Starting phenix.real_space_refine on Thu Aug 6 23:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9m_52964/08_2026/9q9m_52964.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9m_52964/08_2026/9q9m_52964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q9m_52964/08_2026/9q9m_52964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9m_52964/08_2026/9q9m_52964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q9m_52964/08_2026/9q9m_52964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9m_52964/08_2026/9q9m_52964.map" } resolution = 2.81 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= 0.001 sd= 0.071 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 10797 2.51 5 N 3025 2.21 5 O 3388 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 34 residue(s): 0.02s 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: 17361 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: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 681 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "A" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3760 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 456} Chain breaks: 1 Chain: "B" Number of atoms: 3811 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 470, 3803 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 461} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 470, 3803 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 461} Chain breaks: 1 bond proxies already assigned to first conformer: 3845 Chain: "D" Number of atoms: 3898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3898 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 20, 'TRANS': 457} 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: 4.77, per 1000 atoms: 0.27 Number of scatterers: 17361 At special positions: 0 Unit cell: (105.415, 113.412, 180.296, 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 3388 8.00 N 3025 7.00 C 10797 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: 1.63 Conformation dependent library (CDL) restraints added in 813.1 milliseconds 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 16 sheets defined 43.9% alpha, 18.3% beta 25 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'J' and resid 467 through 472 Processing helix chain 'F' and resid 716 through 746 removed outlier: 3.500A pdb=" N LEU F 743 " --> pdb=" O LEU F 739 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG F 745 " --> pdb=" O ASP F 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.775A 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 136 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: 3.856A 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: 3.777A 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 1102 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: 3.576A 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: 3.717A 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 235 removed outlier: 3.775A pdb=" N MET B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1092 Processing helix chain 'B' and resid 1094 through 1099 removed outlier: 3.848A pdb=" N ASP B1099 " --> pdb=" O PRO B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1155 removed outlier: 3.710A pdb=" N LYS B1103 " --> pdb=" O ASP B1099 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B1113 " --> pdb=" O ILE B1109 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) 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: 4.017A pdb=" N LYS B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.857A 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 1278 removed outlier: 3.591A pdb=" N VAL B1274 " --> pdb=" O ASP B1270 " (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 removed outlier: 3.515A pdb=" N VAL D 433 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS D 434 " --> pdb=" O GLU D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 removed outlier: 3.843A 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 507 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: 3.879A 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: 3.647A 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: 6.528A 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: 6.456A 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: 6.642A 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: 6.642A pdb=" N ARG A 87 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU A 93 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 121 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1227 through 1231 removed outlier: 6.281A 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: 8.819A 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: 4.031A 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: 3.798A 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: 3.798A 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: 3.865A 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: 8.336A 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: 7.402A 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: 6.752A pdb=" N LYS D 175 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU D 213 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA D 177 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL D 215 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR D 179 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN D 212 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE D 242 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE D 214 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 264 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 263 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 6.187A 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: 3.594A 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: 6.835A 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: 6.865A 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: 6.082A 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) 820 hydrogen bonds defined for protein. 2346 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: 3.78 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2856 1.31 - 1.43: 4682 1.43 - 1.56: 9985 1.56 - 1.69: 111 1.69 - 1.81: 128 Bond restraints: 17762 Sorted by residual: bond pdb=" C GLY D 453 " pdb=" N MET D 454 " ideal model delta sigma weight residual 1.335 1.240 0.095 1.38e-02 5.25e+03 4.73e+01 bond pdb=" C MET A 208 " pdb=" O MET A 208 " ideal model delta sigma weight residual 1.237 1.315 -0.078 1.16e-02 7.43e+03 4.52e+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 4.51e+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 3.93e+01 bond pdb=" C PHE D 228 " pdb=" N ILE D 229 " ideal model delta sigma weight residual 1.330 1.280 0.050 8.40e-03 1.42e+04 3.59e+01 ... (remaining 17757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 23296 2.54 - 5.08: 687 5.08 - 7.62: 122 7.62 - 10.16: 9 10.16 - 12.70: 7 Bond angle restraints: 24121 Sorted by residual: angle pdb=" N VAL D 429 " pdb=" CA VAL D 429 " pdb=" C VAL D 429 " ideal model delta sigma weight residual 113.00 104.12 8.88 1.30e+00 5.92e-01 4.67e+01 angle pdb=" O GLN A 207 " pdb=" C GLN A 207 " pdb=" N MET A 208 " ideal model delta sigma weight residual 122.22 114.49 7.73 1.17e+00 7.31e-01 4.36e+01 angle pdb=" N LYS D 105 " pdb=" CA LYS D 105 " pdb=" C LYS D 105 " ideal model delta sigma weight residual 113.18 105.46 7.72 1.21e+00 6.83e-01 4.07e+01 angle pdb=" N PRO F 748 " pdb=" CA PRO F 748 " pdb=" C PRO F 748 " ideal model delta sigma weight residual 111.26 100.90 10.36 1.63e+00 3.76e-01 4.04e+01 angle pdb=" N LYS A1090 " pdb=" CA LYS A1090 " pdb=" C LYS A1090 " ideal model delta sigma weight residual 113.88 106.64 7.24 1.23e+00 6.61e-01 3.46e+01 ... (remaining 24116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8864 17.96 - 35.92: 1236 35.92 - 53.89: 524 53.89 - 71.85: 148 71.85 - 89.81: 20 Dihedral angle restraints: 10792 sinusoidal: 4967 harmonic: 5825 Sorted by residual: dihedral pdb=" CD ARG F 745 " pdb=" NE ARG F 745 " pdb=" CZ ARG F 745 " pdb=" NH1 ARG F 745 " ideal model delta sinusoidal sigma weight residual 0.00 60.81 -60.81 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CD ARG D 428 " pdb=" NE ARG D 428 " pdb=" CZ ARG D 428 " pdb=" NH1 ARG D 428 " ideal model delta sinusoidal sigma weight residual 0.00 38.43 -38.43 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CD ARG B1098 " pdb=" NE ARG B1098 " pdb=" CZ ARG B1098 " pdb=" NH1 ARG B1098 " ideal model delta sinusoidal sigma weight residual 0.00 35.39 -35.39 1 1.00e+01 1.00e-02 1.77e+01 ... (remaining 10789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2509 0.120 - 0.240: 122 0.240 - 0.359: 11 0.359 - 0.479: 4 0.479 - 0.599: 20 Chirality restraints: 2666 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 8.97e+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 -2.92 -0.59 2.00e-01 2.50e+01 8.61e+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 8.39e+00 ... (remaining 2663 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 745 " 0.960 9.50e-02 1.11e+02 4.30e-01 1.12e+02 pdb=" NE ARG F 745 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG F 745 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG F 745 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 745 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 428 " -0.665 9.50e-02 1.11e+02 2.98e-01 5.42e+01 pdb=" NE ARG D 428 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG D 428 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 428 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 428 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1098 " 0.623 9.50e-02 1.11e+02 2.79e-01 4.76e+01 pdb=" NE ARG B1098 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B1098 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B1098 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B1098 " 0.019 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 36 2.45 - 3.06: 10874 3.06 - 3.67: 26146 3.67 - 4.29: 41420 4.29 - 4.90: 67392 Nonbonded interactions: 145868 Sorted by model distance: nonbonded pdb=" ND1 HIS D 245 " pdb="MN MN D 802 " model vdw 1.835 2.400 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 ... (remaining 145863 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 235 or resid 1078 through 1 \ 306)) selection = (chain 'B' and (resid 1 through 2 or resid 4 through 1306)) } ncs_group { reference = (chain 'D' and (resid 8 through 402 or resid 426 through 802)) selection = (chain 'E' and (resid 8 through 507 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: 4.440 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: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.070 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.006 0.095 17762 Z= 0.437 Angle : 0.976 12.696 24121 Z= 0.648 Chirality : 0.076 0.599 2666 Planarity : 0.016 0.430 2931 Dihedral : 20.034 89.810 7000 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.88 % Allowed : 21.61 % Favored : 76.51 % 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: -0.17 (0.18), residues: 1972 helix: 1.03 (0.18), residues: 823 sheet: 0.05 (0.27), residues: 349 loop : -1.40 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1256 TYR 0.011 0.002 TYR B1282 PHE 0.027 0.002 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 0.00617 / 0.44 (17762) covalent geometry : angle 0.97576 / 0.65 (24121) hydrogen bonds : bond 0.16420 / 15.49 ( 846) hydrogen bonds : angle 7.12081 / 8.08 ( 2446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 382 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6037 (ttm) cc_final: 0.5559 (mmm) REVERT: A 5 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6634 (mt-10) REVERT: A 89 VAL cc_start: 0.7678 (m) cc_final: 0.7462 (t) REVERT: A 122 LYS cc_start: 0.8187 (tttt) cc_final: 0.7469 (ptpt) REVERT: A 185 TYR cc_start: 0.7526 (m-80) cc_final: 0.7085 (m-80) REVERT: A 205 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 71 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7553 (mtmt) REVERT: B 90 ASN cc_start: 0.7005 (m-40) cc_final: 0.6664 (m-40) REVERT: B 94 ILE cc_start: 0.7835 (mt) cc_final: 0.7545 (mp) REVERT: B 208 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6448 (tmm) REVERT: B 1123 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7903 (tt) REVERT: B 1162 TYR cc_start: 0.8021 (p90) cc_final: 0.7795 (p90) REVERT: B 1189 LEU cc_start: 0.8314 (mp) cc_final: 0.7863 (tt) REVERT: B 1197 MET cc_start: 0.8884 (ttt) cc_final: 0.8591 (ttt) REVERT: D 64 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8146 (mm-30) REVERT: D 259 GLN cc_start: 0.5726 (mm-40) cc_final: 0.5421 (mm110) REVERT: D 325 ASN cc_start: 0.8471 (t0) cc_final: 0.8119 (t160) REVERT: D 374 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7874 (pt0) REVERT: D 378 VAL cc_start: 0.7273 (t) cc_final: 0.6843 (m) REVERT: D 438 GLN cc_start: 0.7612 (pt0) cc_final: 0.7339 (mm-40) REVERT: D 496 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7561 (tptp) REVERT: E 64 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7430 (mm-30) REVERT: E 196 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7656 (tptt) REVERT: E 232 GLN cc_start: 0.8330 (mp10) cc_final: 0.8057 (mm-40) REVERT: E 313 VAL cc_start: 0.8480 (t) cc_final: 0.7947 (t) REVERT: E 330 GLN cc_start: 0.7639 (mt0) cc_final: 0.7352 (mm110) REVERT: E 343 MET cc_start: 0.7086 (mtm) cc_final: 0.6777 (mtm) REVERT: E 356 HIS cc_start: 0.7404 (m-70) cc_final: 0.7165 (m-70) REVERT: E 359 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7241 (pm20) outliers start: 34 outliers final: 3 residues processed: 401 average time/residue: 0.6685 time to fit residues: 297.9223 Evaluate side-chains 226 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 221 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain E residue 199 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1181 ASN A1261 ASN B 152 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS D 317 HIS D 401 HIS D 482 GLN E 219 ASN E 256 ASN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 GLN E 401 HIS E 477 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.181732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139538 restraints weight = 25079.439| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.59 r_work: 0.3596 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17762 Z= 0.166 Angle : 0.642 8.225 24121 Z= 0.342 Chirality : 0.045 0.225 2666 Planarity : 0.004 0.047 2931 Dihedral : 17.338 67.947 2807 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.70 % Allowed : 24.77 % Favored : 71.53 % 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: 0.25 (0.18), residues: 1972 helix: 1.52 (0.18), residues: 829 sheet: 0.20 (0.25), residues: 372 loop : -1.37 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1105 TYR 0.024 0.002 TYR A1104 PHE 0.026 0.002 PHE E 237 TRP 0.006 0.001 TRP A 164 HIS 0.009 0.001 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (17762) covalent geometry : angle 0.64154 / 0.34 (24121) hydrogen bonds : bond 0.04957 / 4.89 ( 846) hydrogen bonds : angle 5.12387 / 5.57 ( 2446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6067 (ttm) cc_final: 0.5662 (ttp) REVERT: A 89 VAL cc_start: 0.7555 (m) cc_final: 0.7316 (t) REVERT: A 185 TYR cc_start: 0.7348 (m-80) cc_final: 0.6877 (m-80) REVERT: A 205 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7104 (mt-10) REVERT: A 1108 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6505 (tmm) REVERT: A 1261 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.6928 (t0) REVERT: B 20 LYS cc_start: 0.8266 (pttp) cc_final: 0.8024 (ptpp) REVERT: B 71 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7575 (mtmt) REVERT: B 79 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7388 (ttp80) REVERT: B 94 ILE cc_start: 0.7603 (mt) cc_final: 0.7021 (mp) REVERT: B 119 THR cc_start: 0.7609 (m) cc_final: 0.7155 (p) REVERT: B 186 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6905 (mt) REVERT: B 1126 LYS cc_start: 0.7358 (ttmm) cc_final: 0.7016 (ttpt) REVERT: B 1189 LEU cc_start: 0.8206 (mp) cc_final: 0.7817 (tt) REVERT: B 1197 MET cc_start: 0.8950 (ttt) cc_final: 0.8544 (ttt) REVERT: B 1260 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6793 (mmm-85) REVERT: D 64 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7906 (mm-30) REVERT: D 161 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6694 (pptt) REVERT: D 192 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.5417 (mtt) REVERT: D 205 GLU cc_start: 0.8024 (pm20) cc_final: 0.7800 (pm20) REVERT: D 325 ASN cc_start: 0.8150 (t0) cc_final: 0.7728 (t0) REVERT: D 327 LYS cc_start: 0.7384 (tptt) cc_final: 0.7096 (pttp) REVERT: D 350 GLU cc_start: 0.7099 (tt0) cc_final: 0.6784 (tm-30) REVERT: D 374 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7931 (pt0) REVERT: D 438 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6882 (mm-40) REVERT: D 439 THR cc_start: 0.6888 (m) cc_final: 0.6208 (t) REVERT: E 64 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7090 (mm-30) REVERT: E 157 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6824 (mtp) REVERT: E 196 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7645 (tptt) REVERT: E 232 GLN cc_start: 0.8299 (mp10) cc_final: 0.7867 (mm-40) REVERT: E 330 GLN cc_start: 0.7289 (mt0) cc_final: 0.6988 (mm110) REVERT: E 356 HIS cc_start: 0.7494 (m-70) cc_final: 0.7071 (m-70) REVERT: E 359 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6849 (pm20) outliers start: 67 outliers final: 19 residues processed: 274 average time/residue: 0.6523 time to fit residues: 200.0843 Evaluate side-chains 223 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1261 ASN Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1260 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 243 TRP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 379 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 29 optimal weight: 0.0470 chunk 60 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 overall best weight: 1.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1181 ASN A1259 GLN B 199 GLN B1269 HIS D 112 GLN D 317 HIS D 401 HIS D 443 ASN D 482 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.177545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134761 restraints weight = 25760.417| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.61 r_work: 0.3541 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17762 Z= 0.173 Angle : 0.616 7.184 24121 Z= 0.325 Chirality : 0.045 0.244 2666 Planarity : 0.004 0.041 2931 Dihedral : 17.194 64.539 2798 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.20 % Allowed : 25.15 % Favored : 70.65 % 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: 0.48 (0.18), residues: 1972 helix: 1.82 (0.18), residues: 818 sheet: 0.22 (0.25), residues: 379 loop : -1.28 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 349 TYR 0.022 0.002 TYR E 369 PHE 0.021 0.002 PHE F 688 TRP 0.005 0.001 TRP A 164 HIS 0.006 0.001 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (17762) covalent geometry : angle 0.61613 / 0.32 (24121) hydrogen bonds : bond 0.04590 / 4.53 ( 846) hydrogen bonds : angle 4.80471 / 5.14 ( 2446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 206 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6576 (p-80) REVERT: F 707 ASP cc_start: 0.5847 (OUTLIER) cc_final: 0.5124 (t0) REVERT: A 1 MET cc_start: 0.6534 (ttm) cc_final: 0.6169 (mtm) REVERT: A 5 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 20 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6992 (ptmt) REVERT: A 89 VAL cc_start: 0.7742 (m) cc_final: 0.7527 (t) REVERT: A 92 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: A 185 TYR cc_start: 0.7405 (m-80) cc_final: 0.7009 (m-80) REVERT: A 1138 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7732 (mpt) REVERT: A 1261 ASN cc_start: 0.7455 (t0) cc_final: 0.6930 (t0) REVERT: A 1289 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 20 LYS cc_start: 0.8333 (pttp) cc_final: 0.8040 (ptpp) REVERT: B 71 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7588 (mtmt) REVERT: B 94 ILE cc_start: 0.7795 (mt) cc_final: 0.7362 (mp) REVERT: B 186 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6918 (mt) REVERT: B 1123 ILE cc_start: 0.7447 (mp) cc_final: 0.7239 (tt) REVERT: B 1189 LEU cc_start: 0.8241 (mp) cc_final: 0.7824 (tt) REVERT: D 64 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7976 (mm-30) REVERT: D 161 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6603 (pptt) REVERT: D 192 MET cc_start: 0.5934 (OUTLIER) cc_final: 0.5420 (mtt) REVERT: D 310 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6737 (mm-30) REVERT: D 366 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.6737 (mtm110) REVERT: D 374 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7949 (pt0) REVERT: D 438 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6743 (mm-40) REVERT: D 439 THR cc_start: 0.6917 (m) cc_final: 0.6437 (t) REVERT: D 443 ASN cc_start: 0.8605 (m-40) cc_final: 0.8124 (m110) REVERT: D 458 VAL cc_start: 0.7827 (t) cc_final: 0.7605 (m) REVERT: E 64 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7102 (mm-30) REVERT: E 157 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6810 (mtp) REVERT: E 196 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7631 (tptt) REVERT: E 232 GLN cc_start: 0.8281 (mp10) cc_final: 0.7913 (mm-40) REVERT: E 309 MET cc_start: 0.7640 (tpt) cc_final: 0.7247 (tpt) REVERT: E 330 GLN cc_start: 0.7434 (mt0) cc_final: 0.7062 (mm110) REVERT: E 359 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6955 (pm20) outliers start: 76 outliers final: 27 residues processed: 260 average time/residue: 0.6168 time to fit residues: 179.1055 Evaluate side-chains 225 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 243 TRP Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 464 LYS Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 394 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 132 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 3 optimal weight: 40.0000 chunk 59 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 701 HIS A1130 GLN A1181 ASN B 85 GLN ** B1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 317 HIS D 325 ASN D 401 HIS D 482 GLN E 259 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.168726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123866 restraints weight = 32601.432| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.90 r_work: 0.3403 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 17762 Z= 0.334 Angle : 0.752 9.004 24121 Z= 0.393 Chirality : 0.052 0.317 2666 Planarity : 0.005 0.048 2931 Dihedral : 17.464 65.120 2798 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.42 % Allowed : 23.38 % Favored : 71.20 % 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: -0.00 (0.18), residues: 1972 helix: 1.45 (0.18), residues: 809 sheet: -0.16 (0.24), residues: 388 loop : -1.49 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 13 TYR 0.032 0.002 TYR A 212 PHE 0.033 0.003 PHE F 688 TRP 0.012 0.002 TRP D 210 HIS 0.009 0.002 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.33 (17762) covalent geometry : angle 0.75179 / 0.39 (24121) hydrogen bonds : bond 0.05646 / 5.51 ( 846) hydrogen bonds : angle 5.05098 / 5.40 ( 2446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 206 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 687 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7275 (mtmt) REVERT: F 707 ASP cc_start: 0.6145 (OUTLIER) cc_final: 0.5351 (t0) REVERT: A 1 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6947 (mtm) REVERT: A 18 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6137 (mm-30) REVERT: A 148 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7884 (tttp) REVERT: A 1271 GLU cc_start: 0.6986 (mp0) cc_final: 0.6046 (mm-30) REVERT: A 1289 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8366 (mm) REVERT: B 1 MET cc_start: 0.6404 (mmm) cc_final: 0.6048 (mmm) REVERT: B 71 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7596 (mtmt) REVERT: B 160 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: B 1108 MET cc_start: 0.7552 (mmm) cc_final: 0.7100 (mmt) REVERT: B 1189 LEU cc_start: 0.8363 (mp) cc_final: 0.7803 (tt) REVERT: D 112 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: D 192 MET cc_start: 0.5798 (OUTLIER) cc_final: 0.5288 (mtt) REVERT: D 292 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6909 (mmm-85) REVERT: D 374 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7994 (pt0) REVERT: D 438 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6892 (mm-40) REVERT: D 439 THR cc_start: 0.6853 (m) cc_final: 0.6124 (t) REVERT: D 443 ASN cc_start: 0.8732 (m-40) cc_final: 0.8281 (m110) REVERT: D 496 LYS cc_start: 0.7624 (mmmt) cc_final: 0.7340 (tptp) REVERT: E 64 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7179 (mm-30) REVERT: E 189 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6068 (tt) REVERT: E 196 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7768 (tptt) REVERT: E 232 GLN cc_start: 0.8292 (mp10) cc_final: 0.8044 (mm-40) REVERT: E 278 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6946 (mt-10) REVERT: E 281 LYS cc_start: 0.7298 (mttt) cc_final: 0.6810 (mmtm) REVERT: E 330 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7272 (mm110) REVERT: E 346 ASN cc_start: 0.7372 (t0) cc_final: 0.7073 (t0) REVERT: E 384 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6751 (mttm) REVERT: E 428 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.6142 (mtt90) REVERT: E 465 GLU cc_start: 0.7082 (mp0) cc_final: 0.6826 (mp0) REVERT: E 467 LYS cc_start: 0.7460 (ttpt) cc_final: 0.7025 (tppt) REVERT: E 471 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6615 (tt0) outliers start: 98 outliers final: 33 residues processed: 277 average time/residue: 0.5965 time to fit residues: 185.4652 Evaluate side-chains 227 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 464 LYS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 ARG Chi-restraints excluded: chain E residue 471 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 24 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN B1183 ASN B1247 HIS D 112 GLN D 317 HIS D 322 ASN D 401 HIS D 482 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.172737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128469 restraints weight = 35340.144| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.02 r_work: 0.3460 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17762 Z= 0.140 Angle : 0.597 7.112 24121 Z= 0.314 Chirality : 0.044 0.319 2666 Planarity : 0.004 0.041 2931 Dihedral : 17.208 64.015 2798 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.21 % Allowed : 26.59 % Favored : 70.20 % 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: 0.35 (0.18), residues: 1972 helix: 1.78 (0.18), residues: 817 sheet: 0.11 (0.25), residues: 377 loop : -1.42 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 745 TYR 0.028 0.002 TYR A 212 PHE 0.023 0.001 PHE F 688 TRP 0.006 0.001 TRP A 164 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (17762) covalent geometry : angle 0.59701 / 0.31 (24121) hydrogen bonds : bond 0.04344 / 4.32 ( 846) hydrogen bonds : angle 4.68539 / 5.00 ( 2446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6424 (p-80) REVERT: F 707 ASP cc_start: 0.6089 (OUTLIER) cc_final: 0.5273 (t0) REVERT: A 1 MET cc_start: 0.7237 (ttm) cc_final: 0.6852 (mtm) REVERT: A 5 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7234 (mt-10) REVERT: A 89 VAL cc_start: 0.7880 (m) cc_final: 0.7669 (t) REVERT: A 92 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: A 148 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7962 (tttp) REVERT: A 160 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: A 177 ASP cc_start: 0.8040 (p0) cc_final: 0.7717 (p0) REVERT: A 1271 GLU cc_start: 0.7012 (mp0) cc_final: 0.6062 (mm-30) REVERT: B 1 MET cc_start: 0.6304 (mmm) cc_final: 0.5961 (mmm) REVERT: B 71 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7516 (mtmt) REVERT: B 79 ARG cc_start: 0.8173 (ttt90) cc_final: 0.7919 (ttp80) REVERT: B 1123 ILE cc_start: 0.7060 (mp) cc_final: 0.6855 (tt) REVERT: B 1158 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: B 1189 LEU cc_start: 0.8262 (mp) cc_final: 0.7717 (tt) REVERT: D 64 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8066 (mm-30) REVERT: D 374 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8054 (pt0) REVERT: D 438 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6826 (mm-40) REVERT: D 439 THR cc_start: 0.6760 (m) cc_final: 0.6105 (t) REVERT: D 443 ASN cc_start: 0.8654 (m-40) cc_final: 0.8271 (m110) REVERT: D 496 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7315 (tptp) REVERT: E 64 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7109 (mm-30) REVERT: E 136 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6450 (t0) REVERT: E 189 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.5802 (tt) REVERT: E 196 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7759 (tptt) REVERT: E 232 GLN cc_start: 0.8224 (mp10) cc_final: 0.7945 (mm-40) REVERT: E 233 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: E 281 LYS cc_start: 0.7222 (mttt) cc_final: 0.6771 (mmtm) REVERT: E 330 GLN cc_start: 0.7603 (mt0) cc_final: 0.7165 (mm110) REVERT: E 428 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.6105 (mtt90) REVERT: E 465 GLU cc_start: 0.6994 (mp0) cc_final: 0.6476 (mp0) REVERT: E 467 LYS cc_start: 0.7407 (ttpt) cc_final: 0.6968 (tppt) REVERT: E 471 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6655 (tt0) outliers start: 58 outliers final: 16 residues processed: 235 average time/residue: 0.6013 time to fit residues: 158.0021 Evaluate side-chains 204 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1158 GLN Chi-restraints excluded: chain B residue 1159 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 438 GLN 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 233 PHE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 428 ARG Chi-restraints excluded: chain E residue 471 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 141 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1183 ASN D 112 GLN D 317 HIS D 325 ASN D 401 HIS D 482 GLN E 401 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.173199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130266 restraints weight = 24344.197| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.52 r_work: 0.3492 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17762 Z= 0.136 Angle : 0.587 8.126 24121 Z= 0.308 Chirality : 0.043 0.292 2666 Planarity : 0.004 0.040 2931 Dihedral : 17.081 63.536 2798 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.99 % Allowed : 27.14 % Favored : 69.87 % 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: 0.45 (0.18), residues: 1972 helix: 1.86 (0.18), residues: 820 sheet: 0.19 (0.26), residues: 377 loop : -1.40 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 488 TYR 0.027 0.002 TYR A 212 PHE 0.027 0.001 PHE E 237 TRP 0.005 0.001 TRP A 164 HIS 0.019 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (17762) covalent geometry : angle 0.58724 / 0.31 (24121) hydrogen bonds : bond 0.04244 / 4.20 ( 846) hydrogen bonds : angle 4.58685 / 4.89 ( 2446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 184 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7173 (OUTLIER) cc_final: 0.6381 (p-80) REVERT: F 707 ASP cc_start: 0.6104 (OUTLIER) cc_final: 0.5316 (t0) REVERT: A 1 MET cc_start: 0.7206 (ttm) cc_final: 0.6876 (mtm) REVERT: A 5 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 148 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7933 (tttp) REVERT: A 160 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: A 177 ASP cc_start: 0.8024 (p0) cc_final: 0.7652 (p0) REVERT: A 1140 MET cc_start: 0.8167 (tpp) cc_final: 0.7831 (mmm) REVERT: A 1271 GLU cc_start: 0.6948 (mp0) cc_final: 0.6535 (pm20) REVERT: B 1 MET cc_start: 0.6266 (mmm) cc_final: 0.5947 (mmm) REVERT: B 71 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7540 (mtmt) REVERT: B 79 ARG cc_start: 0.8141 (ttt90) cc_final: 0.7903 (ttp80) REVERT: B 140 MET cc_start: 0.6837 (mmm) cc_final: 0.6314 (mtm) REVERT: B 1158 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7413 (mt0) REVERT: B 1189 LEU cc_start: 0.8289 (mp) cc_final: 0.7723 (tt) REVERT: D 64 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8034 (mm-30) REVERT: D 366 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7276 (mtm-85) REVERT: D 374 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8093 (mt-10) REVERT: D 438 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6816 (mm-40) REVERT: D 439 THR cc_start: 0.6789 (m) cc_final: 0.6130 (t) REVERT: D 443 ASN cc_start: 0.8656 (m-40) cc_final: 0.8275 (m110) REVERT: E 64 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7089 (mm-30) REVERT: E 136 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6460 (t0) REVERT: E 189 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5746 (tt) REVERT: E 196 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7753 (tptt) REVERT: E 232 GLN cc_start: 0.8217 (mp10) cc_final: 0.7931 (mm-40) REVERT: E 233 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: E 281 LYS cc_start: 0.7149 (mttt) cc_final: 0.6708 (mmtm) REVERT: E 294 MET cc_start: 0.7525 (ttp) cc_final: 0.6869 (ttp) REVERT: E 330 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7140 (mm110) REVERT: E 465 GLU cc_start: 0.6992 (mp0) cc_final: 0.6477 (mp0) REVERT: E 467 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7024 (tppt) REVERT: E 471 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6673 (tt0) outliers start: 54 outliers final: 19 residues processed: 221 average time/residue: 0.6085 time to fit residues: 150.7678 Evaluate side-chains 202 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1158 GLN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 471 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 177 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 29 optimal weight: 0.0170 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1183 ASN D 317 HIS D 325 ASN D 401 HIS D 482 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.173814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131370 restraints weight = 22526.201| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.42 r_work: 0.3512 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17762 Z= 0.126 Angle : 0.573 9.174 24121 Z= 0.301 Chirality : 0.043 0.273 2666 Planarity : 0.004 0.062 2931 Dihedral : 16.945 62.708 2798 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.87 % Allowed : 27.20 % Favored : 69.93 % 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: 0.58 (0.18), residues: 1972 helix: 1.98 (0.18), residues: 820 sheet: 0.29 (0.26), residues: 377 loop : -1.37 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 349 TYR 0.027 0.001 TYR A 212 PHE 0.021 0.001 PHE F 688 TRP 0.006 0.001 TRP B 164 HIS 0.025 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (17762) covalent geometry : angle 0.57330 / 0.30 (24121) hydrogen bonds : bond 0.04069 / 4.03 ( 846) hydrogen bonds : angle 4.48521 / 4.79 ( 2446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7138 (OUTLIER) cc_final: 0.6290 (p-80) REVERT: F 707 ASP cc_start: 0.6115 (OUTLIER) cc_final: 0.5356 (t0) REVERT: F 737 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5087 (pt0) REVERT: A 1 MET cc_start: 0.7327 (ttm) cc_final: 0.6990 (mtm) REVERT: A 5 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7405 (mt-10) REVERT: A 160 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: A 1089 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7432 (pttt) REVERT: A 1140 MET cc_start: 0.8222 (tpp) cc_final: 0.7945 (mmm) REVERT: A 1179 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7674 (ttp80) REVERT: A 1271 GLU cc_start: 0.7034 (mp0) cc_final: 0.6635 (pm20) REVERT: B 1 MET cc_start: 0.6344 (mmm) cc_final: 0.5994 (mmm) REVERT: B 71 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7721 (mtpt) REVERT: B 79 ARG cc_start: 0.8292 (ttt90) cc_final: 0.8074 (ttp80) REVERT: B 119 THR cc_start: 0.7831 (m) cc_final: 0.7385 (p) REVERT: B 1108 MET cc_start: 0.7508 (mmm) cc_final: 0.7191 (mmm) REVERT: B 1189 LEU cc_start: 0.8299 (mp) cc_final: 0.7754 (tt) REVERT: D 64 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8099 (mm-30) REVERT: D 354 ASN cc_start: 0.7568 (t0) cc_final: 0.6937 (t0) REVERT: D 374 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8210 (mt-10) REVERT: D 438 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6809 (mm-40) REVERT: D 439 THR cc_start: 0.6838 (m) cc_final: 0.6171 (t) REVERT: D 443 ASN cc_start: 0.8665 (m-40) cc_final: 0.8279 (m110) REVERT: D 500 GLU cc_start: 0.6765 (tm-30) cc_final: 0.6520 (tm-30) REVERT: E 64 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7190 (mm-30) REVERT: E 136 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6521 (t0) REVERT: E 189 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.5957 (tt) REVERT: E 196 LYS cc_start: 0.8401 (mtmt) cc_final: 0.7784 (tptt) REVERT: E 232 GLN cc_start: 0.8200 (mp10) cc_final: 0.7899 (mm-40) REVERT: E 233 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7802 (m-10) REVERT: E 281 LYS cc_start: 0.7174 (mttt) cc_final: 0.6703 (mmtm) REVERT: E 330 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7174 (mm110) REVERT: E 465 GLU cc_start: 0.6942 (mp0) cc_final: 0.6498 (mp0) REVERT: E 467 LYS cc_start: 0.7496 (ttpt) cc_final: 0.6980 (tppt) REVERT: E 471 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6678 (tt0) outliers start: 52 outliers final: 20 residues processed: 226 average time/residue: 0.6491 time to fit residues: 164.0016 Evaluate side-chains 205 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain F residue 737 GLU Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 243 TRP Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 438 GLN 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 209 SER Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 471 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 94 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS B1183 ASN D 317 HIS D 325 ASN D 401 HIS D 482 GLN E 445 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.170232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125632 restraints weight = 34548.621| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.97 r_work: 0.3424 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17762 Z= 0.238 Angle : 0.649 10.438 24121 Z= 0.338 Chirality : 0.046 0.282 2666 Planarity : 0.004 0.042 2931 Dihedral : 17.047 64.058 2798 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.99 % Allowed : 27.03 % Favored : 69.98 % 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: 0.32 (0.18), residues: 1972 helix: 1.78 (0.18), residues: 819 sheet: 0.00 (0.25), residues: 399 loop : -1.46 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 349 TYR 0.026 0.002 TYR A 212 PHE 0.030 0.002 PHE E 237 TRP 0.008 0.001 TRP D 210 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (17762) covalent geometry : angle 0.64921 / 0.34 (24121) hydrogen bonds : bond 0.04697 / 4.59 ( 846) hydrogen bonds : angle 4.67782 / 5.00 ( 2446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 687 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7328 (mtmt) REVERT: F 701 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6343 (p-80) REVERT: F 707 ASP cc_start: 0.6254 (OUTLIER) cc_final: 0.5434 (t0) REVERT: F 737 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5152 (pt0) REVERT: A 1 MET cc_start: 0.7245 (ttm) cc_final: 0.6907 (mtm) REVERT: A 5 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 18 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6104 (mm-30) REVERT: A 122 LYS cc_start: 0.7662 (tttm) cc_final: 0.6992 (ttpp) REVERT: A 160 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7776 (mm-30) REVERT: A 209 GLU cc_start: 0.7168 (tp30) cc_final: 0.6737 (tp30) REVERT: A 1140 MET cc_start: 0.8285 (tpp) cc_final: 0.8061 (mmm) REVERT: A 1179 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7562 (ttp80) REVERT: A 1271 GLU cc_start: 0.6923 (mp0) cc_final: 0.5983 (mm-30) REVERT: B 1 MET cc_start: 0.6372 (mmm) cc_final: 0.6012 (mmm) REVERT: B 71 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7671 (mtmt) REVERT: B 1108 MET cc_start: 0.7475 (mmm) cc_final: 0.7239 (mmm) REVERT: B 1158 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: B 1223 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8188 (mt) REVERT: D 112 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: D 374 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8102 (pt0) REVERT: D 438 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6837 (mm-40) REVERT: D 439 THR cc_start: 0.6817 (m) cc_final: 0.6149 (t) REVERT: D 443 ASN cc_start: 0.8713 (m-40) cc_final: 0.8324 (m110) REVERT: E 64 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7151 (mm-30) REVERT: E 136 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6499 (t0) REVERT: E 189 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.5971 (tt) REVERT: E 196 LYS cc_start: 0.8389 (mtmt) cc_final: 0.7782 (tptt) REVERT: E 232 GLN cc_start: 0.8215 (mp10) cc_final: 0.7945 (mm-40) REVERT: E 233 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: E 281 LYS cc_start: 0.7239 (mttt) cc_final: 0.6751 (mmtm) REVERT: E 330 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7269 (mm110) REVERT: E 346 ASN cc_start: 0.7264 (t0) cc_final: 0.7013 (t0) REVERT: E 465 GLU cc_start: 0.7085 (mp0) cc_final: 0.6616 (mp0) REVERT: E 467 LYS cc_start: 0.7510 (ttpt) cc_final: 0.6969 (tppt) REVERT: E 471 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6744 (tt0) outliers start: 54 outliers final: 25 residues processed: 225 average time/residue: 0.6414 time to fit residues: 160.7806 Evaluate side-chains 214 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain F residue 737 GLU Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1158 GLN Chi-restraints excluded: chain B residue 1223 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 471 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1183 ASN D 297 HIS D 317 HIS D 325 ASN D 401 HIS D 482 GLN E 401 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.173192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129764 restraints weight = 29225.661| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.74 r_work: 0.3484 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17762 Z= 0.133 Angle : 0.595 11.971 24121 Z= 0.310 Chirality : 0.043 0.252 2666 Planarity : 0.004 0.040 2931 Dihedral : 16.929 63.480 2798 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.65 % Allowed : 27.81 % Favored : 69.54 % 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: 0.47 (0.18), residues: 1972 helix: 1.93 (0.18), residues: 818 sheet: 0.13 (0.26), residues: 387 loop : -1.41 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 366 TYR 0.027 0.002 TYR A 212 PHE 0.021 0.001 PHE F 688 TRP 0.006 0.001 TRP A 164 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (17762) covalent geometry : angle 0.59471 / 0.31 (24121) hydrogen bonds : bond 0.04112 / 4.07 ( 846) hydrogen bonds : angle 4.52485 / 4.85 ( 2446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: F 687 LYS cc_start: 0.7634 (mtmm) cc_final: 0.7242 (mtmt) REVERT: F 701 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6259 (p-80) REVERT: F 707 ASP cc_start: 0.5974 (m-30) cc_final: 0.5540 (t0) REVERT: F 737 GLU cc_start: 0.5887 (OUTLIER) cc_final: 0.5129 (pt0) REVERT: A 1 MET cc_start: 0.7099 (ttm) cc_final: 0.6719 (mtm) REVERT: A 5 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 122 LYS cc_start: 0.7703 (tttm) cc_final: 0.7002 (ttpp) REVERT: A 160 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: A 209 GLU cc_start: 0.7141 (tp30) cc_final: 0.6633 (tp30) REVERT: A 211 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7681 (mttt) REVERT: A 1089 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7445 (pttt) REVERT: A 1140 MET cc_start: 0.8171 (tpp) cc_final: 0.7886 (mmm) REVERT: A 1179 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7614 (ttp80) REVERT: A 1232 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: A 1271 GLU cc_start: 0.6892 (mp0) cc_final: 0.6002 (mm-30) REVERT: B 1 MET cc_start: 0.6235 (mmm) cc_final: 0.5889 (mmm) REVERT: B 71 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7655 (mtpt) REVERT: B 119 THR cc_start: 0.7839 (m) cc_final: 0.7417 (p) REVERT: B 184 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6352 (mmt180) REVERT: B 208 MET cc_start: 0.6457 (tmm) cc_final: 0.6233 (tmt) REVERT: B 1108 MET cc_start: 0.7470 (mmm) cc_final: 0.7077 (mmm) REVERT: B 1189 LEU cc_start: 0.8095 (mp) cc_final: 0.7545 (tt) REVERT: D 354 ASN cc_start: 0.7515 (t0) cc_final: 0.6881 (t0) REVERT: D 374 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8146 (mt-10) REVERT: D 438 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6789 (mm-40) REVERT: D 439 THR cc_start: 0.6805 (m) cc_final: 0.6187 (t) REVERT: D 443 ASN cc_start: 0.8736 (m-40) cc_final: 0.8344 (m110) REVERT: E 64 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7094 (mm-30) REVERT: E 136 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6465 (t0) REVERT: E 189 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.5827 (tt) REVERT: E 191 ARG cc_start: 0.6652 (ttm-80) cc_final: 0.6155 (ttm-80) REVERT: E 196 LYS cc_start: 0.8389 (mtmt) cc_final: 0.7765 (tptt) REVERT: E 232 GLN cc_start: 0.8160 (mp10) cc_final: 0.7877 (mm-40) REVERT: E 233 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: E 281 LYS cc_start: 0.7171 (mttt) cc_final: 0.6697 (mmtm) REVERT: E 330 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7144 (mm110) REVERT: E 384 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6711 (mtmm) REVERT: E 431 ASP cc_start: 0.7311 (m-30) cc_final: 0.7102 (m-30) REVERT: E 465 GLU cc_start: 0.7046 (mp0) cc_final: 0.6578 (mp0) REVERT: E 467 LYS cc_start: 0.7490 (ttpt) cc_final: 0.6908 (tppt) REVERT: E 471 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6807 (tt0) REVERT: E 488 ARG cc_start: 0.7512 (mmm-85) cc_final: 0.7245 (tmm-80) outliers start: 48 outliers final: 21 residues processed: 221 average time/residue: 0.6420 time to fit residues: 158.0670 Evaluate side-chains 208 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 737 GLU Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain A residue 1232 GLU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 ARG Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 471 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 31 optimal weight: 5.9990 chunk 172 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 711 HIS B1183 ASN D 297 HIS D 317 HIS D 401 HIS D 482 GLN E 401 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.172338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127907 restraints weight = 34515.100| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.98 r_work: 0.3457 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17762 Z= 0.170 Angle : 0.611 12.288 24121 Z= 0.318 Chirality : 0.044 0.258 2666 Planarity : 0.004 0.040 2931 Dihedral : 16.888 63.553 2798 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.54 % Allowed : 28.19 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 1972 helix: 1.90 (0.18), residues: 818 sheet: 0.04 (0.25), residues: 399 loop : -1.44 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 349 TYR 0.031 0.002 TYR A 212 PHE 0.029 0.002 PHE E 237 TRP 0.005 0.001 TRP D 210 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (17762) covalent geometry : angle 0.61109 / 0.32 (24121) hydrogen bonds : bond 0.04232 / 4.17 ( 846) hydrogen bonds : angle 4.53930 / 4.86 ( 2446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: F 687 LYS cc_start: 0.7640 (mtmm) cc_final: 0.7258 (mtmt) REVERT: F 701 HIS cc_start: 0.7155 (OUTLIER) cc_final: 0.6255 (p-80) REVERT: F 707 ASP cc_start: 0.5963 (m-30) cc_final: 0.5504 (t0) REVERT: F 737 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5169 (pt0) REVERT: A 1 MET cc_start: 0.7162 (ttm) cc_final: 0.6788 (mtm) REVERT: A 5 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7248 (mt-10) REVERT: A 122 LYS cc_start: 0.7717 (tttm) cc_final: 0.7012 (ttpp) REVERT: A 160 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: A 209 GLU cc_start: 0.7163 (tp30) cc_final: 0.6784 (pt0) REVERT: A 211 LYS cc_start: 0.7893 (mtmt) cc_final: 0.7665 (mttt) REVERT: A 1089 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7509 (pttt) REVERT: A 1140 MET cc_start: 0.8216 (tpp) cc_final: 0.7977 (mmm) REVERT: A 1179 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7612 (ttp80) REVERT: A 1232 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: A 1271 GLU cc_start: 0.6901 (mp0) cc_final: 0.5966 (mm-30) REVERT: B 1 MET cc_start: 0.6290 (mmm) cc_final: 0.5935 (mmm) REVERT: B 71 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7556 (mtmt) REVERT: B 119 THR cc_start: 0.7747 (m) cc_final: 0.7495 (p) REVERT: B 184 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.6358 (mmt180) REVERT: B 1108 MET cc_start: 0.7522 (mmm) cc_final: 0.7253 (mmm) REVERT: B 1189 LEU cc_start: 0.8135 (mp) cc_final: 0.7558 (tt) REVERT: D 64 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8063 (mm-30) REVERT: D 309 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6243 (tpt) REVERT: D 354 ASN cc_start: 0.7528 (t0) cc_final: 0.6888 (t0) REVERT: D 374 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8170 (mt-10) REVERT: D 438 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6803 (mm-40) REVERT: D 439 THR cc_start: 0.6801 (m) cc_final: 0.6198 (t) REVERT: D 443 ASN cc_start: 0.8743 (m-40) cc_final: 0.8358 (m110) REVERT: E 64 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7119 (mm-30) REVERT: E 136 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6489 (t0) REVERT: E 189 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5865 (tt) REVERT: E 191 ARG cc_start: 0.6661 (ttm-80) cc_final: 0.6163 (ttm-80) REVERT: E 196 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7768 (tptt) REVERT: E 232 GLN cc_start: 0.8177 (mp10) cc_final: 0.7903 (mm-40) REVERT: E 233 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: E 281 LYS cc_start: 0.7192 (mttt) cc_final: 0.6714 (mmtm) REVERT: E 330 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7163 (mm110) REVERT: E 384 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6703 (mtmm) REVERT: E 465 GLU cc_start: 0.7093 (mp0) cc_final: 0.6626 (mp0) REVERT: E 467 LYS cc_start: 0.7495 (ttpt) cc_final: 0.6940 (tppt) REVERT: E 471 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6819 (tt0) REVERT: E 488 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.7206 (tmm-80) outliers start: 46 outliers final: 24 residues processed: 215 average time/residue: 0.5873 time to fit residues: 141.5855 Evaluate side-chains 212 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 737 GLU Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain A residue 1232 GLU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 ARG Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 471 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1183 ASN D 297 HIS D 317 HIS D 401 HIS D 482 GLN E 401 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.173766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131065 restraints weight = 22656.696| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.43 r_work: 0.3509 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17762 Z= 0.129 Angle : 0.588 11.812 24121 Z= 0.308 Chirality : 0.043 0.250 2666 Planarity : 0.004 0.040 2931 Dihedral : 16.815 62.859 2798 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.54 % Allowed : 28.14 % Favored : 69.32 % 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: 0.51 (0.19), residues: 1972 helix: 1.97 (0.18), residues: 819 sheet: 0.13 (0.26), residues: 387 loop : -1.41 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 349 TYR 0.030 0.002 TYR A 212 PHE 0.020 0.001 PHE F 688 TRP 0.006 0.001 TRP A 164 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (17762) covalent geometry : angle 0.58803 / 0.31 (24121) hydrogen bonds : bond 0.04045 / 3.99 ( 846) hydrogen bonds : angle 4.47332 / 4.80 ( 2446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6842.56 seconds wall clock time: 117 minutes 12.86 seconds (7032.86 seconds total)