Starting phenix.real_space_refine on Sat Jul 4 03:18:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9j_52961/07_2026/9q9j_52961.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9j_52961/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9q9j_52961/07_2026/9q9j_52961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9j_52961/07_2026/9q9j_52961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q9j_52961/07_2026/9q9j_52961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9j_52961/07_2026/9q9j_52961.map" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 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: 5.05, per 1000 atoms: 0.29 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: 1.60 Conformation dependent library (CDL) restraints added in 1.1 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: 2.21 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: 3.25 Time building geometry restraints manager: 2.10 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: 23722 2.54 - 5.08: 430 5.08 - 7.62: 101 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 - 0.119: 2597 0.119 - 0.239: 51 0.239 - 0.358: 7 0.358 - 0.478: 4 0.478 - 0.597: 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 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.91e+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 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.70e+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 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.36e+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: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.110 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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= 0.363 Angle : 0.830 12.708 24265 Z= 0.522 Chirality : 0.070 0.597 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/Z covalent geometry : bond 0.00528 / 0.36 (17870) covalent geometry : angle 0.82987 / 0.52 (24265) hydrogen bonds : bond 0.15370 / 14.90 ( 865) hydrogen bonds : angle 6.63357 / 7.29 ( 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 : 0.619 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: 0.5977 time to fit residues: 206.3366 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 : 0.605 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 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... A1181 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3881 r_free = 0.3881 target = 0.156347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116279 restraints weight = 37859.484| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.65 r_work: 0.3178 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17870 Z= 0.147 Angle : 0.593 8.529 24265 Z= 0.312 Chirality : 0.044 0.184 2679 Planarity : 0.004 0.038 2950 Dihedral : 17.460 76.783 2846 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.57 % Allowed : 23.12 % Favored : 73.31 % 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: 0.75 (0.18), residues: 1985 helix: 2.01 (0.18), residues: 827 sheet: 0.55 (0.26), residues: 353 loop : -1.17 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1260 TYR 0.012 0.001 TYR B1282 PHE 0.014 0.001 PHE A 15 TRP 0.006 0.001 TRP A 164 HIS 0.006 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (17870) covalent geometry : angle 0.59299 / 0.31 (24265) hydrogen bonds : bond 0.04670 / 4.71 ( 865) hydrogen bonds : angle 4.87300 / 5.32 ( 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 296 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 231 time to evaluate : 0.505 Fit side-chains REVERT: J 461 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: A 1 MET cc_start: 0.7541 (ttm) cc_final: 0.6831 (ttm) REVERT: A 71 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8444 (mtpm) REVERT: A 92 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7353 (mt-10) REVERT: A 138 ARG cc_start: 0.8187 (ttp-170) cc_final: 0.7801 (ttm-80) REVERT: A 190 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 201 GLN cc_start: 0.8010 (tp40) cc_final: 0.7460 (mt0) REVERT: A 204 LYS cc_start: 0.7503 (mttp) cc_final: 0.7030 (mppt) REVERT: A 211 LYS cc_start: 0.7675 (mttm) cc_final: 0.7211 (pttp) REVERT: A 1115 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7102 (mt-10) REVERT: A 1126 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7320 (tptt) REVERT: A 1168 ASP cc_start: 0.7522 (m-30) cc_final: 0.7213 (m-30) REVERT: A 1243 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 1254 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7645 (mttt) REVERT: A 1261 ASN cc_start: 0.7703 (m110) cc_final: 0.7454 (m110) REVERT: A 1290 LYS cc_start: 0.8465 (ptpt) cc_final: 0.8074 (ptmt) REVERT: B 1 MET cc_start: 0.6414 (mmm) cc_final: 0.6150 (mmm) REVERT: B 148 LYS cc_start: 0.8361 (tttt) cc_final: 0.8040 (ttmm) REVERT: B 194 GLN cc_start: 0.8207 (tp40) cc_final: 0.7173 (tt0) REVERT: B 1260 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6628 (tmm160) REVERT: B 1294 ASP cc_start: 0.8177 (m-30) cc_final: 0.7771 (m-30) REVERT: D 105 LYS cc_start: 0.7688 (mttp) cc_final: 0.7428 (mtmm) REVERT: D 274 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7764 (mt) REVERT: D 310 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6405 (mm-30) REVERT: D 327 LYS cc_start: 0.7726 (mttt) cc_final: 0.7339 (ptmt) REVERT: D 341 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6438 (tm-30) REVERT: D 348 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: D 442 LYS cc_start: 0.7449 (mtmt) cc_final: 0.6752 (ttpp) REVERT: D 451 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7626 (mt-10) REVERT: D 452 ARG cc_start: 0.8145 (mtp-110) cc_final: 0.7716 (mtm-85) REVERT: D 467 LYS cc_start: 0.6602 (tttt) cc_final: 0.6319 (mppt) REVERT: D 480 LYS cc_start: 0.7455 (ttmm) cc_final: 0.7000 (ttmt) REVERT: D 503 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7138 (mmm160) REVERT: E 64 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7387 (mp0) REVERT: E 157 MET cc_start: 0.7792 (mtt) cc_final: 0.6634 (pmm) REVERT: E 227 ASN cc_start: 0.6935 (p0) cc_final: 0.6080 (m-40) REVERT: E 229 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8472 (mp) REVERT: E 281 LYS cc_start: 0.7597 (mttt) cc_final: 0.7047 (mtpt) REVERT: E 290 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8171 (tttt) REVERT: E 341 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6796 (tt0) REVERT: E 345 GLU cc_start: 0.6738 (tt0) cc_final: 0.6326 (mt-10) REVERT: E 387 ASP cc_start: 0.7966 (m-30) cc_final: 0.7729 (p0) REVERT: E 430 GLU cc_start: 0.7767 (mp0) cc_final: 0.7525 (mp0) REVERT: E 431 ASP cc_start: 0.7990 (m-30) cc_final: 0.7711 (t0) REVERT: E 435 GLN cc_start: 0.7581 (mt0) cc_final: 0.6695 (mt0) REVERT: E 452 ARG cc_start: 0.7934 (ptp90) cc_final: 0.7315 (ptm160) REVERT: E 459 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6457 (mt0) REVERT: E 479 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7295 (pp20) outliers start: 65 outliers final: 24 residues processed: 268 average time/residue: 0.5952 time to fit residues: 176.5378 Evaluate side-chains 245 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 215 GLN 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 92 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 159 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 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 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: 0.0770 chunk 140 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 91 optimal weight: 0.0870 chunk 72 optimal weight: 3.9990 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: 2.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 317 HIS D 401 HIS D 477 GLN E 259 GLN E 297 HIS E 317 HIS E 330 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.153411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113081 restraints weight = 32079.925| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.36 r_work: 0.3159 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- 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 = 0.47 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 = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17870 Z= 0.204 Angle : 0.608 7.315 24265 Z= 0.321 Chirality : 0.045 0.193 2679 Planarity : 0.004 0.045 2950 Dihedral : 17.300 63.444 2818 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.34 % Allowed : 22.62 % Favored : 73.04 % 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: 0.76 (0.18), residues: 1985 helix: 2.06 (0.18), residues: 821 sheet: 0.47 (0.26), residues: 363 loop : -1.17 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 87 TYR 0.019 0.002 TYR B1282 PHE 0.016 0.002 PHE E 54 TRP 0.007 0.001 TRP A 164 HIS 0.007 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (17870) covalent geometry : angle 0.60814 / 0.32 (24265) hydrogen bonds : bond 0.04845 / 4.83 ( 865) hydrogen bonds : angle 4.61536 / 5.02 ( 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 308 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 229 time to evaluate : 0.748 Fit side-chains REVERT: J 461 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7149 (pp20) REVERT: A 1 MET cc_start: 0.7620 (ttm) cc_final: 0.6736 (ttm) REVERT: A 92 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7242 (mt-10) REVERT: A 138 ARG cc_start: 0.8270 (ttp-170) cc_final: 0.7794 (ttm-80) REVERT: A 190 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7217 (mm-30) REVERT: A 201 GLN cc_start: 0.7966 (tp40) cc_final: 0.7382 (mt0) REVERT: A 204 LYS cc_start: 0.7388 (mttp) cc_final: 0.6860 (mppt) REVERT: A 211 LYS cc_start: 0.7634 (mttm) cc_final: 0.7130 (pttp) REVERT: A 215 GLN cc_start: 0.7460 (tt0) cc_final: 0.7020 (pt0) REVERT: A 1115 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7410 (mt-10) REVERT: A 1126 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7186 (tptt) REVERT: A 1145 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7837 (mtpt) REVERT: A 1168 ASP cc_start: 0.7608 (m-30) cc_final: 0.7313 (m-30) REVERT: A 1178 LYS cc_start: 0.8898 (mttm) cc_final: 0.8423 (mttp) REVERT: A 1254 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7599 (mttt) REVERT: A 1261 ASN cc_start: 0.7747 (m110) cc_final: 0.7436 (m110) REVERT: A 1290 LYS cc_start: 0.8401 (ptpt) cc_final: 0.7954 (ptmt) REVERT: B 1 MET cc_start: 0.6403 (mmm) cc_final: 0.6148 (mmm) REVERT: B 106 SER cc_start: 0.7823 (OUTLIER) cc_final: 0.7409 (t) REVERT: B 148 LYS cc_start: 0.8316 (tttt) cc_final: 0.8025 (ttmm) REVERT: B 194 GLN cc_start: 0.8131 (tp40) cc_final: 0.7067 (tt0) REVERT: B 1197 MET cc_start: 0.9057 (ttt) cc_final: 0.8678 (ttt) REVERT: B 1260 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6524 (tmm160) REVERT: B 1294 ASP cc_start: 0.8230 (m-30) cc_final: 0.7817 (m-30) REVERT: D 274 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7703 (mt) REVERT: D 310 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6468 (mm-30) REVERT: D 327 LYS cc_start: 0.7837 (mttt) cc_final: 0.7455 (ptmt) REVERT: D 338 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: D 341 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6467 (tm-30) REVERT: D 348 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: D 438 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: D 442 LYS cc_start: 0.7441 (mtmt) cc_final: 0.6829 (ttpp) REVERT: D 451 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7645 (tt0) REVERT: D 452 ARG cc_start: 0.8151 (mtp-110) cc_final: 0.7679 (mtm-85) REVERT: D 467 LYS cc_start: 0.6594 (tttt) cc_final: 0.6337 (mppt) REVERT: D 473 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6981 (tp) REVERT: D 480 LYS cc_start: 0.7468 (ttmm) cc_final: 0.7061 (ttmt) REVERT: D 503 ARG cc_start: 0.7531 (mtt180) cc_final: 0.7077 (mmm160) REVERT: E 64 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7331 (mp0) REVERT: E 192 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7914 (mtt) REVERT: E 227 ASN cc_start: 0.6937 (p0) cc_final: 0.6073 (m-40) REVERT: E 229 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8432 (mp) REVERT: E 281 LYS cc_start: 0.7604 (mttt) cc_final: 0.7068 (mtpt) REVERT: E 290 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8050 (tttp) REVERT: E 341 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6916 (tt0) REVERT: E 387 ASP cc_start: 0.8042 (m-30) cc_final: 0.7776 (p0) REVERT: E 430 GLU cc_start: 0.7779 (mp0) cc_final: 0.7453 (mp0) REVERT: E 431 ASP cc_start: 0.7993 (m-30) cc_final: 0.7677 (t0) REVERT: E 435 GLN cc_start: 0.7516 (mt0) cc_final: 0.6597 (mt0) REVERT: E 452 ARG cc_start: 0.7989 (ptp90) cc_final: 0.7392 (ptm160) REVERT: E 459 GLN cc_start: 0.6993 (mm-40) cc_final: 0.6545 (tt0) REVERT: E 479 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7372 (pp20) REVERT: E 487 GLU cc_start: 0.6627 (mm-30) cc_final: 0.6225 (mt-10) outliers start: 79 outliers final: 36 residues processed: 283 average time/residue: 0.6412 time to fit residues: 202.1824 Evaluate side-chains 258 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 76 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 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 106 SER 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 192 MET 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 338 GLU 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 192 MET 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: 0.9990 chunk 150 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 1 optimal weight: 30.0000 chunk 182 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 725 GLN D 256 ASN D 317 HIS D 401 HIS 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 = 0.3868 r_free = 0.3868 target = 0.155223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114971 restraints weight = 35980.252| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.27 r_work: 0.3196 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17870 Z= 0.142 Angle : 0.557 6.750 24265 Z= 0.294 Chirality : 0.043 0.279 2679 Planarity : 0.003 0.037 2950 Dihedral : 17.140 65.410 2818 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.79 % Allowed : 24.00 % Favored : 72.21 % 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: 0.89 (0.18), residues: 1985 helix: 2.16 (0.18), residues: 822 sheet: 0.56 (0.26), residues: 362 loop : -1.12 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 120 TYR 0.013 0.001 TYR B1282 PHE 0.013 0.001 PHE E 461 TRP 0.009 0.001 TRP A 164 HIS 0.006 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (17870) covalent geometry : angle 0.55730 / 0.29 (24265) hydrogen bonds : bond 0.04108 / 4.19 ( 865) hydrogen bonds : angle 4.40927 / 4.83 ( 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 292 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 223 time to evaluate : 0.609 Fit side-chains REVERT: J 461 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7257 (pp20) REVERT: A 1 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6917 (ttm) REVERT: A 92 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7506 (mt-10) REVERT: A 138 ARG cc_start: 0.8453 (ttp-170) cc_final: 0.7952 (ttm-80) REVERT: A 190 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 201 GLN cc_start: 0.8130 (tp40) cc_final: 0.7532 (mt0) REVERT: A 204 LYS cc_start: 0.7527 (mttp) cc_final: 0.7013 (mppt) REVERT: A 211 LYS cc_start: 0.7686 (mttm) cc_final: 0.7177 (pttp) REVERT: A 215 GLN cc_start: 0.7560 (tt0) cc_final: 0.7109 (pt0) REVERT: A 1115 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 1126 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7507 (tptt) REVERT: A 1168 ASP cc_start: 0.7774 (m-30) cc_final: 0.7479 (m-30) REVERT: A 1178 LYS cc_start: 0.8956 (mttm) cc_final: 0.8496 (mttp) REVERT: A 1254 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7701 (mttt) REVERT: A 1261 ASN cc_start: 0.7794 (m110) cc_final: 0.7481 (m110) REVERT: A 1290 LYS cc_start: 0.8503 (ptpt) cc_final: 0.8069 (ptmt) REVERT: B 1 MET cc_start: 0.6647 (mmm) cc_final: 0.6360 (mmm) REVERT: B 92 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: B 106 SER cc_start: 0.7841 (OUTLIER) cc_final: 0.7433 (t) REVERT: B 138 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7814 (ptp-170) REVERT: B 148 LYS cc_start: 0.8420 (tttt) cc_final: 0.8153 (ttmm) REVERT: B 194 GLN cc_start: 0.8388 (tp40) cc_final: 0.7355 (tt0) REVERT: B 1111 MET cc_start: 0.6612 (ttp) cc_final: 0.6381 (ttp) REVERT: B 1260 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6518 (ttm110) REVERT: B 1294 ASP cc_start: 0.8385 (m-30) cc_final: 0.7984 (m-30) REVERT: D 274 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7711 (mt) REVERT: D 310 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6614 (mm-30) REVERT: D 327 LYS cc_start: 0.7864 (mttt) cc_final: 0.7463 (ptmt) REVERT: D 341 GLU cc_start: 0.7571 (mm-30) cc_final: 0.6599 (tm-30) REVERT: D 348 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: D 438 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7564 (pt0) REVERT: D 442 LYS cc_start: 0.7637 (mtmt) cc_final: 0.6956 (tmtm) REVERT: D 451 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7662 (tt0) REVERT: D 452 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7708 (mtm-85) REVERT: D 467 LYS cc_start: 0.6654 (tttt) cc_final: 0.6358 (mppt) REVERT: D 480 LYS cc_start: 0.7572 (ttmm) cc_final: 0.7151 (ttmt) REVERT: D 503 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7116 (mmm160) REVERT: E 64 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7516 (mp0) REVERT: E 192 MET cc_start: 0.8363 (mmm) cc_final: 0.8141 (mtt) REVERT: E 227 ASN cc_start: 0.6974 (p0) cc_final: 0.6130 (m-40) REVERT: E 229 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8512 (mp) REVERT: E 281 LYS cc_start: 0.7571 (mttt) cc_final: 0.7037 (mtpt) REVERT: E 290 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8269 (tttm) REVERT: E 341 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7051 (tt0) REVERT: E 387 ASP cc_start: 0.8211 (m-30) cc_final: 0.7895 (p0) REVERT: E 430 GLU cc_start: 0.7791 (mp0) cc_final: 0.7432 (mp0) REVERT: E 431 ASP cc_start: 0.8136 (m-30) cc_final: 0.7829 (t0) REVERT: E 435 GLN cc_start: 0.7641 (mt0) cc_final: 0.6864 (mt0) REVERT: E 452 ARG cc_start: 0.8043 (ptp90) cc_final: 0.7402 (ptm160) REVERT: E 459 GLN cc_start: 0.7112 (mm-40) cc_final: 0.6647 (tt0) REVERT: E 479 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7393 (pp20) REVERT: E 487 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6328 (mt-10) outliers start: 69 outliers final: 37 residues processed: 266 average time/residue: 0.5683 time to fit residues: 168.4510 Evaluate side-chains 253 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 GLU 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 92 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 201 GLN 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 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 156 SER Chi-restraints excluded: chain D residue 159 VAL 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 294 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 438 GLN 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 162 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 53 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 193 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN D 256 ASN D 317 HIS D 401 HIS 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 = 0.3857 r_free = 0.3857 target = 0.154232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113644 restraints weight = 33479.620| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.47 r_work: 0.3149 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 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 = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17870 Z= 0.173 Angle : 0.584 9.600 24265 Z= 0.306 Chirality : 0.045 0.432 2679 Planarity : 0.004 0.037 2950 Dihedral : 17.050 63.672 2818 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.39 % Allowed : 23.50 % 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: 0.88 (0.18), residues: 1985 helix: 2.16 (0.18), residues: 822 sheet: 0.58 (0.26), residues: 363 loop : -1.13 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 87 TYR 0.017 0.001 TYR B1282 PHE 0.015 0.001 PHE E 54 TRP 0.008 0.001 TRP A 164 HIS 0.006 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (17870) covalent geometry : angle 0.58355 / 0.31 (24265) hydrogen bonds : bond 0.04341 / 4.40 ( 865) hydrogen bonds : angle 4.35808 / 4.76 ( 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 296 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 216 time to evaluate : 0.696 Fit side-chains REVERT: J 461 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: A 1 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.6720 (ttm) REVERT: A 92 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7359 (mt-10) REVERT: A 138 ARG cc_start: 0.8331 (ttp-170) cc_final: 0.7845 (ttm-80) REVERT: A 190 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7327 (mm-30) REVERT: A 201 GLN cc_start: 0.7997 (tp40) cc_final: 0.7439 (mt0) REVERT: A 204 LYS cc_start: 0.7402 (mttp) cc_final: 0.6872 (mppt) REVERT: A 211 LYS cc_start: 0.7636 (mttm) cc_final: 0.7109 (pttp) REVERT: A 215 GLN cc_start: 0.7534 (tt0) cc_final: 0.7096 (pt0) REVERT: A 218 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: A 1115 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7464 (mt-10) REVERT: A 1126 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7296 (tptt) REVERT: A 1145 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7836 (mtpt) REVERT: A 1168 ASP cc_start: 0.7638 (m-30) cc_final: 0.7355 (m-30) REVERT: A 1178 LYS cc_start: 0.8913 (mttm) cc_final: 0.8453 (mttp) REVERT: A 1254 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7648 (mttt) REVERT: A 1261 ASN cc_start: 0.7732 (m110) cc_final: 0.7449 (m110) REVERT: A 1290 LYS cc_start: 0.8403 (ptpt) cc_final: 0.7825 (mmtp) REVERT: B 92 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: B 106 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7457 (t) REVERT: B 148 LYS cc_start: 0.8340 (tttt) cc_final: 0.8091 (ttmm) REVERT: B 194 GLN cc_start: 0.8175 (tp40) cc_final: 0.7170 (tt0) REVERT: B 1099 ASP cc_start: 0.5927 (OUTLIER) cc_final: 0.5697 (OUTLIER) REVERT: B 1111 MET cc_start: 0.6505 (ttp) cc_final: 0.6291 (ttp) REVERT: B 1294 ASP cc_start: 0.8293 (m-30) cc_final: 0.7897 (m-30) REVERT: D 51 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: D 274 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7701 (mt) REVERT: D 310 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6639 (mm-30) REVERT: D 327 LYS cc_start: 0.7825 (mttt) cc_final: 0.7469 (ptmt) REVERT: D 341 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6428 (tm-30) REVERT: D 348 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: D 438 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: D 442 LYS cc_start: 0.7604 (mtmt) cc_final: 0.6938 (tmtm) REVERT: D 451 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7658 (tt0) REVERT: D 452 ARG cc_start: 0.8191 (mtp-110) cc_final: 0.7723 (mtm-85) REVERT: D 467 LYS cc_start: 0.6670 (tttt) cc_final: 0.6412 (mppt) REVERT: D 473 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7085 (tp) REVERT: D 480 LYS cc_start: 0.7586 (ttmm) cc_final: 0.7133 (ttmt) REVERT: D 503 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7257 (mmm160) REVERT: E 64 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7391 (mp0) REVERT: E 227 ASN cc_start: 0.6958 (p0) cc_final: 0.6126 (m-40) REVERT: E 229 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8457 (mp) REVERT: E 281 LYS cc_start: 0.7599 (mttt) cc_final: 0.7078 (mtpt) REVERT: E 290 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8248 (tttm) REVERT: E 341 GLU cc_start: 0.7684 (mm-30) cc_final: 0.6978 (tt0) REVERT: E 387 ASP cc_start: 0.8095 (m-30) cc_final: 0.7826 (p0) REVERT: E 430 GLU cc_start: 0.7780 (mp0) cc_final: 0.7473 (mp0) REVERT: E 435 GLN cc_start: 0.7525 (mt0) cc_final: 0.6677 (mt0) REVERT: E 452 ARG cc_start: 0.8071 (ptp90) cc_final: 0.7430 (ptm160) REVERT: E 459 GLN cc_start: 0.6993 (mm-40) cc_final: 0.6577 (tt0) REVERT: E 479 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7422 (pp20) REVERT: E 487 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6353 (mt-10) outliers start: 80 outliers final: 44 residues processed: 271 average time/residue: 0.5844 time to fit residues: 176.3997 Evaluate side-chains 262 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 205 GLU 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 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 210 LEU Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 1099 ASP 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 156 SER Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 159 VAL 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 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 162 ILE 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 342 GLU 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: 9.9990 chunk 33 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 684 ASN D 256 ASN D 317 HIS D 401 HIS 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 = 0.3879 r_free = 0.3879 target = 0.156528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113022 restraints weight = 44997.149| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.85 r_work: 0.3196 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17870 Z= 0.123 Angle : 0.545 6.730 24265 Z= 0.287 Chirality : 0.042 0.272 2679 Planarity : 0.003 0.036 2950 Dihedral : 16.935 64.253 2818 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.13 % Allowed : 25.10 % 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: 1.04 (0.18), residues: 1985 helix: 2.31 (0.17), residues: 817 sheet: 0.65 (0.26), residues: 363 loop : -1.05 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1260 TYR 0.016 0.001 TYR B1282 PHE 0.014 0.001 PHE E 504 TRP 0.010 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17870) covalent geometry : angle 0.54516 / 0.29 (24265) hydrogen bonds : bond 0.03865 / 3.96 ( 865) hydrogen bonds : angle 4.22615 / 4.62 ( 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 269 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 0.512 Fit side-chains REVERT: J 461 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7158 (pp20) REVERT: A 1 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.6702 (ttm) REVERT: A 92 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 138 ARG cc_start: 0.8328 (ttp-170) cc_final: 0.7829 (ttm-80) REVERT: A 190 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 201 GLN cc_start: 0.7976 (tp40) cc_final: 0.7418 (mt0) REVERT: A 204 LYS cc_start: 0.7344 (mttp) cc_final: 0.6811 (mppt) REVERT: A 211 LYS cc_start: 0.7616 (mttm) cc_final: 0.7109 (pttp) REVERT: A 215 GLN cc_start: 0.7523 (tt0) cc_final: 0.7082 (pt0) REVERT: A 218 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: A 1115 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7417 (mt-10) REVERT: A 1126 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7319 (tptt) REVERT: A 1168 ASP cc_start: 0.7586 (m-30) cc_final: 0.7296 (m-30) REVERT: A 1178 LYS cc_start: 0.8903 (mttm) cc_final: 0.8457 (mttp) REVERT: A 1254 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7634 (mttt) REVERT: A 1261 ASN cc_start: 0.7615 (m110) cc_final: 0.7327 (m110) REVERT: A 1290 LYS cc_start: 0.8400 (ptpt) cc_final: 0.7808 (mmtp) REVERT: B 148 LYS cc_start: 0.8305 (tttt) cc_final: 0.8053 (ttmm) REVERT: B 194 GLN cc_start: 0.8172 (tp40) cc_final: 0.7199 (tt0) REVERT: B 1111 MET cc_start: 0.6526 (ttp) cc_final: 0.6281 (ttp) REVERT: B 1260 ARG cc_start: 0.7806 (mmt180) cc_final: 0.6664 (tmm160) REVERT: B 1294 ASP cc_start: 0.8251 (m-30) cc_final: 0.7841 (m-30) REVERT: D 51 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: D 274 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7643 (mt) REVERT: D 310 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6627 (mm-30) REVERT: D 327 LYS cc_start: 0.7914 (mttt) cc_final: 0.7540 (ptmt) REVERT: D 341 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6468 (tm-30) REVERT: D 348 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: D 438 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7548 (pt0) REVERT: D 442 LYS cc_start: 0.7590 (mtmt) cc_final: 0.6922 (tmtm) REVERT: D 451 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7636 (tt0) REVERT: D 452 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7721 (mtm-85) REVERT: D 467 LYS cc_start: 0.6642 (tttt) cc_final: 0.6375 (mppt) REVERT: D 473 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7030 (tp) REVERT: D 480 LYS cc_start: 0.7503 (ttmm) cc_final: 0.7049 (ttmt) REVERT: D 503 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7258 (mmm160) REVERT: E 64 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7423 (mp0) REVERT: E 227 ASN cc_start: 0.6894 (p0) cc_final: 0.6109 (m-40) REVERT: E 281 LYS cc_start: 0.7533 (mttt) cc_final: 0.7016 (mtpt) REVERT: E 290 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8264 (tttm) REVERT: E 341 GLU cc_start: 0.7628 (mm-30) cc_final: 0.6948 (tt0) REVERT: E 387 ASP cc_start: 0.8092 (m-30) cc_final: 0.7820 (p0) REVERT: E 452 ARG cc_start: 0.8060 (ptp90) cc_final: 0.7425 (ptm160) REVERT: E 459 GLN cc_start: 0.6963 (mm-40) cc_final: 0.6577 (tt0) REVERT: E 487 GLU cc_start: 0.6609 (mm-30) cc_final: 0.6393 (mt-10) outliers start: 57 outliers final: 34 residues processed: 253 average time/residue: 0.5632 time to fit residues: 159.6570 Evaluate side-chains 244 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 183 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 218 GLU 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 201 GLN 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 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 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 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 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 168 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 435 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.154310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114293 restraints weight = 32032.207| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.34 r_work: 0.3166 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 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 = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17870 Z= 0.176 Angle : 0.584 10.657 24265 Z= 0.305 Chirality : 0.044 0.249 2679 Planarity : 0.003 0.038 2950 Dihedral : 16.942 63.011 2818 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.79 % Allowed : 24.71 % Favored : 71.50 % 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: 2.20 (0.18), residues: 824 sheet: 0.64 (0.26), residues: 362 loop : -1.07 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1260 TYR 0.017 0.001 TYR B1282 PHE 0.014 0.001 PHE E 54 TRP 0.007 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (17870) covalent geometry : angle 0.58378 / 0.30 (24265) hydrogen bonds : bond 0.04231 / 4.31 ( 865) hydrogen bonds : angle 4.27143 / 4.65 ( 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 277 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 208 time to evaluate : 0.620 Fit side-chains REVERT: J 461 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7157 (pp20) REVERT: A 1 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6667 (ttm) REVERT: A 92 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7343 (mt-10) REVERT: A 138 ARG cc_start: 0.8329 (ttp-170) cc_final: 0.8100 (tmm160) REVERT: A 190 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7289 (mm-30) REVERT: A 201 GLN cc_start: 0.7989 (tp40) cc_final: 0.7436 (mt0) REVERT: A 204 LYS cc_start: 0.7359 (mttp) cc_final: 0.6823 (mppt) REVERT: A 211 LYS cc_start: 0.7639 (mttm) cc_final: 0.7143 (pttp) REVERT: A 215 GLN cc_start: 0.7583 (tt0) cc_final: 0.7161 (pt0) REVERT: A 218 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: A 1115 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7437 (mt-10) REVERT: A 1126 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7302 (tptt) REVERT: A 1145 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7758 (mtpt) REVERT: A 1168 ASP cc_start: 0.7621 (m-30) cc_final: 0.7342 (m-30) REVERT: A 1178 LYS cc_start: 0.8912 (mttm) cc_final: 0.8454 (mttp) REVERT: A 1254 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7669 (mttt) REVERT: A 1261 ASN cc_start: 0.7691 (m110) cc_final: 0.7417 (m110) REVERT: A 1290 LYS cc_start: 0.8384 (ptpt) cc_final: 0.7809 (mmtp) REVERT: B 92 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: B 106 SER cc_start: 0.7851 (OUTLIER) cc_final: 0.7467 (t) REVERT: B 148 LYS cc_start: 0.8328 (tttt) cc_final: 0.8075 (ttmm) REVERT: B 194 GLN cc_start: 0.8171 (tp40) cc_final: 0.7171 (tt0) REVERT: B 1099 ASP cc_start: 0.5997 (OUTLIER) cc_final: 0.5792 (p0) REVERT: B 1111 MET cc_start: 0.6531 (ttp) cc_final: 0.6302 (ttp) REVERT: B 1260 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6615 (ttm110) REVERT: B 1294 ASP cc_start: 0.8277 (m-30) cc_final: 0.7882 (m-30) REVERT: D 51 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: D 274 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7647 (mt) REVERT: D 310 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6627 (mm-30) REVERT: D 327 LYS cc_start: 0.7901 (mttt) cc_final: 0.7542 (ptmt) REVERT: D 341 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6506 (tm-30) REVERT: D 348 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: D 438 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: D 442 LYS cc_start: 0.7612 (mtmt) cc_final: 0.6943 (tmtm) REVERT: D 451 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7435 (mt-10) REVERT: D 452 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7742 (mtm-85) REVERT: D 467 LYS cc_start: 0.6644 (tttt) cc_final: 0.6410 (mppt) REVERT: D 473 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7065 (tp) REVERT: D 480 LYS cc_start: 0.7589 (ttmm) cc_final: 0.7161 (ttmt) REVERT: D 503 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7236 (mmm160) REVERT: E 64 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7432 (mp0) REVERT: E 227 ASN cc_start: 0.6898 (p0) cc_final: 0.6128 (m-40) REVERT: E 281 LYS cc_start: 0.7563 (mttt) cc_final: 0.7040 (mtpt) REVERT: E 290 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8293 (tttm) REVERT: E 341 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6972 (tt0) REVERT: E 452 ARG cc_start: 0.8074 (ptp90) cc_final: 0.7444 (ptm160) REVERT: E 459 GLN cc_start: 0.6954 (mm-40) cc_final: 0.6568 (tt0) REVERT: E 487 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6383 (mt-10) outliers start: 69 outliers final: 42 residues processed: 255 average time/residue: 0.6045 time to fit residues: 171.4116 Evaluate side-chains 255 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 205 GLU 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 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 210 LEU Chi-restraints excluded: chain B residue 1099 ASP 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 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 159 VAL 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 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 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 342 GLU Chi-restraints excluded: chain E residue 355 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 187 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 125 optimal weight: 0.0470 chunk 32 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 256 ASN D 317 HIS D 401 HIS E 232 GLN E 259 GLN 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 = 0.3878 r_free = 0.3878 target = 0.156279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115283 restraints weight = 35834.995| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.62 r_work: 0.3176 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- 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 = 0.46 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1904 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= 0.118 Angle : 0.545 8.451 24265 Z= 0.286 Chirality : 0.042 0.220 2679 Planarity : 0.003 0.037 2950 Dihedral : 16.863 63.273 2818 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.19 % Allowed : 25.10 % 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: 1.12 (0.18), residues: 1985 helix: 2.36 (0.17), residues: 819 sheet: 0.70 (0.26), residues: 362 loop : -1.00 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.012 0.001 TYR D 262 PHE 0.013 0.001 PHE E 504 TRP 0.009 0.001 TRP A 164 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (17870) covalent geometry : angle 0.54463 / 0.29 (24265) hydrogen bonds : bond 0.03835 / 3.93 ( 865) hydrogen bonds : angle 4.17750 / 4.56 ( 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 270 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 0.562 Fit side-chains REVERT: J 461 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: A 1 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6627 (ttm) REVERT: A 92 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 138 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.8109 (tmm160) REVERT: A 190 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7320 (mm-30) REVERT: A 201 GLN cc_start: 0.7991 (tp40) cc_final: 0.7427 (mt0) REVERT: A 204 LYS cc_start: 0.7350 (mttp) cc_final: 0.6808 (mppt) REVERT: A 211 LYS cc_start: 0.7632 (mttm) cc_final: 0.7141 (pttp) REVERT: A 215 GLN cc_start: 0.7574 (tt0) cc_final: 0.7151 (pt0) REVERT: A 216 TYR cc_start: 0.7905 (m-10) cc_final: 0.7705 (m-10) REVERT: A 1115 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 1126 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7322 (tptt) REVERT: A 1168 ASP cc_start: 0.7643 (m-30) cc_final: 0.7362 (m-30) REVERT: A 1178 LYS cc_start: 0.8914 (mttm) cc_final: 0.8451 (mttp) REVERT: A 1254 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7663 (mttt) REVERT: A 1261 ASN cc_start: 0.7628 (m110) cc_final: 0.7333 (m110) REVERT: A 1290 LYS cc_start: 0.8394 (ptpt) cc_final: 0.7833 (mmtp) REVERT: B 148 LYS cc_start: 0.8317 (tttt) cc_final: 0.8065 (ttmm) REVERT: B 194 GLN cc_start: 0.8167 (tp40) cc_final: 0.7215 (tt0) REVERT: B 1111 MET cc_start: 0.6476 (ttp) cc_final: 0.6259 (ttp) REVERT: B 1260 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6605 (ttm110) REVERT: B 1294 ASP cc_start: 0.8250 (m-30) cc_final: 0.7842 (m-30) REVERT: B 1310 ASN cc_start: 0.7798 (m-40) cc_final: 0.7547 (m110) REVERT: D 274 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7596 (mt) REVERT: D 310 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6566 (mm-30) REVERT: D 327 LYS cc_start: 0.7893 (mttt) cc_final: 0.7525 (ptmt) REVERT: D 341 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6495 (tm-30) REVERT: D 348 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: D 354 ASN cc_start: 0.7600 (t0) cc_final: 0.7322 (t0) REVERT: D 438 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7540 (pt0) REVERT: D 442 LYS cc_start: 0.7624 (mtmt) cc_final: 0.6931 (tmtm) REVERT: D 451 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7583 (tt0) REVERT: D 452 ARG cc_start: 0.8179 (mtp-110) cc_final: 0.7718 (mtm-85) REVERT: D 467 LYS cc_start: 0.6631 (tttt) cc_final: 0.6415 (mppt) REVERT: D 473 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7047 (tp) REVERT: D 479 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7010 (mt-10) REVERT: D 480 LYS cc_start: 0.7566 (ttmm) cc_final: 0.7110 (ttmt) REVERT: D 503 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7180 (mmm160) REVERT: E 64 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7404 (mp0) REVERT: E 157 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7804 (mmm) REVERT: E 227 ASN cc_start: 0.6869 (p0) cc_final: 0.6104 (m-40) REVERT: E 281 LYS cc_start: 0.7492 (mttt) cc_final: 0.6960 (mtpt) REVERT: E 290 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8107 (tttp) REVERT: E 341 GLU cc_start: 0.7684 (mm-30) cc_final: 0.6978 (tt0) REVERT: E 452 ARG cc_start: 0.8053 (ptp90) cc_final: 0.7417 (ptm160) REVERT: E 459 GLN cc_start: 0.6954 (mm-40) cc_final: 0.6549 (tt0) REVERT: E 479 GLU cc_start: 0.7619 (pp20) cc_final: 0.7363 (pp20) REVERT: E 487 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6372 (mt-10) outliers start: 58 outliers final: 37 residues processed: 250 average time/residue: 0.5855 time to fit residues: 163.6149 Evaluate side-chains 251 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 128 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 210 LEU 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 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 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 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 136 ASP Chi-restraints excluded: chain E residue 157 MET 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 342 GLU Chi-restraints excluded: chain E residue 355 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 51 optimal weight: 0.0970 chunk 54 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 0.0770 chunk 115 optimal weight: 5.9990 overall best weight: 1.1538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3875 r_free = 0.3875 target = 0.156009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114842 restraints weight = 36960.748| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.70 r_work: 0.3170 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17870 Z= 0.133 Angle : 0.558 8.287 24265 Z= 0.292 Chirality : 0.042 0.203 2679 Planarity : 0.003 0.038 2950 Dihedral : 16.802 62.332 2817 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.35 % Allowed : 25.15 % Favored : 71.50 % 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: 1.12 (0.18), residues: 1985 helix: 2.36 (0.17), residues: 818 sheet: 0.70 (0.26), residues: 362 loop : -1.00 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 120 TYR 0.014 0.001 TYR D 262 PHE 0.014 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/Z covalent geometry : bond 0.00300 / 0.13 (17870) covalent geometry : angle 0.55775 / 0.29 (24265) hydrogen bonds : bond 0.03880 / 3.97 ( 865) hydrogen bonds : angle 4.15477 / 4.53 ( 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 270 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 0.493 Fit side-chains REVERT: J 461 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7071 (pp20) REVERT: A 1 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.6673 (ttm) REVERT: A 92 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7383 (mt-10) REVERT: A 138 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.8126 (tmm160) REVERT: A 190 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 201 GLN cc_start: 0.7999 (tp40) cc_final: 0.7447 (mt0) REVERT: A 204 LYS cc_start: 0.7333 (mttp) cc_final: 0.6785 (mppt) REVERT: A 211 LYS cc_start: 0.7607 (mttm) cc_final: 0.7106 (pttp) REVERT: A 215 GLN cc_start: 0.7537 (tt0) cc_final: 0.7088 (pt0) REVERT: A 1115 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 1126 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7301 (tptt) REVERT: A 1168 ASP cc_start: 0.7655 (m-30) cc_final: 0.7364 (m-30) REVERT: A 1178 LYS cc_start: 0.8908 (mttm) cc_final: 0.8436 (mttp) REVERT: A 1254 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7649 (mttt) REVERT: A 1261 ASN cc_start: 0.7622 (m110) cc_final: 0.7309 (m110) REVERT: A 1290 LYS cc_start: 0.8403 (ptpt) cc_final: 0.7828 (mmtp) REVERT: B 106 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7467 (t) REVERT: B 148 LYS cc_start: 0.8321 (tttt) cc_final: 0.8071 (ttmm) REVERT: B 194 GLN cc_start: 0.8154 (tp40) cc_final: 0.7087 (pt0) REVERT: B 1111 MET cc_start: 0.6405 (ttp) cc_final: 0.6199 (ttp) REVERT: B 1260 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6502 (ttm110) REVERT: B 1294 ASP cc_start: 0.8244 (m-30) cc_final: 0.7831 (m-30) REVERT: B 1310 ASN cc_start: 0.7791 (m-40) cc_final: 0.7537 (m110) REVERT: D 274 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7567 (mt) REVERT: D 310 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6603 (mm-30) REVERT: D 327 LYS cc_start: 0.7903 (mttt) cc_final: 0.7534 (ptmt) REVERT: D 341 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6520 (tm-30) REVERT: D 348 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: D 354 ASN cc_start: 0.7596 (t0) cc_final: 0.7323 (t0) REVERT: D 438 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7513 (pt0) REVERT: D 442 LYS cc_start: 0.7607 (mtmt) cc_final: 0.6913 (tmtm) REVERT: D 451 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7594 (tt0) REVERT: D 452 ARG cc_start: 0.8178 (mtp-110) cc_final: 0.7706 (mtm-85) REVERT: D 467 LYS cc_start: 0.6653 (tttt) cc_final: 0.6426 (mppt) REVERT: D 473 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7015 (tp) REVERT: D 480 LYS cc_start: 0.7564 (ttmm) cc_final: 0.7109 (ttmt) REVERT: D 503 ARG cc_start: 0.7598 (mtt180) cc_final: 0.7153 (mmm160) REVERT: E 64 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7458 (mp0) REVERT: E 157 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7747 (mmm) REVERT: E 227 ASN cc_start: 0.6871 (p0) cc_final: 0.6140 (m-40) REVERT: E 229 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8465 (mp) REVERT: E 281 LYS cc_start: 0.7489 (mttt) cc_final: 0.6951 (mtpt) REVERT: E 290 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8090 (tttp) REVERT: E 341 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6940 (tt0) REVERT: E 452 ARG cc_start: 0.8054 (ptp90) cc_final: 0.7419 (ptm160) REVERT: E 459 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6565 (tt0) REVERT: E 479 GLU cc_start: 0.7603 (pp20) cc_final: 0.7348 (pp20) REVERT: E 487 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6351 (mt-10) outliers start: 61 outliers final: 40 residues processed: 250 average time/residue: 0.5231 time to fit residues: 146.7052 Evaluate side-chains 256 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 106 SER Chi-restraints excluded: chain B residue 210 LEU 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 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 158 SER Chi-restraints excluded: chain D residue 159 VAL 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 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 157 MET 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 342 GLU 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: 0.8980 chunk 115 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3876 r_free = 0.3876 target = 0.156157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115751 restraints weight = 33263.113| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.49 r_work: 0.3184 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17870 Z= 0.132 Angle : 0.559 9.240 24265 Z= 0.292 Chirality : 0.042 0.208 2679 Planarity : 0.003 0.077 2950 Dihedral : 16.768 61.988 2817 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.24 % Allowed : 25.54 % 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: 1.13 (0.18), residues: 1985 helix: 2.34 (0.17), residues: 825 sheet: 0.71 (0.26), residues: 362 loop : -0.98 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B1105 TYR 0.011 0.001 TYR B1282 PHE 0.014 0.001 PHE D 228 TRP 0.009 0.001 TRP A 164 HIS 0.006 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (17870) covalent geometry : angle 0.55902 / 0.29 (24265) hydrogen bonds : bond 0.03858 / 3.95 ( 865) hydrogen bonds : angle 4.13923 / 4.51 ( 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 267 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 0.609 Fit side-chains REVERT: J 461 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7022 (pp20) REVERT: A 1 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.6644 (ttm) REVERT: A 92 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7395 (mt-10) REVERT: A 138 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.8112 (tmm160) REVERT: A 190 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7306 (mm-30) REVERT: A 201 GLN cc_start: 0.7980 (tp40) cc_final: 0.7455 (mt0) REVERT: A 204 LYS cc_start: 0.7337 (mttp) cc_final: 0.6798 (mppt) REVERT: A 211 LYS cc_start: 0.7635 (mttm) cc_final: 0.7142 (pttp) REVERT: A 215 GLN cc_start: 0.7549 (tt0) cc_final: 0.7111 (pt0) REVERT: A 1096 GLN cc_start: 0.6119 (pm20) cc_final: 0.5871 (pm20) REVERT: A 1115 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7385 (mt-10) REVERT: A 1126 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7296 (tptt) REVERT: A 1168 ASP cc_start: 0.7621 (m-30) cc_final: 0.7332 (m-30) REVERT: A 1178 LYS cc_start: 0.8903 (mttm) cc_final: 0.8452 (mttp) REVERT: A 1254 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7640 (mttt) REVERT: A 1261 ASN cc_start: 0.7605 (m110) cc_final: 0.7304 (m110) REVERT: A 1290 LYS cc_start: 0.8383 (ptpt) cc_final: 0.7825 (mmtp) REVERT: B 71 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8583 (mtpm) REVERT: B 106 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7474 (t) REVERT: B 108 LYS cc_start: 0.6699 (mtpp) cc_final: 0.5579 (ttmt) REVERT: B 148 LYS cc_start: 0.8310 (tttt) cc_final: 0.8068 (ttmm) REVERT: B 194 GLN cc_start: 0.8124 (tp40) cc_final: 0.7074 (pt0) REVERT: B 1105 ARG cc_start: 0.7503 (mmm160) cc_final: 0.6881 (mmp-170) REVERT: B 1111 MET cc_start: 0.6392 (ttp) cc_final: 0.6186 (ttp) REVERT: B 1260 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6506 (ttm110) REVERT: B 1294 ASP cc_start: 0.8241 (m-30) cc_final: 0.7831 (m-30) REVERT: B 1310 ASN cc_start: 0.7779 (m-40) cc_final: 0.7551 (m110) REVERT: D 274 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7564 (mt) REVERT: D 310 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6621 (mm-30) REVERT: D 327 LYS cc_start: 0.7923 (mttt) cc_final: 0.7537 (ptmt) REVERT: D 348 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7094 (tt0) REVERT: D 354 ASN cc_start: 0.7606 (t0) cc_final: 0.7346 (t0) REVERT: D 438 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: D 442 LYS cc_start: 0.7597 (mtmt) cc_final: 0.6872 (tmtm) REVERT: D 451 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7532 (tt0) REVERT: D 452 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7707 (mtm-85) REVERT: D 467 LYS cc_start: 0.6599 (tttt) cc_final: 0.6398 (mppt) REVERT: D 473 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7015 (tp) REVERT: D 479 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7071 (mt-10) REVERT: D 480 LYS cc_start: 0.7571 (ttmm) cc_final: 0.7115 (ttmt) REVERT: D 503 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7126 (mmm160) REVERT: E 64 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7474 (mp0) REVERT: E 157 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7732 (mmm) REVERT: E 227 ASN cc_start: 0.6824 (p0) cc_final: 0.6122 (m-40) REVERT: E 229 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8475 (mp) REVERT: E 232 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7786 (mm-40) REVERT: E 281 LYS cc_start: 0.7485 (mttt) cc_final: 0.6951 (mtpt) REVERT: E 290 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8080 (tttp) REVERT: E 341 GLU cc_start: 0.7654 (mm-30) cc_final: 0.6938 (tt0) REVERT: E 452 ARG cc_start: 0.8057 (ptp90) cc_final: 0.7419 (ptm160) REVERT: E 459 GLN cc_start: 0.6931 (mm-40) cc_final: 0.6569 (tt0) REVERT: E 479 GLU cc_start: 0.7595 (pp20) cc_final: 0.7339 (pp20) REVERT: E 487 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6374 (mt-10) outliers start: 59 outliers final: 41 residues processed: 247 average time/residue: 0.5735 time to fit residues: 158.5270 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 : 0.677 ------------------------------------------------------------------------------- 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 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 106 SER Chi-restraints excluded: chain B residue 210 LEU 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 B residue 1260 ARG 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 158 SER Chi-restraints excluded: chain D residue 159 VAL 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 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 157 MET 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 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 342 GLU 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 193 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3880 r_free = 0.3880 target = 0.156541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115639 restraints weight = 35628.789| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.59 r_work: 0.3180 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2008 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= 0.123 Angle : 0.553 9.331 24265 Z= 0.289 Chirality : 0.042 0.213 2679 Planarity : 0.003 0.083 2950 Dihedral : 16.733 61.754 2817 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.02 % Allowed : 25.48 % Favored : 71.50 % 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: 1.17 (0.18), residues: 1985 helix: 2.42 (0.17), residues: 818 sheet: 0.73 (0.26), residues: 362 loop : -0.99 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B1105 TYR 0.011 0.001 TYR B1282 PHE 0.014 0.001 PHE E 101 TRP 0.009 0.001 TRP A 164 HIS 0.006 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (17870) covalent geometry : angle 0.55293 / 0.29 (24265) hydrogen bonds : bond 0.03788 / 3.88 ( 865) hydrogen bonds : angle 4.12719 / 4.49 ( 2502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6485.79 seconds wall clock time: 111 minutes 7.08 seconds (6667.08 seconds total)