Starting phenix.real_space_refine on Thu Aug 6 23:24:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9j_52961/08_2026/9q9j_52961.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9j_52961/08_2026/9q9j_52961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q9j_52961/08_2026/9q9j_52961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9j_52961/08_2026/9q9j_52961.map" model { file = "/net/cci-nas-00/data/ceres_data/9q9j_52961/08_2026/9q9j_52961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9j_52961/08_2026/9q9j_52961.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Mn 4 7.51 5 P 56 5.49 5 Mg 2 5.21 5 S 81 5.16 5 Be 2 3.05 5 C 10862 2.51 5 N 3049 2.21 5 O 3403 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.13, 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: 1.73 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: 1.86 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: 3.97 Time building geometry restraints manager: 2.20 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.740 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- 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 : 0.832 12.708 24265 Z= 0.524 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 0.83174 / 0.52 (24265) hydrogen bonds : bond 0.15370 / 14.95 ( 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 : 0.674 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: 0.6771 time to fit residues: 233.4974 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 : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 342 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1181 ASN D 256 ASN D 317 HIS D 401 HIS E 218 GLN E 256 ASN E 259 GLN E 316 ASN E 317 HIS E 330 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116093 restraints weight = 37947.607| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.62 r_work: 0.3177 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17870 Z= 0.148 Angle : 0.595 8.402 24265 Z= 0.313 Chirality : 0.043 0.185 2679 Planarity : 0.004 0.041 2950 Dihedral : 17.383 77.462 2846 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.51 % Allowed : 23.28 % Favored : 73.20 % 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: 2.00 (0.18), residues: 827 sheet: 0.56 (0.26), residues: 353 loop : -1.17 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.00330 / 0.15 (17870) covalent geometry : angle 0.59483 / 0.31 (24265) hydrogen bonds : bond 0.04620 / 4.67 ( 865) hydrogen bonds : angle 4.88857 / 5.33 ( 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 295 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 231 time to evaluate : 0.564 Fit side-chains REVERT: J 461 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7141 (pp20) REVERT: A 1 MET cc_start: 0.7538 (ttm) cc_final: 0.6845 (ttm) REVERT: A 71 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8451 (mtpm) REVERT: A 92 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 138 ARG cc_start: 0.8186 (ttp-170) cc_final: 0.7801 (ttm-80) REVERT: A 190 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7177 (mt-10) REVERT: A 201 GLN cc_start: 0.8007 (tp40) cc_final: 0.7445 (mt0) REVERT: A 204 LYS cc_start: 0.7501 (mttp) cc_final: 0.7032 (mppt) REVERT: A 211 LYS cc_start: 0.7662 (mttm) cc_final: 0.7196 (pttp) REVERT: A 1111 MET cc_start: 0.7583 (tmm) cc_final: 0.6987 (tmm) REVERT: A 1115 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7089 (mt-10) REVERT: A 1126 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7315 (tptt) REVERT: A 1168 ASP cc_start: 0.7527 (m-30) cc_final: 0.7217 (m-30) REVERT: A 1243 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7826 (mt-10) REVERT: A 1254 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7646 (mttt) REVERT: A 1261 ASN cc_start: 0.7738 (m110) cc_final: 0.7470 (m110) REVERT: A 1290 LYS cc_start: 0.8468 (ptpt) cc_final: 0.8086 (ptmt) REVERT: B 1 MET cc_start: 0.6415 (mmm) cc_final: 0.6154 (mmm) REVERT: B 148 LYS cc_start: 0.8354 (tttt) cc_final: 0.8036 (ttmm) REVERT: B 194 GLN cc_start: 0.8208 (tp40) cc_final: 0.7173 (tt0) REVERT: B 1260 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6610 (tmm160) REVERT: B 1294 ASP cc_start: 0.8190 (m-30) cc_final: 0.7771 (m-30) REVERT: D 105 LYS cc_start: 0.7689 (mttp) cc_final: 0.7428 (mtmm) REVERT: D 274 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7736 (mt) REVERT: D 310 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6398 (mm-30) REVERT: D 327 LYS cc_start: 0.7717 (mttt) cc_final: 0.7314 (ptmt) REVERT: D 341 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6402 (tm-30) REVERT: D 348 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: D 442 LYS cc_start: 0.7453 (mtmt) cc_final: 0.6759 (ttpp) REVERT: D 451 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7605 (mt-10) REVERT: D 452 ARG cc_start: 0.8151 (mtp-110) cc_final: 0.7721 (mtm-85) REVERT: D 467 LYS cc_start: 0.6595 (tttt) cc_final: 0.6335 (mppt) REVERT: D 480 LYS cc_start: 0.7440 (ttmm) cc_final: 0.6984 (ttmt) REVERT: D 503 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7131 (mmm160) REVERT: E 64 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7343 (mp0) REVERT: E 157 MET cc_start: 0.7801 (mtt) cc_final: 0.6660 (pmm) REVERT: E 227 ASN cc_start: 0.6940 (p0) cc_final: 0.6085 (m-40) REVERT: E 229 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8466 (mp) REVERT: E 281 LYS cc_start: 0.7616 (mttt) cc_final: 0.7068 (mtpt) REVERT: E 290 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8123 (tttp) REVERT: E 341 GLU cc_start: 0.7655 (mm-30) cc_final: 0.6807 (tt0) REVERT: E 345 GLU cc_start: 0.6740 (tt0) cc_final: 0.6324 (mt-10) REVERT: E 387 ASP cc_start: 0.7968 (m-30) cc_final: 0.7731 (p0) REVERT: E 430 GLU cc_start: 0.7758 (mp0) cc_final: 0.7434 (mp0) REVERT: E 431 ASP cc_start: 0.7991 (m-30) cc_final: 0.7715 (t0) REVERT: E 435 GLN cc_start: 0.7581 (mt0) cc_final: 0.6698 (mt0) REVERT: E 452 ARG cc_start: 0.7934 (ptp90) cc_final: 0.7309 (ptm160) REVERT: E 459 GLN cc_start: 0.7015 (mm-40) cc_final: 0.6502 (mt0) REVERT: E 479 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7288 (pp20) outliers start: 64 outliers final: 24 residues processed: 267 average time/residue: 0.5983 time to fit residues: 177.6171 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 : 0.559 ------------------------------------------------------------------------------- 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: 0.4980 chunk 24 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 256 ASN D 317 HIS D 401 HIS D 477 GLN E 297 HIS E 317 HIS E 330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112629 restraints weight = 32191.027| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.63 r_work: 0.3161 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 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 = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17870 Z= 0.183 Angle : 0.596 7.245 24265 Z= 0.313 Chirality : 0.045 0.193 2679 Planarity : 0.004 0.047 2950 Dihedral : 17.210 63.685 2818 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.28 % Allowed : 22.79 % Favored : 72.93 % 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: 0.82 (0.18), residues: 1985 helix: 2.10 (0.18), residues: 821 sheet: 0.53 (0.26), residues: 362 loop : -1.15 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 488 TYR 0.018 0.001 TYR B1282 PHE 0.015 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 0.00425 / 0.18 (17870) covalent geometry : angle 0.59623 / 0.31 (24265) hydrogen bonds : bond 0.04656 / 4.68 ( 865) hydrogen bonds : angle 4.57284 / 4.98 ( 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 307 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 229 time to evaluate : 0.641 Fit side-chains REVERT: J 461 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7154 (pp20) REVERT: A 1 MET cc_start: 0.7633 (ttm) cc_final: 0.6769 (ttm) REVERT: A 92 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 138 ARG cc_start: 0.8330 (ttp-170) cc_final: 0.7862 (ttm-80) REVERT: A 190 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7245 (mm-30) REVERT: A 201 GLN cc_start: 0.7974 (tp40) cc_final: 0.7406 (mt0) REVERT: A 204 LYS cc_start: 0.7429 (mttp) cc_final: 0.6888 (mppt) REVERT: A 211 LYS cc_start: 0.7640 (mttm) cc_final: 0.7169 (pttp) REVERT: A 218 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: A 1115 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7457 (mt-10) REVERT: A 1126 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7249 (tptt) REVERT: A 1145 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7852 (mtpt) REVERT: A 1168 ASP cc_start: 0.7604 (m-30) cc_final: 0.7317 (m-30) REVERT: A 1254 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7619 (mttt) REVERT: A 1261 ASN cc_start: 0.7746 (m110) cc_final: 0.7429 (m110) REVERT: A 1290 LYS cc_start: 0.8410 (ptpt) cc_final: 0.7978 (ptmt) REVERT: B 1 MET cc_start: 0.6380 (mmm) cc_final: 0.6161 (mmm) REVERT: B 106 SER cc_start: 0.7846 (OUTLIER) cc_final: 0.7441 (t) REVERT: B 148 LYS cc_start: 0.8332 (tttt) cc_final: 0.8057 (ttmm) REVERT: B 194 GLN cc_start: 0.8155 (tp40) cc_final: 0.7109 (tt0) REVERT: B 1197 MET cc_start: 0.9049 (ttt) cc_final: 0.8660 (ttt) REVERT: B 1260 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6606 (tmm160) REVERT: B 1294 ASP cc_start: 0.8237 (m-30) cc_final: 0.7832 (m-30) REVERT: D 274 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7718 (mt) REVERT: D 310 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6499 (mm-30) REVERT: D 327 LYS cc_start: 0.7857 (mttt) cc_final: 0.7451 (ptmt) REVERT: D 338 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: D 341 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6501 (tm-30) REVERT: D 348 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: D 438 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: D 442 LYS cc_start: 0.7479 (mtmt) cc_final: 0.6847 (ttpp) REVERT: D 451 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7651 (tt0) REVERT: D 452 ARG cc_start: 0.8157 (mtp-110) cc_final: 0.7694 (mtm-85) REVERT: D 467 LYS cc_start: 0.6601 (tttt) cc_final: 0.6342 (mppt) REVERT: D 480 LYS cc_start: 0.7479 (ttmm) cc_final: 0.7079 (ttmt) REVERT: D 503 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7104 (mmm160) REVERT: E 64 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7344 (mp0) REVERT: E 192 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7941 (mtt) REVERT: E 227 ASN cc_start: 0.6960 (p0) cc_final: 0.6106 (m-40) REVERT: E 229 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8432 (mp) REVERT: E 281 LYS cc_start: 0.7619 (mttt) cc_final: 0.7093 (mtpt) REVERT: E 290 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8073 (tttp) REVERT: E 341 GLU cc_start: 0.7661 (mm-30) cc_final: 0.6949 (tt0) REVERT: E 387 ASP cc_start: 0.8035 (m-30) cc_final: 0.7776 (p0) REVERT: E 430 GLU cc_start: 0.7795 (mp0) cc_final: 0.7473 (mp0) REVERT: E 431 ASP cc_start: 0.7998 (m-30) cc_final: 0.7705 (t0) REVERT: E 435 GLN cc_start: 0.7556 (mt0) cc_final: 0.6636 (mt0) REVERT: E 452 ARG cc_start: 0.7985 (ptp90) cc_final: 0.7365 (ptm160) REVERT: E 459 GLN cc_start: 0.7007 (mm-40) cc_final: 0.6536 (tt0) REVERT: E 479 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7384 (pp20) REVERT: E 487 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6265 (mt-10) outliers start: 78 outliers final: 34 residues processed: 281 average time/residue: 0.5998 time to fit residues: 187.9268 Evaluate side-chains 256 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 2.9990 chunk 150 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 182 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.154067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113440 restraints weight = 35930.472| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.53 r_work: 0.3150 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- 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 = 0.46 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: 0.8550 moved from start: 0.1550 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= 0.162 Angle : 0.577 6.799 24265 Z= 0.303 Chirality : 0.044 0.254 2679 Planarity : 0.003 0.037 2950 Dihedral : 17.100 64.766 2818 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.17 % Allowed : 24.00 % Favored : 71.83 % 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: 0.87 (0.18), residues: 1985 helix: 2.15 (0.18), residues: 823 sheet: 0.53 (0.26), residues: 363 loop : -1.13 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 120 TYR 0.014 0.001 TYR B1282 PHE 0.014 0.001 PHE E 54 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 0.00372 / 0.16 (17870) covalent geometry : angle 0.57651 / 0.30 (24265) hydrogen bonds : bond 0.04263 / 4.35 ( 865) hydrogen bonds : angle 4.43740 / 4.86 ( 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 291 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 215 time to evaluate : 0.704 Fit side-chains REVERT: J 461 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7208 (pp20) REVERT: A 1 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6793 (ttm) REVERT: A 92 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7395 (mt-10) REVERT: A 138 ARG cc_start: 0.8329 (ttp-170) cc_final: 0.7864 (ttm-80) REVERT: A 190 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7291 (mm-30) REVERT: A 201 GLN cc_start: 0.7982 (tp40) cc_final: 0.7419 (mt0) REVERT: A 204 LYS cc_start: 0.7417 (mttp) cc_final: 0.6889 (mppt) REVERT: A 211 LYS cc_start: 0.7620 (mttm) cc_final: 0.7101 (pttp) REVERT: A 215 GLN cc_start: 0.7451 (tt0) cc_final: 0.7014 (pt0) REVERT: A 218 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: A 1115 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7466 (mt-10) REVERT: A 1126 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7294 (tptt) REVERT: A 1145 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7825 (mtpt) REVERT: A 1168 ASP cc_start: 0.7643 (m-30) cc_final: 0.7364 (m-30) REVERT: A 1178 LYS cc_start: 0.8907 (mttm) cc_final: 0.8445 (mttp) REVERT: A 1254 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7636 (mttt) REVERT: A 1261 ASN cc_start: 0.7740 (m110) cc_final: 0.7446 (m110) REVERT: A 1290 LYS cc_start: 0.8418 (ptpt) cc_final: 0.7993 (ptmt) REVERT: B 1 MET cc_start: 0.6448 (mmm) cc_final: 0.6245 (mmm) REVERT: B 92 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: B 106 SER cc_start: 0.7842 (OUTLIER) cc_final: 0.7441 (t) REVERT: B 138 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7672 (ptp-170) REVERT: B 148 LYS cc_start: 0.8342 (tttt) cc_final: 0.8077 (ttmm) REVERT: B 194 GLN cc_start: 0.8178 (tp40) cc_final: 0.7146 (tt0) REVERT: B 1197 MET cc_start: 0.9043 (ttt) cc_final: 0.8701 (ttt) REVERT: B 1260 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6557 (ttm110) REVERT: B 1294 ASP cc_start: 0.8279 (m-30) cc_final: 0.7881 (m-30) REVERT: D 274 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7760 (mt) REVERT: D 310 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6532 (mm-30) REVERT: D 327 LYS cc_start: 0.7835 (mttt) cc_final: 0.7461 (ptmt) REVERT: D 338 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: D 341 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6499 (tm-30) REVERT: D 348 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: D 438 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: D 442 LYS cc_start: 0.7556 (mtmt) cc_final: 0.6864 (ttpp) REVERT: D 451 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7633 (tt0) REVERT: D 452 ARG cc_start: 0.8177 (mtp-110) cc_final: 0.7710 (mtm-85) REVERT: D 467 LYS cc_start: 0.6589 (tttt) cc_final: 0.6331 (mppt) REVERT: D 473 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7060 (tp) REVERT: D 480 LYS cc_start: 0.7484 (ttmm) cc_final: 0.7067 (ttmt) REVERT: D 503 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7091 (mmm160) REVERT: E 64 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7390 (mp0) REVERT: E 192 MET cc_start: 0.8229 (mmm) cc_final: 0.7999 (mtt) REVERT: E 227 ASN cc_start: 0.6973 (p0) cc_final: 0.6144 (m-40) REVERT: E 229 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8449 (mp) REVERT: E 281 LYS cc_start: 0.7601 (mttt) cc_final: 0.7080 (mtpt) REVERT: E 290 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8182 (tttm) REVERT: E 341 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6949 (tt0) REVERT: E 387 ASP cc_start: 0.8083 (m-30) cc_final: 0.7829 (p0) REVERT: E 430 GLU cc_start: 0.7789 (mp0) cc_final: 0.7477 (mp0) REVERT: E 431 ASP cc_start: 0.8029 (m-30) cc_final: 0.7758 (t0) REVERT: E 435 GLN cc_start: 0.7567 (mt0) cc_final: 0.6645 (mt0) REVERT: E 452 ARG cc_start: 0.8038 (ptp90) cc_final: 0.7391 (ptm160) REVERT: E 459 GLN cc_start: 0.7003 (mm-40) cc_final: 0.6560 (tt0) REVERT: E 479 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7363 (pp20) REVERT: E 487 GLU cc_start: 0.6563 (mm-30) cc_final: 0.6311 (mt-10) outliers start: 76 outliers final: 40 residues processed: 265 average time/residue: 0.5780 time to fit residues: 171.5190 Evaluate side-chains 255 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 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 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 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 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 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 355 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 53 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 60 optimal weight: 0.0470 chunk 193 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 256 ASN D 317 HIS D 401 HIS E 317 HIS E 330 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.156070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115777 restraints weight = 33670.041| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.47 r_work: 0.3177 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 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 = 0.3195 r_free = 0.3195 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: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17870 Z= 0.121 Angle : 0.549 10.002 24265 Z= 0.287 Chirality : 0.043 0.461 2679 Planarity : 0.003 0.037 2950 Dihedral : 16.915 64.319 2818 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.24 % Allowed : 24.71 % Favored : 72.05 % 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: 1.02 (0.18), residues: 1985 helix: 2.27 (0.18), residues: 821 sheet: 0.65 (0.26), residues: 363 loop : -1.06 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 488 TYR 0.013 0.001 TYR B1282 PHE 0.013 0.001 PHE E 461 TRP 0.009 0.001 TRP A 164 HIS 0.007 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17870) covalent geometry : angle 0.54900 / 0.29 (24265) hydrogen bonds : bond 0.03921 / 4.01 ( 865) hydrogen bonds : angle 4.26758 / 4.68 ( 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 277 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.646 Fit side-chains REVERT: J 461 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7148 (pp20) REVERT: A 1 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6748 (ttm) REVERT: A 92 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7370 (mt-10) REVERT: A 138 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.7901 (ttm-80) REVERT: A 190 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 201 GLN cc_start: 0.7987 (tp40) cc_final: 0.7436 (mt0) REVERT: A 204 LYS cc_start: 0.7387 (mttp) cc_final: 0.6856 (mppt) REVERT: A 211 LYS cc_start: 0.7642 (mttm) cc_final: 0.7152 (pttp) REVERT: A 215 GLN cc_start: 0.7508 (tt0) cc_final: 0.7081 (pt0) REVERT: A 1115 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7429 (mt-10) REVERT: A 1126 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7333 (tptt) REVERT: A 1168 ASP cc_start: 0.7583 (m-30) cc_final: 0.7307 (m-30) REVERT: A 1178 LYS cc_start: 0.8897 (mttm) cc_final: 0.8426 (mttp) REVERT: A 1254 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7643 (mttt) REVERT: A 1261 ASN cc_start: 0.7664 (m110) cc_final: 0.7377 (m110) REVERT: A 1290 LYS cc_start: 0.8410 (ptpt) cc_final: 0.7826 (mmtp) REVERT: B 138 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7642 (ptp-170) REVERT: B 148 LYS cc_start: 0.8321 (tttt) cc_final: 0.8106 (ttmm) REVERT: B 194 GLN cc_start: 0.8144 (tp40) cc_final: 0.7163 (tt0) REVERT: B 1197 MET cc_start: 0.9020 (ttt) cc_final: 0.8704 (ttt) REVERT: B 1260 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6558 (tmm160) REVERT: B 1294 ASP cc_start: 0.8238 (m-30) cc_final: 0.7838 (m-30) REVERT: D 51 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: D 274 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7697 (mt) REVERT: D 310 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6557 (mm-30) REVERT: D 327 LYS cc_start: 0.7833 (mttt) cc_final: 0.7456 (ptmt) REVERT: D 341 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6458 (tm-30) REVERT: D 348 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: D 438 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7570 (pt0) REVERT: D 442 LYS cc_start: 0.7578 (mtmt) cc_final: 0.6910 (tmtm) REVERT: D 451 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7617 (tt0) REVERT: D 452 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7701 (mtm-85) REVERT: D 467 LYS cc_start: 0.6635 (tttt) cc_final: 0.6377 (mppt) REVERT: D 473 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7044 (tp) REVERT: D 480 LYS cc_start: 0.7500 (ttmm) cc_final: 0.7036 (ttmt) REVERT: D 503 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7254 (mmm160) REVERT: E 64 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7417 (mp0) REVERT: E 227 ASN cc_start: 0.6923 (p0) cc_final: 0.6101 (m-40) REVERT: E 281 LYS cc_start: 0.7576 (mttt) cc_final: 0.7050 (mtpt) REVERT: E 290 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8258 (tttm) REVERT: E 341 GLU cc_start: 0.7657 (mm-30) cc_final: 0.6952 (tt0) REVERT: E 387 ASP cc_start: 0.8054 (m-30) cc_final: 0.7794 (p0) REVERT: E 430 GLU cc_start: 0.7744 (mp0) cc_final: 0.7433 (mp0) REVERT: E 431 ASP cc_start: 0.8017 (m-30) cc_final: 0.7785 (t0) REVERT: E 435 GLN cc_start: 0.7524 (mt0) cc_final: 0.6555 (mt0) REVERT: E 452 ARG cc_start: 0.8042 (ptp90) cc_final: 0.7408 (ptm160) REVERT: E 459 GLN cc_start: 0.6977 (mm-40) cc_final: 0.6557 (tt0) REVERT: E 479 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7375 (pp20) REVERT: E 487 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6371 (mt-10) outliers start: 59 outliers final: 36 residues processed: 260 average time/residue: 0.6271 time to fit residues: 182.3532 Evaluate side-chains 249 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 126 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 317 HIS E 330 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112249 restraints weight = 44891.034| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.06 r_work: 0.3177 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 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 = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17870 Z= 0.129 Angle : 0.547 6.635 24265 Z= 0.287 Chirality : 0.043 0.295 2679 Planarity : 0.003 0.037 2950 Dihedral : 16.854 63.569 2818 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.68 % Allowed : 24.71 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 1985 helix: 2.37 (0.18), residues: 816 sheet: 0.69 (0.26), residues: 362 loop : -1.05 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1260 TYR 0.014 0.001 TYR B1282 PHE 0.013 0.001 PHE E 54 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 0.00289 / 0.13 (17870) covalent geometry : angle 0.54730 / 0.29 (24265) hydrogen bonds : bond 0.03901 / 3.99 ( 865) hydrogen bonds : angle 4.21423 / 4.61 ( 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 279 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 212 time to evaluate : 0.679 Fit side-chains REVERT: J 461 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7099 (pp20) REVERT: A 1 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.6648 (ttm) REVERT: A 92 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7281 (mt-10) REVERT: A 110 GLU cc_start: 0.7979 (tt0) cc_final: 0.7730 (tt0) REVERT: A 138 ARG cc_start: 0.8291 (ttp-170) cc_final: 0.7772 (ttm-80) REVERT: A 190 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 201 GLN cc_start: 0.7957 (tp40) cc_final: 0.7371 (mt0) REVERT: A 204 LYS cc_start: 0.7326 (mttp) cc_final: 0.6778 (mppt) REVERT: A 211 LYS cc_start: 0.7617 (mttm) cc_final: 0.7128 (pttp) REVERT: A 215 GLN cc_start: 0.7505 (tt0) cc_final: 0.7083 (pt0) REVERT: A 218 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: A 1115 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7360 (mt-10) REVERT: A 1126 LYS cc_start: 0.7936 (ttpt) cc_final: 0.7242 (tptt) REVERT: A 1168 ASP cc_start: 0.7572 (m-30) cc_final: 0.7272 (m-30) REVERT: A 1178 LYS cc_start: 0.8893 (mttm) cc_final: 0.8395 (mttp) REVERT: A 1254 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7591 (mttt) REVERT: A 1261 ASN cc_start: 0.7625 (m110) cc_final: 0.7325 (m110) REVERT: A 1290 LYS cc_start: 0.8378 (ptpt) cc_final: 0.7767 (mmtp) REVERT: B 106 SER cc_start: 0.7852 (OUTLIER) cc_final: 0.7460 (t) REVERT: B 148 LYS cc_start: 0.8286 (tttt) cc_final: 0.8032 (ttmm) REVERT: B 194 GLN cc_start: 0.8109 (tp40) cc_final: 0.7135 (tt0) REVERT: B 1099 ASP cc_start: 0.5835 (OUTLIER) cc_final: 0.5580 (OUTLIER) REVERT: B 1294 ASP cc_start: 0.8210 (m-30) cc_final: 0.7780 (m-30) REVERT: D 274 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7631 (mt) REVERT: D 310 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6520 (mm-30) REVERT: D 327 LYS cc_start: 0.7869 (mttt) cc_final: 0.7475 (ptmt) REVERT: D 341 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6399 (tm-30) REVERT: D 348 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: D 438 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: D 442 LYS cc_start: 0.7568 (mtmt) cc_final: 0.6904 (tmtm) REVERT: D 451 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7604 (tt0) REVERT: D 452 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7676 (mtm-85) REVERT: D 467 LYS cc_start: 0.6555 (tttt) cc_final: 0.6324 (mppt) REVERT: D 473 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6969 (tp) REVERT: D 480 LYS cc_start: 0.7497 (ttmm) cc_final: 0.7033 (ttmt) REVERT: D 503 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7226 (mmm160) REVERT: E 64 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7390 (mp0) REVERT: E 227 ASN cc_start: 0.6844 (p0) cc_final: 0.6059 (m-40) REVERT: E 281 LYS cc_start: 0.7494 (mttt) cc_final: 0.6949 (mtpt) REVERT: E 290 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8207 (tttm) REVERT: E 341 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6873 (tt0) REVERT: E 387 ASP cc_start: 0.8052 (m-30) cc_final: 0.7763 (p0) REVERT: E 430 GLU cc_start: 0.7701 (mp0) cc_final: 0.7451 (mp0) REVERT: E 431 ASP cc_start: 0.7989 (m-30) cc_final: 0.7736 (t0) REVERT: E 435 GLN cc_start: 0.7469 (mt0) cc_final: 0.6579 (mt0) REVERT: E 452 ARG cc_start: 0.8039 (ptp90) cc_final: 0.7392 (ptm160) REVERT: E 459 GLN cc_start: 0.6939 (mm-40) cc_final: 0.6524 (tt0) REVERT: E 479 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7350 (pp20) REVERT: E 487 GLU cc_start: 0.6572 (mm-30) cc_final: 0.6365 (mt-10) outliers start: 67 outliers final: 42 residues processed: 260 average time/residue: 0.6071 time to fit residues: 176.5640 Evaluate side-chains 257 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 218 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 168 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 140 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 256 ASN D 317 HIS D 401 HIS E 317 HIS E 330 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.156193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113582 restraints weight = 32487.890| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.35 r_work: 0.3227 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17870 Z= 0.136 Angle : 0.559 7.519 24265 Z= 0.292 Chirality : 0.043 0.250 2679 Planarity : 0.003 0.038 2950 Dihedral : 16.821 63.256 2817 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.68 % Allowed : 24.66 % Favored : 71.66 % 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: 1.11 (0.18), residues: 1985 helix: 2.36 (0.18), residues: 818 sheet: 0.72 (0.26), residues: 361 loop : -1.02 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1260 TYR 0.013 0.001 TYR B1282 PHE 0.015 0.001 PHE E 504 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 0.00309 / 0.14 (17870) covalent geometry : angle 0.55904 / 0.29 (24265) hydrogen bonds : bond 0.03924 / 4.01 ( 865) hydrogen bonds : angle 4.19028 / 4.57 ( 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 281 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 0.677 Fit side-chains REVERT: J 461 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7210 (pp20) REVERT: A 1 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.6800 (ttm) REVERT: A 92 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 110 GLU cc_start: 0.8168 (tt0) cc_final: 0.7963 (tt0) REVERT: A 138 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.8204 (tmm160) REVERT: A 190 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7463 (mm-30) REVERT: A 201 GLN cc_start: 0.8068 (tp40) cc_final: 0.7468 (mt0) REVERT: A 204 LYS cc_start: 0.7437 (mttp) cc_final: 0.6890 (mppt) REVERT: A 211 LYS cc_start: 0.7698 (mttm) cc_final: 0.7204 (pttp) REVERT: A 215 GLN cc_start: 0.7590 (tt0) cc_final: 0.7173 (pt0) REVERT: A 218 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: A 1115 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7575 (mt-10) REVERT: A 1126 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7472 (tptt) REVERT: A 1168 ASP cc_start: 0.7724 (m-30) cc_final: 0.7453 (m-30) REVERT: A 1178 LYS cc_start: 0.8963 (mttm) cc_final: 0.8499 (mttp) REVERT: A 1254 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7689 (mttt) REVERT: A 1261 ASN cc_start: 0.7688 (m110) cc_final: 0.7365 (m110) REVERT: A 1290 LYS cc_start: 0.8460 (ptpt) cc_final: 0.7844 (mmtp) REVERT: B 92 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: B 106 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7436 (t) REVERT: B 138 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7772 (ptp-170) REVERT: B 148 LYS cc_start: 0.8369 (tttt) cc_final: 0.8134 (ttmm) REVERT: B 194 GLN cc_start: 0.8315 (tp40) cc_final: 0.7354 (tt0) REVERT: B 1099 ASP cc_start: 0.5884 (OUTLIER) cc_final: 0.5645 (OUTLIER) REVERT: B 1260 ARG cc_start: 0.7857 (mmt180) cc_final: 0.6598 (tmm160) REVERT: B 1294 ASP cc_start: 0.8333 (m-30) cc_final: 0.7909 (m-30) REVERT: D 51 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: D 274 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7656 (mt) REVERT: D 310 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6688 (mm-30) REVERT: D 327 LYS cc_start: 0.7938 (mttt) cc_final: 0.7560 (ptmt) REVERT: D 341 GLU cc_start: 0.7518 (mm-30) cc_final: 0.6570 (tm-30) REVERT: D 348 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: D 354 ASN cc_start: 0.7634 (t0) cc_final: 0.7345 (t0) REVERT: D 438 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: D 442 LYS cc_start: 0.7627 (mtmt) cc_final: 0.6946 (tmtm) REVERT: D 451 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7632 (tt0) REVERT: D 452 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7700 (mtm-85) REVERT: D 467 LYS cc_start: 0.6654 (tttt) cc_final: 0.6387 (mppt) REVERT: D 473 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7115 (tp) REVERT: D 479 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7073 (mt-10) REVERT: D 480 LYS cc_start: 0.7609 (ttmm) cc_final: 0.7138 (ttmt) REVERT: D 503 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7284 (mmm160) REVERT: E 64 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7547 (mp0) REVERT: E 227 ASN cc_start: 0.6869 (p0) cc_final: 0.6102 (m-40) REVERT: E 281 LYS cc_start: 0.7517 (mttt) cc_final: 0.6979 (mtpt) REVERT: E 290 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8132 (tttp) REVERT: E 341 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7029 (tt0) REVERT: E 387 ASP cc_start: 0.8179 (m-30) cc_final: 0.7860 (p0) REVERT: E 430 GLU cc_start: 0.7764 (mp0) cc_final: 0.7526 (mp0) REVERT: E 431 ASP cc_start: 0.8113 (m-30) cc_final: 0.7828 (t0) REVERT: E 435 GLN cc_start: 0.7558 (mt0) cc_final: 0.6704 (mt0) REVERT: E 452 ARG cc_start: 0.8084 (ptp90) cc_final: 0.7435 (ptm160) REVERT: E 459 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6631 (tt0) REVERT: E 487 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6431 (mt-10) outliers start: 67 outliers final: 40 residues processed: 260 average time/residue: 0.6223 time to fit residues: 180.9441 Evaluate side-chains 260 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 218 GLU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 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 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 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 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: 3.9990 chunk 22 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 125 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.154630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.111063 restraints weight = 36073.807| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.51 r_work: 0.3188 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17870 Z= 0.163 Angle : 0.577 8.518 24265 Z= 0.301 Chirality : 0.044 0.223 2679 Planarity : 0.003 0.039 2950 Dihedral : 16.850 62.507 2817 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.62 % Allowed : 24.99 % Favored : 71.39 % 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: 1.07 (0.18), residues: 1985 helix: 2.33 (0.18), residues: 817 sheet: 0.69 (0.26), residues: 361 loop : -1.04 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 87 TYR 0.016 0.001 TYR B1282 PHE 0.014 0.001 PHE E 504 TRP 0.007 0.001 TRP A 164 HIS 0.006 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (17870) covalent geometry : angle 0.57691 / 0.30 (24265) hydrogen bonds : bond 0.04132 / 4.22 ( 865) hydrogen bonds : angle 4.22666 / 4.60 ( 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 278 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 212 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: J 461 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7165 (pp20) REVERT: A 1 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6726 (ttm) REVERT: A 92 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7431 (mt-10) REVERT: A 138 ARG cc_start: 0.8396 (ttp-170) cc_final: 0.8164 (tmm160) REVERT: A 190 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7472 (mm-30) REVERT: A 201 GLN cc_start: 0.8090 (tp40) cc_final: 0.7461 (mt0) REVERT: A 204 LYS cc_start: 0.7415 (mttp) cc_final: 0.6861 (mppt) REVERT: A 211 LYS cc_start: 0.7659 (mttm) cc_final: 0.7157 (pttp) REVERT: A 215 GLN cc_start: 0.7587 (tt0) cc_final: 0.7149 (pt0) REVERT: A 218 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: A 1115 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7571 (mt-10) REVERT: A 1126 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7414 (tptt) REVERT: A 1145 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7792 (mtpt) REVERT: A 1168 ASP cc_start: 0.7804 (m-30) cc_final: 0.7518 (m-30) REVERT: A 1178 LYS cc_start: 0.8957 (mttm) cc_final: 0.8458 (mttp) REVERT: A 1254 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7669 (mttt) REVERT: A 1261 ASN cc_start: 0.7789 (m110) cc_final: 0.7423 (m110) REVERT: A 1290 LYS cc_start: 0.8471 (ptpt) cc_final: 0.7803 (mmtp) REVERT: B 92 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 106 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7432 (t) REVERT: B 138 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7809 (ptp-170) REVERT: B 148 LYS cc_start: 0.8382 (tttt) cc_final: 0.8118 (ttmm) REVERT: B 194 GLN cc_start: 0.8302 (tp40) cc_final: 0.7301 (tt0) REVERT: B 1260 ARG cc_start: 0.7727 (mmt180) cc_final: 0.6411 (ttm110) REVERT: B 1294 ASP cc_start: 0.8371 (m-30) cc_final: 0.7938 (m-30) REVERT: D 51 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: D 274 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7624 (mt) REVERT: D 310 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6633 (mm-30) REVERT: D 327 LYS cc_start: 0.7915 (mttt) cc_final: 0.7516 (ptmt) REVERT: D 341 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6538 (tm-30) REVERT: D 348 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: D 354 ASN cc_start: 0.7591 (t0) cc_final: 0.7301 (t0) REVERT: D 438 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: D 442 LYS cc_start: 0.7611 (mtmt) cc_final: 0.6896 (tmtm) REVERT: D 451 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7401 (mt-10) REVERT: D 452 ARG cc_start: 0.8205 (mtp-110) cc_final: 0.7696 (mtm-85) REVERT: D 467 LYS cc_start: 0.6610 (tttt) cc_final: 0.6347 (mppt) REVERT: D 473 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7095 (tp) REVERT: D 480 LYS cc_start: 0.7644 (ttmm) cc_final: 0.7178 (ttmt) REVERT: D 503 ARG cc_start: 0.7598 (mtt180) cc_final: 0.7156 (mmm160) REVERT: E 64 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7583 (mp0) REVERT: E 227 ASN cc_start: 0.6847 (p0) cc_final: 0.6080 (m-40) REVERT: E 229 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8484 (mp) REVERT: E 281 LYS cc_start: 0.7492 (mttt) cc_final: 0.6938 (mtpt) REVERT: E 290 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8099 (tttp) REVERT: E 341 GLU cc_start: 0.7777 (mm-30) cc_final: 0.6973 (tt0) REVERT: E 387 ASP cc_start: 0.8216 (m-30) cc_final: 0.7854 (p0) REVERT: E 431 ASP cc_start: 0.8095 (m-30) cc_final: 0.7774 (t0) REVERT: E 435 GLN cc_start: 0.7545 (mt0) cc_final: 0.6697 (mt0) REVERT: E 452 ARG cc_start: 0.8062 (ptp90) cc_final: 0.7414 (ptm160) REVERT: E 459 GLN cc_start: 0.7001 (mm-40) cc_final: 0.6597 (tt0) REVERT: E 487 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6407 (mt-10) outliers start: 66 outliers final: 42 residues processed: 257 average time/residue: 0.6016 time to fit residues: 172.4238 Evaluate side-chains 259 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 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 1189 LEU Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 173 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.155324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114927 restraints weight = 37226.458| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.60 r_work: 0.3162 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 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 = 0.3176 r_free = 0.3176 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: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17870 Z= 0.141 Angle : 0.567 9.044 24265 Z= 0.296 Chirality : 0.043 0.212 2679 Planarity : 0.003 0.038 2950 Dihedral : 16.807 62.411 2817 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.24 % Allowed : 25.15 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.18), residues: 1985 helix: 2.37 (0.18), 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 E 483 TYR 0.014 0.001 TYR B1282 PHE 0.014 0.001 PHE E 504 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 0.00321 / 0.14 (17870) covalent geometry : angle 0.56704 / 0.30 (24265) hydrogen bonds : bond 0.03954 / 4.06 ( 865) hydrogen bonds : angle 4.17505 / 4.56 ( 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: 59 poor density : 211 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: J 461 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7137 (pp20) REVERT: A 1 MET cc_start: 0.7676 (ttm) cc_final: 0.6640 (ttm) REVERT: A 92 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 138 ARG cc_start: 0.8351 (ttp-170) cc_final: 0.8125 (tmm160) REVERT: A 190 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 201 GLN cc_start: 0.7994 (tp40) cc_final: 0.7437 (mt0) REVERT: A 204 LYS cc_start: 0.7360 (mttp) cc_final: 0.6835 (mppt) REVERT: A 211 LYS cc_start: 0.7645 (mttm) cc_final: 0.7166 (pttp) REVERT: A 215 GLN cc_start: 0.7568 (tt0) cc_final: 0.7171 (pt0) REVERT: A 218 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: A 1115 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7420 (mt-10) REVERT: A 1126 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7323 (tptt) REVERT: A 1168 ASP cc_start: 0.7651 (m-30) cc_final: 0.7389 (m-30) REVERT: A 1178 LYS cc_start: 0.8923 (mttm) cc_final: 0.8469 (mttp) REVERT: A 1254 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7679 (mttt) REVERT: A 1261 ASN cc_start: 0.7644 (m110) cc_final: 0.7336 (m110) REVERT: A 1290 LYS cc_start: 0.8409 (ptpt) cc_final: 0.7850 (mmtp) REVERT: B 92 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: B 106 SER cc_start: 0.7845 (OUTLIER) cc_final: 0.7482 (t) REVERT: B 138 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7686 (ptp90) REVERT: B 148 LYS cc_start: 0.8323 (tttt) cc_final: 0.8077 (ttmm) REVERT: B 194 GLN cc_start: 0.8158 (tp40) cc_final: 0.7234 (tt0) REVERT: B 1260 ARG cc_start: 0.7705 (mmt180) cc_final: 0.6550 (ttm110) REVERT: B 1294 ASP cc_start: 0.8277 (m-30) cc_final: 0.7867 (m-30) REVERT: B 1310 ASN cc_start: 0.7824 (m-40) cc_final: 0.7576 (m110) REVERT: D 51 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: D 274 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7636 (mt) REVERT: D 310 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6627 (mm-30) REVERT: D 327 LYS cc_start: 0.7931 (mttt) cc_final: 0.7546 (ptmt) REVERT: D 348 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: D 354 ASN cc_start: 0.7587 (t0) cc_final: 0.7328 (t0) REVERT: D 438 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: D 442 LYS cc_start: 0.7621 (mtmt) cc_final: 0.6927 (tmtm) REVERT: D 451 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7568 (tt0) REVERT: D 452 ARG cc_start: 0.8179 (mtp-110) cc_final: 0.7719 (mtm-85) REVERT: D 467 LYS cc_start: 0.6645 (tttt) cc_final: 0.6386 (mppt) REVERT: D 473 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7043 (tp) REVERT: D 479 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7133 (mt-10) REVERT: D 480 LYS cc_start: 0.7606 (ttmm) cc_final: 0.7146 (ttmt) REVERT: D 503 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7149 (mmm160) REVERT: E 64 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7463 (mp0) REVERT: E 227 ASN cc_start: 0.6880 (p0) cc_final: 0.6128 (m-40) REVERT: E 232 GLN cc_start: 0.8249 (mp-120) cc_final: 0.7885 (mm-40) REVERT: E 281 LYS cc_start: 0.7516 (mttt) cc_final: 0.6984 (mtpt) REVERT: E 290 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8124 (tttp) REVERT: E 341 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6969 (tt0) REVERT: E 435 GLN cc_start: 0.7519 (mt0) cc_final: 0.6589 (mt0) REVERT: E 452 ARG cc_start: 0.8068 (ptp90) cc_final: 0.7439 (ptm160) REVERT: E 459 GLN cc_start: 0.6961 (mm-40) cc_final: 0.6590 (tt0) REVERT: E 479 GLU cc_start: 0.7616 (pp20) cc_final: 0.7360 (pp20) REVERT: E 487 GLU cc_start: 0.6588 (mm-30) cc_final: 0.6371 (mt-10) outliers start: 59 outliers final: 41 residues processed: 252 average time/residue: 0.5893 time to fit residues: 165.6541 Evaluate side-chains 255 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 256 ASN D 317 HIS D 401 HIS 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 = 0.3857 r_free = 0.3857 target = 0.154501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113796 restraints weight = 33518.912| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.49 r_work: 0.3159 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 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 = 0.3172 r_free = 0.3172 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: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.004 0.050 17870 Z= 0.163 Angle : 0.585 9.939 24265 Z= 0.305 Chirality : 0.044 0.211 2679 Planarity : 0.003 0.038 2950 Dihedral : 16.799 61.474 2817 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.35 % Allowed : 25.21 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.18), residues: 1985 helix: 2.35 (0.18), residues: 818 sheet: 0.67 (0.26), residues: 361 loop : -1.03 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 87 TYR 0.015 0.001 TYR B1282 PHE 0.014 0.001 PHE E 54 TRP 0.007 0.001 TRP A 164 HIS 0.006 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (17870) covalent geometry : angle 0.58499 / 0.30 (24265) hydrogen bonds : bond 0.04113 / 4.22 ( 865) hydrogen bonds : angle 4.20741 / 4.58 ( 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 271 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: J 461 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7160 (pp20) REVERT: A 1 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6602 (ttm) REVERT: A 92 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 138 ARG cc_start: 0.8366 (ttp-170) cc_final: 0.8140 (tmm160) REVERT: A 190 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7326 (mm-30) REVERT: A 201 GLN cc_start: 0.7998 (tp40) cc_final: 0.7469 (mt0) REVERT: A 204 LYS cc_start: 0.7367 (mttp) cc_final: 0.6814 (mppt) REVERT: A 211 LYS cc_start: 0.7654 (mttm) cc_final: 0.7173 (pttp) REVERT: A 215 GLN cc_start: 0.7570 (tt0) cc_final: 0.7158 (pt0) REVERT: A 218 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: A 1096 GLN cc_start: 0.6182 (pm20) cc_final: 0.5935 (pm20) REVERT: A 1115 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7434 (mt-10) REVERT: A 1126 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7329 (tptt) REVERT: A 1168 ASP cc_start: 0.7670 (m-30) cc_final: 0.7400 (m-30) REVERT: A 1178 LYS cc_start: 0.8922 (mttm) cc_final: 0.8411 (mttp) REVERT: A 1254 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7691 (mttt) REVERT: A 1261 ASN cc_start: 0.7682 (m110) cc_final: 0.7377 (m110) REVERT: A 1290 LYS cc_start: 0.8404 (ptpt) cc_final: 0.7855 (mmtp) REVERT: B 92 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: B 106 SER cc_start: 0.7873 (OUTLIER) cc_final: 0.7514 (t) REVERT: B 138 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7676 (ptp90) REVERT: B 148 LYS cc_start: 0.8329 (tttt) cc_final: 0.8086 (ttmm) REVERT: B 194 GLN cc_start: 0.8167 (tp40) cc_final: 0.7227 (tt0) REVERT: B 1260 ARG cc_start: 0.7650 (mmt180) cc_final: 0.6525 (ttm110) REVERT: B 1294 ASP cc_start: 0.8298 (m-30) cc_final: 0.7896 (m-30) REVERT: B 1310 ASN cc_start: 0.7845 (m-40) cc_final: 0.7600 (m110) REVERT: D 51 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: D 274 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7642 (mt) REVERT: D 310 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6637 (mm-30) REVERT: D 327 LYS cc_start: 0.7936 (mttt) cc_final: 0.7564 (ptmt) REVERT: D 348 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: D 354 ASN cc_start: 0.7604 (t0) cc_final: 0.7331 (t0) REVERT: D 438 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: D 442 LYS cc_start: 0.7617 (mtmt) cc_final: 0.6921 (tmtm) REVERT: D 451 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7475 (tt0) REVERT: D 452 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7731 (mtm-85) REVERT: D 467 LYS cc_start: 0.6716 (tttt) cc_final: 0.6477 (mppt) REVERT: D 473 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7075 (tp) REVERT: D 480 LYS cc_start: 0.7639 (ttmm) cc_final: 0.7186 (ttmt) REVERT: D 503 ARG cc_start: 0.7562 (mtt180) cc_final: 0.7140 (mmm160) REVERT: E 64 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7481 (mp0) REVERT: E 157 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7781 (mmt) REVERT: E 227 ASN cc_start: 0.6851 (p0) cc_final: 0.6127 (m-40) REVERT: E 229 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8530 (mp) REVERT: E 232 GLN cc_start: 0.8262 (mp-120) cc_final: 0.7947 (mm-40) REVERT: E 281 LYS cc_start: 0.7559 (mttt) cc_final: 0.7033 (mtpt) REVERT: E 290 LYS cc_start: 0.8480 (ttpt) cc_final: 0.8146 (tttp) REVERT: E 341 GLU cc_start: 0.7673 (mm-30) cc_final: 0.6994 (tt0) REVERT: E 452 ARG cc_start: 0.8090 (ptp90) cc_final: 0.7454 (ptm160) REVERT: E 459 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6614 (tt0) REVERT: E 479 GLU cc_start: 0.7612 (pp20) cc_final: 0.7356 (pp20) REVERT: E 487 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6399 (mt-10) outliers start: 61 outliers final: 42 residues processed: 252 average time/residue: 0.5817 time to fit residues: 164.0147 Evaluate side-chains 259 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 92 GLU 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 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 157 MET Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 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: 4.9990 chunk 51 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 256 ASN D 317 HIS D 401 HIS E 317 HIS E 330 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.155326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115085 restraints weight = 35870.444| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.51 r_work: 0.3168 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- 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 = 0.47 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 = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2023 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= 0.142 Angle : 0.577 10.814 24265 Z= 0.300 Chirality : 0.043 0.377 2679 Planarity : 0.003 0.038 2950 Dihedral : 16.757 61.386 2817 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.24 % Allowed : 25.15 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.18), residues: 1985 helix: 2.37 (0.18), residues: 818 sheet: 0.70 (0.26), residues: 362 loop : -1.01 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 87 TYR 0.014 0.001 TYR B1282 PHE 0.015 0.001 PHE D 228 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 0.00323 / 0.14 (17870) covalent geometry : angle 0.57713 / 0.30 (24265) hydrogen bonds : bond 0.03971 / 4.08 ( 865) hydrogen bonds : angle 4.17892 / 4.54 ( 2502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7014.88 seconds wall clock time: 119 minutes 56.01 seconds (7196.01 seconds total)