Starting phenix.real_space_refine on Sat Jul 4 02:52:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9m_52964/07_2026/9q9m_52964.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9m_52964/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9q9m_52964/07_2026/9q9m_52964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9m_52964/07_2026/9q9m_52964.map" model { file = "/net/cci-nas-00/data/ceres_data/9q9m_52964/07_2026/9q9m_52964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9m_52964/07_2026/9q9m_52964.cif" } 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-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.25 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: 1.25 Conformation dependent library (CDL) restraints added in 852.9 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: 2.06 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: 3.60 Time building geometry restraints manager: 1.73 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: 23297 2.54 - 5.08: 686 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 3.140 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: 4.350 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.630 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- 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 : 0.974 12.696 24121 Z= 0.647 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 0.97415 / 0.65 (24121) hydrogen bonds : bond 0.16420 / 15.40 ( 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 : 0.524 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: 0.6169 time to fit residues: 274.6827 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 : 0.665 ------------------------------------------------------------------------------- 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: 0.3980 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: 1.0800 ------------------------------------------------------------------------------- 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 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4163 r_free = 0.4163 target = 0.182350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140316 restraints weight = 25053.851| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.58 r_work: 0.3611 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 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 = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17762 Z= 0.162 Angle : 0.635 8.100 24121 Z= 0.340 Chirality : 0.045 0.232 2666 Planarity : 0.004 0.050 2931 Dihedral : 17.379 68.004 2807 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 0.27 (0.18), residues: 1972 helix: 1.57 (0.18), residues: 823 sheet: 0.22 (0.26), residues: 372 loop : -1.37 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1105 TYR 0.025 0.002 TYR E 369 PHE 0.028 0.002 PHE E 237 TRP 0.006 0.001 TRP A 164 HIS 0.011 0.001 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (17762) covalent geometry : angle 0.63546 / 0.34 (24121) hydrogen bonds : bond 0.04896 / 4.82 ( 846) hydrogen bonds : angle 5.11407 / 5.56 ( 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 : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6055 (ttm) cc_final: 0.5656 (ttp) REVERT: A 5 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 20 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6828 (ptmt) REVERT: A 89 VAL cc_start: 0.7555 (m) cc_final: 0.7314 (t) REVERT: A 118 ILE cc_start: 0.7518 (mt) cc_final: 0.7273 (mp) REVERT: A 185 TYR cc_start: 0.7328 (m-80) cc_final: 0.6861 (m-80) REVERT: A 205 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7133 (mt-10) REVERT: A 1108 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6309 (tmm) REVERT: A 1261 ASN cc_start: 0.7460 (OUTLIER) cc_final: 0.6926 (t0) REVERT: B 20 LYS cc_start: 0.8272 (pttp) cc_final: 0.8030 (ptpp) REVERT: B 71 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7606 (mtmt) REVERT: B 79 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7244 (ttp80) REVERT: B 94 ILE cc_start: 0.7585 (mt) cc_final: 0.7318 (mp) REVERT: B 119 THR cc_start: 0.7592 (m) cc_final: 0.7140 (p) REVERT: B 160 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: B 186 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6928 (mt) REVERT: B 1126 LYS cc_start: 0.7345 (ttmm) cc_final: 0.7006 (ttpt) REVERT: B 1189 LEU cc_start: 0.8183 (mp) cc_final: 0.7784 (tt) REVERT: B 1197 MET cc_start: 0.8942 (ttt) cc_final: 0.8543 (ttt) REVERT: B 1260 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6793 (mmm-85) REVERT: D 64 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7904 (mm-30) REVERT: D 161 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6703 (pptt) REVERT: D 192 MET cc_start: 0.5852 (OUTLIER) cc_final: 0.5383 (mtt) REVERT: D 205 GLU cc_start: 0.8023 (pm20) cc_final: 0.7799 (pm20) REVERT: D 325 ASN cc_start: 0.8148 (t0) cc_final: 0.7719 (t0) REVERT: D 327 LYS cc_start: 0.7372 (tptt) cc_final: 0.7099 (pttt) REVERT: D 350 GLU cc_start: 0.7092 (tt0) cc_final: 0.6779 (tm-30) REVERT: D 374 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7900 (pt0) REVERT: D 438 GLN cc_start: 0.7357 (pt0) cc_final: 0.6877 (mm-40) REVERT: D 439 THR cc_start: 0.6873 (m) cc_final: 0.6195 (t) REVERT: E 64 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7072 (mm-30) REVERT: E 157 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6854 (mtp) REVERT: E 196 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7637 (tptt) REVERT: E 232 GLN cc_start: 0.8308 (mp10) cc_final: 0.7873 (mm-40) REVERT: E 330 GLN cc_start: 0.7273 (mt0) cc_final: 0.6975 (mm110) REVERT: E 356 HIS cc_start: 0.7465 (m-70) cc_final: 0.7046 (m-70) REVERT: E 359 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6855 (pm20) outliers start: 67 outliers final: 19 residues processed: 272 average time/residue: 0.5819 time to fit residues: 176.9125 Evaluate side-chains 223 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 160 GLU 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 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 263 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 471 GLU 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 317 HIS 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: 0.5980 chunk 60 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 167 optimal weight: 0.0770 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1181 ASN A1259 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1269 HIS D 112 GLN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.176959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.134024 restraints weight = 25705.901| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.61 r_work: 0.3533 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17762 Z= 0.188 Angle : 0.621 6.955 24121 Z= 0.329 Chirality : 0.045 0.248 2666 Planarity : 0.004 0.037 2931 Dihedral : 17.284 64.449 2798 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.48 % Allowed : 25.04 % Favored : 70.48 % 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: 0.46 (0.18), residues: 1972 helix: 1.79 (0.18), residues: 819 sheet: 0.21 (0.25), residues: 379 loop : -1.29 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1098 TYR 0.023 0.002 TYR A1081 PHE 0.023 0.002 PHE B 176 TRP 0.005 0.001 TRP A 164 HIS 0.006 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (17762) covalent geometry : angle 0.62093 / 0.33 (24121) hydrogen bonds : bond 0.04693 / 4.60 ( 846) hydrogen bonds : angle 4.82290 / 5.15 ( 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 292 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 211 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6583 (p-80) REVERT: F 707 ASP cc_start: 0.5908 (OUTLIER) cc_final: 0.5211 (t0) REVERT: A 1 MET cc_start: 0.6587 (ttm) cc_final: 0.6220 (mtm) REVERT: A 89 VAL cc_start: 0.7771 (m) cc_final: 0.7550 (t) REVERT: A 92 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: A 185 TYR cc_start: 0.7397 (m-80) cc_final: 0.6990 (m-80) REVERT: A 205 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7223 (mt-10) REVERT: A 1261 ASN cc_start: 0.7630 (t0) cc_final: 0.7118 (t0) REVERT: A 1289 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8307 (mm) REVERT: B 20 LYS cc_start: 0.8346 (pttp) cc_final: 0.8050 (ptpp) REVERT: B 71 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7602 (mtmt) REVERT: B 94 ILE cc_start: 0.7822 (mt) cc_final: 0.7380 (mp) REVERT: B 160 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: B 1108 MET cc_start: 0.7451 (mmm) cc_final: 0.7246 (mmm) REVERT: B 1123 ILE cc_start: 0.7439 (mp) cc_final: 0.7221 (tt) REVERT: B 1189 LEU cc_start: 0.8244 (mp) cc_final: 0.7814 (tt) REVERT: D 64 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7963 (mm-30) REVERT: D 161 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6629 (pptt) REVERT: D 310 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6556 (mm-30) REVERT: D 366 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.6740 (mtm110) REVERT: D 374 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7919 (pt0) REVERT: D 438 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6775 (mm-40) REVERT: D 439 THR cc_start: 0.6877 (m) cc_final: 0.6377 (t) REVERT: D 443 ASN cc_start: 0.8636 (m-40) cc_final: 0.8130 (m110) REVERT: D 458 VAL cc_start: 0.7842 (t) cc_final: 0.7623 (m) REVERT: E 64 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: E 157 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6769 (mtp) REVERT: E 196 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7630 (tptt) REVERT: E 232 GLN cc_start: 0.8285 (mp10) cc_final: 0.7895 (mm-40) REVERT: E 309 MET cc_start: 0.7680 (tpt) cc_final: 0.7290 (tpt) REVERT: E 330 GLN cc_start: 0.7453 (mt0) cc_final: 0.7079 (mm110) outliers start: 81 outliers final: 26 residues processed: 268 average time/residue: 0.6031 time to fit residues: 180.5379 Evaluate side-chains 220 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 61 THR 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 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 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 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 161 LYS 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 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: 1.9990 chunk 157 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 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: 10.0000 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1181 ASN B 64 ASN B 199 GLN D 112 GLN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 325 ASN D 401 HIS D 482 GLN E 259 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.173112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128962 restraints weight = 32584.538| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.91 r_work: 0.3466 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17762 Z= 0.215 Angle : 0.634 9.646 24121 Z= 0.333 Chirality : 0.046 0.299 2666 Planarity : 0.004 0.042 2931 Dihedral : 17.220 65.092 2798 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.92 % Allowed : 24.05 % Favored : 71.03 % 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: 0.40 (0.18), residues: 1972 helix: 1.77 (0.18), residues: 816 sheet: 0.12 (0.25), residues: 388 loop : -1.33 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1098 TYR 0.022 0.002 TYR A1104 PHE 0.029 0.002 PHE F 688 TRP 0.007 0.001 TRP D 210 HIS 0.005 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (17762) covalent geometry : angle 0.63402 / 0.33 (24121) hydrogen bonds : bond 0.04671 / 4.63 ( 846) hydrogen bonds : angle 4.71011 / 5.05 ( 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 285 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 196 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7218 (OUTLIER) cc_final: 0.6445 (p-80) REVERT: F 703 ILE cc_start: 0.6782 (pt) cc_final: 0.6465 (pp) REVERT: F 707 ASP cc_start: 0.5996 (OUTLIER) cc_final: 0.5265 (t0) REVERT: A 1 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6793 (mtm) REVERT: A 5 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: A 20 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7215 (ptmt) REVERT: A 148 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7893 (tttp) REVERT: A 177 ASP cc_start: 0.8177 (p0) cc_final: 0.7864 (p0) REVERT: A 1138 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7619 (mpt) REVERT: A 1289 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8357 (mm) REVERT: B 1 MET cc_start: 0.6105 (mmm) cc_final: 0.5792 (mmm) REVERT: B 71 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7709 (mtpt) REVERT: B 94 ILE cc_start: 0.7915 (mt) cc_final: 0.7531 (mp) REVERT: B 177 ASP cc_start: 0.7740 (p0) cc_final: 0.7516 (p0) REVERT: B 1189 LEU cc_start: 0.8284 (mp) cc_final: 0.7789 (tt) REVERT: D 64 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8009 (mm-30) REVERT: D 309 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6749 (tpt) REVERT: D 374 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7929 (pt0) REVERT: D 428 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.5448 (mpt-90) REVERT: D 438 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6875 (mm-40) REVERT: D 439 THR cc_start: 0.6973 (m) cc_final: 0.6299 (t) REVERT: D 443 ASN cc_start: 0.8707 (m-40) cc_final: 0.8250 (m110) REVERT: D 458 VAL cc_start: 0.7921 (t) cc_final: 0.7698 (m) REVERT: D 479 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7778 (pp20) REVERT: E 64 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7112 (mm-30) REVERT: E 157 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7226 (mmt) REVERT: E 189 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5815 (tt) REVERT: E 196 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7687 (tptt) REVERT: E 232 GLN cc_start: 0.8255 (mp10) cc_final: 0.7957 (mm-40) REVERT: E 330 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7151 (mm110) REVERT: E 374 GLU cc_start: 0.7670 (pm20) cc_final: 0.7399 (pm20) REVERT: E 471 GLU cc_start: 0.7504 (tp30) cc_final: 0.7080 (tt0) outliers start: 89 outliers final: 30 residues processed: 262 average time/residue: 0.5850 time to fit residues: 172.6835 Evaluate side-chains 230 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 20 LYS 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 1138 MET Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain B residue 147 SER 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 1159 ASP Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 428 ARG 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 98 SER 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 24 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 187 optimal weight: 0.0060 chunk 154 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 112 GLN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 322 ASN 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 = 0.4097 r_free = 0.4097 target = 0.175254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131012 restraints weight = 35133.678| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.02 r_work: 0.3494 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 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: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3481 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= 0.130 Angle : 0.571 8.181 24121 Z= 0.301 Chirality : 0.043 0.276 2666 Planarity : 0.003 0.039 2931 Dihedral : 17.069 63.933 2798 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.37 % Allowed : 26.15 % Favored : 70.48 % 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: 0.60 (0.18), residues: 1972 helix: 1.98 (0.18), residues: 816 sheet: 0.27 (0.25), residues: 377 loop : -1.30 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 79 TYR 0.019 0.002 TYR B 212 PHE 0.012 0.001 PHE E 461 TRP 0.005 0.001 TRP A 164 HIS 0.007 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (17762) covalent geometry : angle 0.57133 / 0.30 (24121) hydrogen bonds : bond 0.04174 / 4.14 ( 846) hydrogen bonds : angle 4.55085 / 4.86 ( 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 258 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 197 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 707 ASP cc_start: 0.5931 (OUTLIER) cc_final: 0.5237 (t0) REVERT: A 1 MET cc_start: 0.7093 (ttm) cc_final: 0.6689 (mtm) REVERT: A 5 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7151 (mt-10) REVERT: A 20 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7228 (ptmt) REVERT: A 89 VAL cc_start: 0.7798 (m) cc_final: 0.7597 (t) REVERT: A 92 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: A 177 ASP cc_start: 0.8000 (p0) cc_final: 0.7638 (p0) REVERT: A 211 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7820 (mttt) REVERT: A 1138 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8081 (mtt) REVERT: A 1289 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8262 (mm) REVERT: B 1 MET cc_start: 0.5998 (mmm) cc_final: 0.5683 (mmm) REVERT: B 71 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7529 (mtmt) REVERT: B 94 ILE cc_start: 0.7801 (mt) cc_final: 0.7395 (mp) REVERT: B 119 THR cc_start: 0.7802 (m) cc_final: 0.7364 (p) REVERT: B 184 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6320 (mmt180) REVERT: B 1158 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7455 (mt0) REVERT: B 1189 LEU cc_start: 0.8255 (mp) cc_final: 0.7752 (tt) REVERT: D 64 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7998 (mm-30) REVERT: D 366 ARG cc_start: 0.7596 (mtm-85) cc_final: 0.7291 (mtm-85) REVERT: D 374 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8019 (pt0) REVERT: D 438 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6790 (mm-40) REVERT: D 439 THR cc_start: 0.6876 (m) cc_final: 0.6255 (t) REVERT: D 443 ASN cc_start: 0.8715 (m-40) cc_final: 0.8287 (m110) REVERT: D 479 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7726 (pp20) REVERT: E 64 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7068 (mm-30) REVERT: E 157 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6929 (mmt) REVERT: E 189 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5706 (tt) REVERT: E 196 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7671 (tptt) REVERT: E 232 GLN cc_start: 0.8215 (mp10) cc_final: 0.7884 (mm-40) REVERT: E 281 LYS cc_start: 0.7110 (mttt) cc_final: 0.6620 (mmtm) REVERT: E 330 GLN cc_start: 0.7510 (mt0) cc_final: 0.7097 (mm110) REVERT: E 374 GLU cc_start: 0.7647 (pm20) cc_final: 0.7368 (pm20) REVERT: E 384 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6438 (mttm) REVERT: E 467 LYS cc_start: 0.7355 (ttpt) cc_final: 0.6994 (tppt) REVERT: E 471 GLU cc_start: 0.7580 (tp30) cc_final: 0.7146 (tt0) outliers start: 61 outliers final: 19 residues processed: 240 average time/residue: 0.6548 time to fit residues: 174.8470 Evaluate side-chains 208 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 119 THR Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1289 ILE 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 B residue 1142 GLU Chi-restraints excluded: chain B residue 1158 GLN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 243 TRP Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 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 367 VAL Chi-restraints excluded: chain E residue 384 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 322 ASN 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 = 0.4095 r_free = 0.4095 target = 0.175061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132481 restraints weight = 24272.698| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.51 r_work: 0.3519 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3654 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= 0.140 Angle : 0.566 9.359 24121 Z= 0.297 Chirality : 0.043 0.264 2666 Planarity : 0.003 0.040 2931 Dihedral : 16.982 63.178 2798 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.26 % Allowed : 26.59 % Favored : 70.15 % 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: 0.65 (0.18), residues: 1972 helix: 2.00 (0.18), residues: 820 sheet: 0.41 (0.26), residues: 365 loop : -1.31 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 745 TYR 0.019 0.002 TYR A 212 PHE 0.031 0.001 PHE E 237 TRP 0.005 0.001 TRP A 164 HIS 0.005 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (17762) covalent geometry : angle 0.56589 / 0.30 (24121) hydrogen bonds : bond 0.04122 / 4.07 ( 846) hydrogen bonds : angle 4.47938 / 4.79 ( 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 245 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 186 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6371 (p-80) REVERT: F 707 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5301 (t0) REVERT: A 1 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6767 (mtm) REVERT: A 5 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 92 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: A 177 ASP cc_start: 0.8024 (p0) cc_final: 0.7636 (p0) REVERT: A 1138 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8039 (mtt) REVERT: A 1140 MET cc_start: 0.8115 (tpp) cc_final: 0.7728 (mmm) REVERT: A 1271 GLU cc_start: 0.6937 (mp0) cc_final: 0.6563 (pm20) REVERT: A 1289 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8248 (mm) REVERT: B 1 MET cc_start: 0.6050 (mmm) cc_final: 0.5759 (mmm) REVERT: B 71 LYS cc_start: 0.7922 (mtpt) cc_final: 0.7543 (mtmt) REVERT: B 94 ILE cc_start: 0.7800 (mt) cc_final: 0.7294 (mp) REVERT: B 119 THR cc_start: 0.7810 (m) cc_final: 0.7390 (p) REVERT: B 140 MET cc_start: 0.6768 (mmm) cc_final: 0.6222 (mtm) REVERT: B 177 ASP cc_start: 0.7613 (p0) cc_final: 0.7353 (p0) REVERT: B 184 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.6370 (mmt180) REVERT: B 1189 LEU cc_start: 0.8244 (mp) cc_final: 0.7712 (tt) REVERT: D 64 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7985 (mm-30) REVERT: D 309 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.6864 (tpt) REVERT: D 366 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.7326 (mtm-85) REVERT: D 374 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7992 (pt0) REVERT: D 438 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6803 (mm-40) REVERT: D 439 THR cc_start: 0.6961 (m) cc_final: 0.6331 (t) REVERT: D 443 ASN cc_start: 0.8758 (m-40) cc_final: 0.8343 (m110) REVERT: D 479 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7742 (pp20) REVERT: E 64 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: E 157 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7062 (mmt) REVERT: E 189 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5706 (tt) REVERT: E 196 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7733 (tptt) REVERT: E 232 GLN cc_start: 0.8204 (mp10) cc_final: 0.7877 (mm-40) REVERT: E 281 LYS cc_start: 0.7106 (mttt) cc_final: 0.6662 (mmtm) REVERT: E 294 MET cc_start: 0.7556 (ttp) cc_final: 0.6824 (ttp) REVERT: E 330 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7099 (mm110) REVERT: E 374 GLU cc_start: 0.7599 (pm20) cc_final: 0.7330 (pm20) REVERT: E 384 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6658 (mtmm) REVERT: E 467 LYS cc_start: 0.7415 (ttpt) cc_final: 0.7015 (tppt) REVERT: E 471 GLU cc_start: 0.7588 (tp30) cc_final: 0.7190 (tt0) outliers start: 59 outliers final: 24 residues processed: 231 average time/residue: 0.5617 time to fit residues: 144.9491 Evaluate side-chains 214 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 69 ASP 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 119 THR Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1289 ILE 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 B residue 1142 GLU Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 243 TRP Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 64 GLU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 177 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 317 HIS D 325 ASN D 401 HIS D 482 GLN E 401 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.175659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.133589 restraints weight = 22489.935| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.40 r_work: 0.3533 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3799 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= 0.127 Angle : 0.560 9.305 24121 Z= 0.293 Chirality : 0.043 0.269 2666 Planarity : 0.003 0.044 2931 Dihedral : 16.908 62.365 2798 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.10 % Allowed : 26.92 % 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: 0.69 (0.19), residues: 1972 helix: 2.05 (0.18), residues: 820 sheet: 0.34 (0.26), residues: 383 loop : -1.28 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 349 TYR 0.020 0.001 TYR A 212 PHE 0.016 0.001 PHE E 193 TRP 0.005 0.001 TRP A 164 HIS 0.004 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (17762) covalent geometry : angle 0.55958 / 0.29 (24121) hydrogen bonds : bond 0.03983 / 3.93 ( 846) hydrogen bonds : angle 4.39853 / 4.72 ( 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 244 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 687 LYS cc_start: 0.7657 (mtmm) cc_final: 0.7269 (mtmt) REVERT: F 701 HIS cc_start: 0.7140 (OUTLIER) cc_final: 0.6327 (p-80) REVERT: F 707 ASP cc_start: 0.6100 (OUTLIER) cc_final: 0.5389 (t0) REVERT: A 1 MET cc_start: 0.7359 (ttm) cc_final: 0.7016 (mtm) REVERT: A 5 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7529 (mt-10) REVERT: A 20 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7360 (ptmt) REVERT: A 92 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: A 1138 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8187 (mtt) REVERT: A 1140 MET cc_start: 0.8186 (tpp) cc_final: 0.7833 (mmm) REVERT: A 1179 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7650 (ttp80) REVERT: A 1271 GLU cc_start: 0.7005 (mp0) cc_final: 0.6616 (pm20) REVERT: A 1289 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8314 (mm) REVERT: B 1 MET cc_start: 0.6205 (mmm) cc_final: 0.5877 (mmm) REVERT: B 71 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7586 (mtmt) REVERT: B 94 ILE cc_start: 0.7964 (mt) cc_final: 0.7501 (mp) REVERT: B 119 THR cc_start: 0.7835 (m) cc_final: 0.7466 (p) REVERT: B 177 ASP cc_start: 0.7658 (p0) cc_final: 0.7413 (p0) REVERT: B 184 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6415 (mmt180) REVERT: B 1108 MET cc_start: 0.7487 (mmm) cc_final: 0.7142 (mmm) REVERT: B 1189 LEU cc_start: 0.8343 (mp) cc_final: 0.7779 (tt) REVERT: D 64 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8097 (mm-30) REVERT: D 309 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7115 (tpt) REVERT: D 354 ASN cc_start: 0.7528 (t0) cc_final: 0.6908 (t0) REVERT: D 366 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7423 (mtm-85) REVERT: D 374 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8211 (mt-10) REVERT: D 438 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6785 (mm-40) REVERT: D 439 THR cc_start: 0.6944 (m) cc_final: 0.6323 (t) REVERT: D 443 ASN cc_start: 0.8815 (m-40) cc_final: 0.8408 (m110) REVERT: D 479 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7751 (pp20) REVERT: D 500 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6482 (tm-30) REVERT: E 64 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: E 157 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7007 (mmt) REVERT: E 189 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.5916 (tt) REVERT: E 191 ARG cc_start: 0.6783 (ttm-80) cc_final: 0.6259 (ttm-80) REVERT: E 196 LYS cc_start: 0.8388 (mtmt) cc_final: 0.7769 (tptt) REVERT: E 232 GLN cc_start: 0.8205 (mp10) cc_final: 0.7879 (mm-40) REVERT: E 281 LYS cc_start: 0.7135 (mttt) cc_final: 0.6666 (mmtm) REVERT: E 330 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7176 (mm110) REVERT: E 374 GLU cc_start: 0.7685 (pm20) cc_final: 0.7408 (pm20) REVERT: E 384 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6714 (mtmm) REVERT: E 467 LYS cc_start: 0.7433 (ttpt) cc_final: 0.6962 (tppt) REVERT: E 471 GLU cc_start: 0.7624 (tp30) cc_final: 0.7249 (tt0) outliers start: 56 outliers final: 21 residues processed: 227 average time/residue: 0.6331 time to fit residues: 160.1660 Evaluate side-chains 214 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 69 ASP 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 119 THR Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1153 SER Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain A residue 1289 ILE 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 251 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 64 GLU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 94 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 25 optimal weight: 0.0040 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 173 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS 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 = 0.4086 r_free = 0.4086 target = 0.174125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130025 restraints weight = 34522.712| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.98 r_work: 0.3476 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3921 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= 0.166 Angle : 0.586 10.116 24121 Z= 0.306 Chirality : 0.043 0.239 2666 Planarity : 0.004 0.040 2931 Dihedral : 16.931 62.500 2798 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.32 % Allowed : 27.03 % Favored : 69.65 % 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: 0.62 (0.18), residues: 1972 helix: 2.01 (0.18), residues: 820 sheet: 0.24 (0.26), residues: 387 loop : -1.31 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 349 TYR 0.021 0.002 TYR E 476 PHE 0.031 0.002 PHE E 237 TRP 0.005 0.001 TRP D 210 HIS 0.011 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (17762) covalent geometry : angle 0.58589 / 0.31 (24121) hydrogen bonds : bond 0.04161 / 4.08 ( 846) hydrogen bonds : angle 4.44362 / 4.76 ( 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 244 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 687 LYS cc_start: 0.7674 (mtmm) cc_final: 0.7313 (mtmt) REVERT: F 701 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6285 (p-80) REVERT: F 707 ASP cc_start: 0.6068 (OUTLIER) cc_final: 0.5376 (t0) REVERT: A 1 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6884 (mtm) REVERT: A 20 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7398 (ptmt) REVERT: A 122 LYS cc_start: 0.7611 (tttm) cc_final: 0.6974 (ttpp) REVERT: A 1140 MET cc_start: 0.8180 (tpp) cc_final: 0.7766 (mmm) REVERT: A 1179 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7804 (ttp80) REVERT: A 1271 GLU cc_start: 0.6971 (mp0) cc_final: 0.6587 (pm20) REVERT: A 1289 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8266 (mm) REVERT: B 1 MET cc_start: 0.6143 (mmm) cc_final: 0.5826 (mmm) REVERT: B 71 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7666 (mtpt) REVERT: B 94 ILE cc_start: 0.7865 (mt) cc_final: 0.7459 (mp) REVERT: B 119 THR cc_start: 0.7858 (m) cc_final: 0.7433 (p) REVERT: B 177 ASP cc_start: 0.7606 (p0) cc_final: 0.7341 (p0) REVERT: B 184 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6383 (mmt180) REVERT: B 1108 MET cc_start: 0.7452 (mmm) cc_final: 0.7152 (mmm) REVERT: B 1158 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: B 1189 LEU cc_start: 0.8256 (mp) cc_final: 0.7695 (tt) REVERT: D 64 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8058 (mm-30) REVERT: D 112 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: D 354 ASN cc_start: 0.7546 (t0) cc_final: 0.6926 (t0) REVERT: D 374 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7952 (pt0) REVERT: D 438 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6790 (mm-40) REVERT: D 439 THR cc_start: 0.6918 (m) cc_final: 0.6280 (t) REVERT: D 443 ASN cc_start: 0.8771 (m-40) cc_final: 0.8342 (m110) REVERT: D 479 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7757 (pp20) REVERT: D 500 GLU cc_start: 0.6696 (tm-30) cc_final: 0.6472 (tm-30) REVERT: E 64 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: E 157 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7055 (mmt) REVERT: E 189 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.5812 (tt) REVERT: E 196 LYS cc_start: 0.8377 (mtmt) cc_final: 0.7759 (tptt) REVERT: E 232 GLN cc_start: 0.8198 (mp10) cc_final: 0.7888 (mm-40) REVERT: E 281 LYS cc_start: 0.7162 (mttt) cc_final: 0.6715 (mmtm) REVERT: E 330 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7148 (mm110) REVERT: E 374 GLU cc_start: 0.7630 (pm20) cc_final: 0.7351 (pm20) REVERT: E 384 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6738 (mttm) REVERT: E 467 LYS cc_start: 0.7466 (ttpt) cc_final: 0.6941 (tppt) REVERT: E 471 GLU cc_start: 0.7613 (tp30) cc_final: 0.7287 (tt0) outliers start: 60 outliers final: 28 residues processed: 231 average time/residue: 0.6528 time to fit residues: 168.5700 Evaluate side-chains 219 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 THR 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 1289 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 ARG Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 198 THR 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 1304 VAL 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 251 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 64 GLU 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 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 384 LYS Chi-restraints excluded: chain E residue 394 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 178 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 711 HIS D 297 HIS D 317 HIS 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 = 0.4101 r_free = 0.4101 target = 0.175644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132074 restraints weight = 29118.319| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.75 r_work: 0.3510 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4010 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= 0.126 Angle : 0.565 10.979 24121 Z= 0.297 Chirality : 0.042 0.247 2666 Planarity : 0.003 0.039 2931 Dihedral : 16.868 61.962 2798 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.54 % Allowed : 27.64 % Favored : 69.82 % 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: 0.73 (0.19), residues: 1972 helix: 2.11 (0.18), residues: 814 sheet: 0.36 (0.26), residues: 383 loop : -1.27 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 349 TYR 0.023 0.001 TYR E 476 PHE 0.012 0.001 PHE E 461 TRP 0.005 0.001 TRP A 164 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (17762) covalent geometry : angle 0.56540 / 0.30 (24121) hydrogen bonds : bond 0.03950 / 3.89 ( 846) hydrogen bonds : angle 4.39458 / 4.71 ( 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 233 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6238 (p-80) REVERT: F 707 ASP cc_start: 0.6048 (OUTLIER) cc_final: 0.5403 (t0) REVERT: A 1 MET cc_start: 0.7184 (ttm) cc_final: 0.6851 (mtm) REVERT: A 5 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7106 (mt-10) REVERT: A 20 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7384 (ptmt) REVERT: A 69 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7665 (t0) REVERT: A 92 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: A 122 LYS cc_start: 0.7691 (tttm) cc_final: 0.7002 (ttpp) REVERT: A 1089 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7414 (pttt) REVERT: A 1140 MET cc_start: 0.8131 (tpp) cc_final: 0.7796 (mmm) REVERT: A 1179 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7598 (ttp80) REVERT: A 1271 GLU cc_start: 0.6930 (mp0) cc_final: 0.6571 (pm20) REVERT: A 1289 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8209 (mm) REVERT: B 1 MET cc_start: 0.6069 (mmm) cc_final: 0.5764 (mmm) REVERT: B 71 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7647 (mtpt) REVERT: B 94 ILE cc_start: 0.7810 (mt) cc_final: 0.7316 (mp) REVERT: B 119 THR cc_start: 0.7825 (m) cc_final: 0.7428 (p) REVERT: B 177 ASP cc_start: 0.7523 (p0) cc_final: 0.7304 (p0) REVERT: B 184 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6371 (mmt180) REVERT: B 1108 MET cc_start: 0.7410 (mmm) cc_final: 0.7087 (mmm) REVERT: B 1184 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8396 (t80) REVERT: B 1189 LEU cc_start: 0.8219 (mp) cc_final: 0.7645 (tt) REVERT: D 64 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8015 (mm-30) REVERT: D 92 GLU cc_start: 0.7359 (pm20) cc_final: 0.7103 (pm20) REVERT: D 310 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6963 (mm-30) REVERT: D 354 ASN cc_start: 0.7451 (t0) cc_final: 0.6828 (t0) REVERT: D 366 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7320 (mtm-85) REVERT: D 374 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8065 (mt-10) REVERT: D 438 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6783 (mm-40) REVERT: D 439 THR cc_start: 0.6902 (m) cc_final: 0.6270 (t) REVERT: D 443 ASN cc_start: 0.8822 (m-40) cc_final: 0.8396 (m110) REVERT: D 479 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7752 (pp20) REVERT: D 500 GLU cc_start: 0.6695 (tm-30) cc_final: 0.6459 (tm-30) REVERT: E 64 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: E 157 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7077 (mmt) REVERT: E 189 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5756 (tt) REVERT: E 191 ARG cc_start: 0.6655 (ttm-80) cc_final: 0.6171 (ttm-80) REVERT: E 196 LYS cc_start: 0.8361 (mtmt) cc_final: 0.7737 (tptt) REVERT: E 232 GLN cc_start: 0.8179 (mp10) cc_final: 0.7863 (mm-40) REVERT: E 281 LYS cc_start: 0.7108 (mttt) cc_final: 0.6687 (mmtm) REVERT: E 330 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7181 (mm110) REVERT: E 374 GLU cc_start: 0.7619 (pm20) cc_final: 0.7312 (pm20) REVERT: E 384 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6726 (mtmm) REVERT: E 467 LYS cc_start: 0.7471 (ttpt) cc_final: 0.6947 (tppt) REVERT: E 471 GLU cc_start: 0.7568 (tp30) cc_final: 0.7284 (tt0) outliers start: 46 outliers final: 20 residues processed: 222 average time/residue: 0.6104 time to fit residues: 151.2087 Evaluate side-chains 216 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 69 ASP 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 119 THR Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain A residue 1289 ILE 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 B residue 1184 TYR Chi-restraints excluded: chain B residue 1304 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 64 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 31 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 182 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 297 HIS D 317 HIS D 401 HIS D 482 GLN E 401 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.176138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132046 restraints weight = 34255.039| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.99 r_work: 0.3506 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4103 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= 0.122 Angle : 0.567 12.930 24121 Z= 0.296 Chirality : 0.042 0.255 2666 Planarity : 0.003 0.039 2931 Dihedral : 16.768 61.311 2798 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.21 % Allowed : 28.47 % 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: 0.79 (0.19), residues: 1972 helix: 2.15 (0.18), residues: 813 sheet: 0.51 (0.27), residues: 365 loop : -1.25 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 349 TYR 0.022 0.001 TYR E 476 PHE 0.029 0.001 PHE E 237 TRP 0.005 0.001 TRP A 164 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (17762) covalent geometry : angle 0.56725 / 0.30 (24121) hydrogen bonds : bond 0.03872 / 3.80 ( 846) hydrogen bonds : angle 4.33985 / 4.65 ( 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: 40 poor density : 185 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 707 ASP cc_start: 0.6039 (OUTLIER) cc_final: 0.5423 (t0) REVERT: A 1 MET cc_start: 0.7196 (ttm) cc_final: 0.6852 (mtm) REVERT: A 5 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 20 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7389 (ptmt) REVERT: A 69 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7641 (t0) REVERT: A 122 LYS cc_start: 0.7701 (tttm) cc_final: 0.6912 (ttpt) REVERT: A 1089 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7515 (pttt) REVERT: A 1140 MET cc_start: 0.8157 (tpp) cc_final: 0.7854 (mmm) REVERT: A 1179 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7599 (ttp80) REVERT: A 1271 GLU cc_start: 0.6929 (mp0) cc_final: 0.6574 (pm20) REVERT: A 1289 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8175 (mm) REVERT: B 1 MET cc_start: 0.6074 (mmm) cc_final: 0.5763 (mmm) REVERT: B 71 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7630 (mtpt) REVERT: B 94 ILE cc_start: 0.7783 (mt) cc_final: 0.7304 (mp) REVERT: B 119 THR cc_start: 0.7796 (m) cc_final: 0.7486 (p) REVERT: B 177 ASP cc_start: 0.7528 (p0) cc_final: 0.7312 (p0) REVERT: B 184 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.6389 (mmt180) REVERT: B 1189 LEU cc_start: 0.8165 (mp) cc_final: 0.7613 (tt) REVERT: D 64 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8026 (mm-30) REVERT: D 309 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.6507 (tpt) REVERT: D 310 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6951 (mm-30) REVERT: D 354 ASN cc_start: 0.7437 (t0) cc_final: 0.6835 (t0) REVERT: D 374 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8054 (mt-10) REVERT: D 438 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6782 (mm-40) REVERT: D 439 THR cc_start: 0.6891 (m) cc_final: 0.6243 (t) REVERT: D 443 ASN cc_start: 0.8828 (m-40) cc_final: 0.8394 (m110) REVERT: D 479 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7721 (pp20) REVERT: D 500 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6481 (tm-30) REVERT: E 64 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: E 157 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7050 (mmt) REVERT: E 189 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.5802 (tt) REVERT: E 191 ARG cc_start: 0.6664 (ttm-80) cc_final: 0.6173 (ttm-80) REVERT: E 196 LYS cc_start: 0.8357 (mtmt) cc_final: 0.7739 (tptt) REVERT: E 232 GLN cc_start: 0.8167 (mp10) cc_final: 0.7861 (mm-40) REVERT: E 275 SER cc_start: 0.8457 (m) cc_final: 0.8102 (t) REVERT: E 281 LYS cc_start: 0.7062 (mttt) cc_final: 0.6606 (mmtm) REVERT: E 330 GLN cc_start: 0.7475 (mt0) cc_final: 0.7098 (mm110) REVERT: E 374 GLU cc_start: 0.7610 (pm20) cc_final: 0.7310 (pm20) REVERT: E 467 LYS cc_start: 0.7467 (ttpt) cc_final: 0.6954 (tppt) REVERT: E 471 GLU cc_start: 0.7581 (tp30) cc_final: 0.7309 (tt0) outliers start: 40 outliers final: 20 residues processed: 216 average time/residue: 0.5976 time to fit residues: 143.4125 Evaluate side-chains 206 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 69 ASP 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 221 CYS Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain A residue 1289 ILE 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 B residue 1293 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 64 GLU 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 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 401 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN D 317 HIS D 401 HIS D 482 GLN E 401 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.172281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129332 restraints weight = 22672.155| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.44 r_work: 0.3485 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17762 Z= 0.239 Angle : 0.650 12.506 24121 Z= 0.338 Chirality : 0.046 0.264 2666 Planarity : 0.004 0.057 2931 Dihedral : 16.867 62.532 2798 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.60 % Allowed : 28.14 % 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: 0.54 (0.18), residues: 1972 helix: 1.95 (0.18), residues: 813 sheet: 0.13 (0.25), residues: 399 loop : -1.32 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 400 TYR 0.023 0.002 TYR A 212 PHE 0.018 0.002 PHE B 176 TRP 0.007 0.001 TRP D 210 HIS 0.026 0.002 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (17762) covalent geometry : angle 0.65006 / 0.34 (24121) hydrogen bonds : bond 0.04422 / 4.29 ( 846) hydrogen bonds : angle 4.51268 / 4.82 ( 2446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6708.41 seconds wall clock time: 114 minutes 58.23 seconds (6898.23 seconds total)