072 (pm20) cc_final: 0.5835 (pm20) REVERT: A 1126 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7270 (tptt) REVERT: A 1168 ASP cc_start: 0.7610 (m-30) cc_final: 0.7325 (m-30) REVERT: A 1178 LYS cc_start: 0.8873 (mttm) cc_final: 0.8350 (mttp) REVERT: A 1254 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7676 (mttt) REVERT: A 1261 ASN cc_start: 0.7508 (m110) cc_final: 0.7202 (m110) REVERT: A 1290 LYS cc_start: 0.8377 (ptpt) cc_final: 0.7813 (mmtp) REVERT: B 92 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: B 106 SER cc_start: 0.7775 (OUTLIER) cc_final: 0.7451 (t) REVERT: B 138 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7720 (ptp90) REVERT: B 148 LYS cc_start: 0.8284 (tttt) cc_final: 0.8011 (ttmm) REVERT: B 194 GLN cc_start: 0.8104 (tp40) cc_final: 0.7041 (pt0) REVERT: B 215 GLN cc_start: 0.7550 (tt0) cc_final: 0.7117 (mt0) REVERT: B 1105 ARG cc_start: 0.7510 (mmm160) cc_final: 0.7080 (mmp-170) REVERT: B 1294 ASP cc_start: 0.8264 (m-30) cc_final: 0.7860 (m-30) REVERT: B 1310 ASN cc_start: 0.7737 (m-40) cc_final: 0.7516 (m110) REVERT: D 232 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7312 (mt0) REVERT: D 274 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7420 (mt) REVERT: D 309 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7455 (tpt) REVERT: D 310 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6581 (mm-30) REVERT: D 327 LYS cc_start: 0.7989 (mttt) cc_final: 0.7629 (ptmt) REVERT: D 442 LYS cc_start: 0.7605 (mtmt) cc_final: 0.6837 (ttpp) REVERT: D 451 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7416 (tt0) REVERT: D 452 ARG cc_start: 0.8128 (mtp-110) cc_final: 0.7720 (mtm-85) REVERT: D 479 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7143 (mt-10) REVERT: D 480 LYS cc_start: 0.7563 (ttmm) cc_final: 0.7102 (ttmt) REVERT: D 503 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7159 (mmm160) REVERT: D 505 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.6025 (ttt-90) REVERT: E 64 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7518 (mp0) REVERT: E 204 LYS cc_start: 0.8287 (ttmm) cc_final: 0.8068 (mtpt) REVERT: E 208 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7299 (m110) REVERT: E 227 ASN cc_start: 0.6826 (p0) cc_final: 0.6109 (m-40) REVERT: E 232 GLN cc_start: 0.8312 (mp-120) cc_final: 0.7893 (mm-40) REVERT: E 281 LYS cc_start: 0.7499 (mttt) cc_final: 0.6964 (mtpt) REVERT: E 290 LYS cc_start: 0.8400 (ttpt) cc_final: 0.8157 (tttm) REVERT: E 324 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7225 (p0) REVERT: E 341 GLU cc_start: 0.7674 (mm-30) cc_final: 0.6934 (tt0) REVERT: E 452 ARG cc_start: 0.8049 (ptp90) cc_final: 0.7311 (ptp-110) REVERT: E 459 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6396 (tt0) REVERT: E 479 GLU cc_start: 0.7544 (pp20) cc_final: 0.7292 (pp20) REVERT: E 487 GLU cc_start: 0.6538 (mm-30) cc_final: 0.6315 (mt-10) outliers start: 46 outliers final: 29 residues processed: 251 average time/residue: 0.5716 time to fit residues: 159.3673 Evaluate side-chains 247 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 505 ARG Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 459 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 193 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 ASN D 317 HIS D 401 HIS E 317 HIS E 330 GLN E 459 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115722 restraints weight = 35944.922| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.49 r_work: 0.3174 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17870 Z= 0.146 Angle : 0.555 11.035 24265 Z= 0.292 Chirality : 0.042 0.156 2679 Planarity : 0.003 0.053 2950 Dihedral : 16.349 62.646 2817 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.69 % Allowed : 26.08 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.14 (0.18), residues: 1985 helix: 2.41 (0.17), residues: 817 sheet: 0.66 (0.26), residues: 362 loop : -0.99 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1105 TYR 0.014 0.001 TYR B1282 PHE 0.015 0.001 PHE D 228 TRP 0.009 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00342 (17870) covalent geometry : angle 0.55453 (24265) hydrogen bonds : bond 0.03835 ( 865) hydrogen bonds : angle 4.10533 ( 2502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6807.59 seconds wall clock time: 116 minutes 28.15 seconds (6988.15 seconds total)