Starting phenix.real_space_refine on Thu Feb 5 13:22:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9m_52964/02_2026/9q9m_52964.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9m_52964/02_2026/9q9m_52964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q9m_52964/02_2026/9q9m_52964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9m_52964/02_2026/9q9m_52964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q9m_52964/02_2026/9q9m_52964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9m_52964/02_2026/9q9m_52964.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Mn 4 7.51 5 P 56 5.49 5 Mg 2 5.21 5 S 81 5.16 5 Be 2 3.05 5 C 10797 2.51 5 N 3025 2.21 5 O 3388 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17361 Number of models: 1 Model: "" Number of chains: 16 Chain: "J" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 154 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "P" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "T" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "F" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 681 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "A" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3760 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 456} Chain breaks: 1 Chain: "B" Number of atoms: 3811 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 470, 3803 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 461} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 470, 3803 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 461} Chain breaks: 1 bond proxies already assigned to first conformer: 3845 Chain: "D" Number of atoms: 3898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3898 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 20, 'TRANS': 457} Chain breaks: 1 Chain: "E" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3917 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 20, 'TRANS': 459} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.23, per 1000 atoms: 0.24 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: 1.60 Conformation dependent library (CDL) restraints added in 713.5 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: 1.90 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: 3.11 Time building geometry restraints manager: 2.06 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: 23320 2.54 - 5.08: 664 5.08 - 7.62: 121 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 - 0.118: 2500 0.118 - 0.236: 130 0.236 - 0.353: 12 0.353 - 0.471: 4 0.471 - 0.589: 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 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" P DT P 27 " pdb=" OP1 DT P 27 " pdb=" OP2 DT P 27 " pdb=" O5' DT P 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.58 2.00e-01 2.50e+01 8.32e+00 chirality pdb=" P DA T 32 " pdb=" OP1 DA T 32 " pdb=" OP2 DA T 32 " pdb=" O5' DA T 32 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.09e+00 ... (remaining 2663 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 745 " 0.960 9.50e-02 1.11e+02 4.30e-01 1.12e+02 pdb=" NE ARG F 745 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG F 745 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG F 745 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 745 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 428 " -0.665 9.50e-02 1.11e+02 2.98e-01 5.42e+01 pdb=" NE ARG D 428 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG D 428 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 428 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 428 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1098 " 0.623 9.50e-02 1.11e+02 2.79e-01 4.76e+01 pdb=" NE ARG B1098 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B1098 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B1098 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B1098 " 0.019 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 36 2.45 - 3.06: 10874 3.06 - 3.67: 26146 3.67 - 4.29: 41420 4.29 - 4.90: 67392 Nonbonded interactions: 145868 Sorted by model distance: nonbonded pdb=" ND1 HIS D 245 " pdb="MN MN D 802 " model vdw 1.835 2.400 nonbonded pdb=" F3 BEF A1403 " pdb="MG MG B1401 " model vdw 1.917 2.120 nonbonded pdb="MG MG A1401 " pdb=" F3 BEF A1404 " model vdw 1.929 2.120 nonbonded pdb=" OG1 THR B 43 " pdb="MG MG B1401 " model vdw 2.000 2.170 nonbonded pdb="MG MG A1401 " pdb=" O HOH A1501 " model vdw 2.020 2.170 ... (remaining 145863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 2 or resid 4 through 235 or resid 1078 through 1 \ 306)) selection = (chain 'B' and (resid 1 through 2 or resid 4 through 1306)) } ncs_group { reference = (chain 'D' and (resid 8 through 402 or resid 426 through 802)) selection = (chain 'E' and (resid 8 through 507 or resid 801 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.840 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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= 0.402 Angle : 0.966 12.696 24121 Z= 0.617 Chirality : 0.075 0.589 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 covalent geometry : bond 0.00600 (17762) covalent geometry : angle 0.96644 (24121) hydrogen bonds : bond 0.16420 ( 846) hydrogen bonds : angle 7.12081 ( 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 : 0.702 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: 0.6135 time to fit residues: 272.0067 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 : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain E residue 199 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1130 GLN A1181 ASN A1261 ASN B 97 GLN B 152 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1269 HIS D 152 HIS D 317 HIS D 401 HIS D 482 GLN E 219 ASN E 256 ASN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 GLN E 401 HIS E 477 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.180064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137354 restraints weight = 25052.919| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.60 r_work: 0.3576 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17762 Z= 0.165 Angle : 0.607 7.588 24121 Z= 0.324 Chirality : 0.043 0.262 2666 Planarity : 0.004 0.044 2931 Dihedral : 17.245 65.638 2807 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.48 % Allowed : 24.93 % Favored : 71.59 % 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: 0.31 (0.18), residues: 1972 helix: 1.59 (0.18), residues: 826 sheet: 0.10 (0.26), residues: 378 loop : -1.28 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 505 TYR 0.028 0.002 TYR E 369 PHE 0.024 0.002 PHE E 237 TRP 0.007 0.001 TRP A 164 HIS 0.008 0.001 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00371 (17762) covalent geometry : angle 0.60653 (24121) hydrogen bonds : bond 0.04660 ( 846) hydrogen bonds : angle 4.96763 ( 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 295 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 232 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 472 PHE cc_start: 0.7279 (m-80) cc_final: 0.6956 (m-80) REVERT: F 701 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6550 (p-80) REVERT: A 1 MET cc_start: 0.6260 (ttm) cc_final: 0.5899 (mtm) REVERT: A 89 VAL cc_start: 0.7636 (m) cc_final: 0.7409 (t) REVERT: A 92 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: A 177 ASP cc_start: 0.8020 (p0) cc_final: 0.7619 (p0) REVERT: A 185 TYR cc_start: 0.7312 (m-80) cc_final: 0.6923 (m-80) REVERT: A 205 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7052 (mt-10) REVERT: A 1261 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.6709 (t0) REVERT: B 20 LYS cc_start: 0.8297 (pttp) cc_final: 0.8003 (ptpp) REVERT: B 71 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7536 (mtmt) REVERT: B 79 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7400 (ttp80) REVERT: B 94 ILE cc_start: 0.7697 (mt) cc_final: 0.7259 (mp) REVERT: B 186 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6809 (mt) REVERT: B 1189 LEU cc_start: 0.8212 (mp) cc_final: 0.7808 (tt) REVERT: D 64 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7933 (mm-30) REVERT: D 192 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5324 (mtt) REVERT: D 205 GLU cc_start: 0.8100 (pm20) cc_final: 0.7872 (pm20) REVERT: D 262 TYR cc_start: 0.6370 (m-80) cc_final: 0.6063 (m-80) REVERT: D 325 ASN cc_start: 0.8133 (t0) cc_final: 0.7709 (t0) REVERT: D 374 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7891 (pt0) REVERT: D 438 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6867 (mm-40) REVERT: D 439 THR cc_start: 0.6838 (m) cc_final: 0.6220 (t) REVERT: E 64 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7071 (mm-30) REVERT: E 157 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6786 (mtp) REVERT: E 196 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7642 (tptt) REVERT: E 232 GLN cc_start: 0.8274 (mp10) cc_final: 0.7912 (mm-40) REVERT: E 294 MET cc_start: 0.7752 (ttp) cc_final: 0.7469 (ttp) REVERT: E 330 GLN cc_start: 0.7376 (mt0) cc_final: 0.7033 (mm110) REVERT: E 356 HIS cc_start: 0.7693 (m-70) cc_final: 0.7360 (m-70) REVERT: E 359 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6867 (pm20) outliers start: 63 outliers final: 20 residues processed: 278 average time/residue: 0.6048 time to fit residues: 188.1761 Evaluate side-chains 220 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 701 HIS 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 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 A residue 1300 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 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 192 MET Chi-restraints excluded: chain D residue 243 TRP Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 379 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 29 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1181 ASN ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN D 112 GLN D 259 GLN D 317 HIS D 322 ASN D 401 HIS D 443 ASN D 459 GLN D 482 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.176554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133921 restraints weight = 25962.588| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.61 r_work: 0.3525 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17762 Z= 0.167 Angle : 0.577 9.297 24121 Z= 0.307 Chirality : 0.043 0.279 2666 Planarity : 0.004 0.038 2931 Dihedral : 16.930 61.167 2798 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.15 % Allowed : 25.21 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 1972 helix: 1.88 (0.18), residues: 824 sheet: 0.30 (0.26), residues: 378 loop : -1.25 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 349 TYR 0.025 0.002 TYR E 369 PHE 0.018 0.002 PHE F 688 TRP 0.006 0.001 TRP A 164 HIS 0.005 0.001 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00381 (17762) covalent geometry : angle 0.57722 (24121) hydrogen bonds : bond 0.04342 ( 846) hydrogen bonds : angle 4.64997 ( 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 275 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 200 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: J 472 PHE cc_start: 0.7380 (m-80) cc_final: 0.6831 (m-80) REVERT: F 703 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.5804 (pp) REVERT: F 707 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5204 (t0) REVERT: A 1 MET cc_start: 0.6836 (ttm) cc_final: 0.6470 (mtm) REVERT: A 5 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7070 (mt-10) REVERT: A 20 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7151 (ptmt) REVERT: A 69 ASP cc_start: 0.8303 (t0) cc_final: 0.8023 (t0) REVERT: A 185 TYR cc_start: 0.7393 (m-80) cc_final: 0.7045 (m-80) REVERT: A 1138 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8203 (mtt) REVERT: A 1275 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6854 (tt0) REVERT: A 1289 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8344 (mm) REVERT: B 71 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7546 (mtmt) REVERT: B 94 ILE cc_start: 0.7850 (mt) cc_final: 0.7410 (mp) REVERT: B 1120 ASP cc_start: 0.7122 (m-30) cc_final: 0.6804 (m-30) REVERT: B 1189 LEU cc_start: 0.8196 (mp) cc_final: 0.7771 (tt) REVERT: D 64 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7972 (mm-30) REVERT: D 309 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6860 (tpt) REVERT: D 374 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7925 (pt0) REVERT: D 438 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6791 (mm-40) REVERT: D 439 THR cc_start: 0.6978 (m) cc_final: 0.6436 (t) REVERT: D 443 ASN cc_start: 0.8676 (m-40) cc_final: 0.8172 (m110) REVERT: D 458 VAL cc_start: 0.7840 (t) cc_final: 0.7618 (m) REVERT: D 479 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7719 (pp20) REVERT: E 64 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: E 157 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6891 (mmt) REVERT: E 196 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7623 (tptt) REVERT: E 232 GLN cc_start: 0.8235 (mp10) cc_final: 0.7867 (mm-40) REVERT: E 294 MET cc_start: 0.7761 (ttp) cc_final: 0.7521 (ttp) REVERT: E 309 MET cc_start: 0.7810 (tpt) cc_final: 0.7343 (tpt) REVERT: E 311 ASP cc_start: 0.7555 (m-30) cc_final: 0.7343 (m-30) REVERT: E 330 GLN cc_start: 0.7490 (mt0) cc_final: 0.7085 (mm110) outliers start: 75 outliers final: 27 residues processed: 254 average time/residue: 0.5495 time to fit residues: 156.6751 Evaluate side-chains 211 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 661 SER Chi-restraints excluded: chain F residue 703 ILE 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 76 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 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 1300 VAL Chi-restraints excluded: chain B residue 147 SER 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 1304 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 243 TRP Chi-restraints excluded: chain D residue 309 MET 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 193 PHE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 132 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1181 ASN B 64 ASN D 112 GLN D 317 HIS D 325 ASN D 401 HIS D 482 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127608 restraints weight = 32598.256| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.92 r_work: 0.3449 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17762 Z= 0.235 Angle : 0.615 7.578 24121 Z= 0.327 Chirality : 0.045 0.260 2666 Planarity : 0.004 0.038 2931 Dihedral : 16.912 62.292 2798 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.81 % Allowed : 24.27 % Favored : 70.92 % 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: 816 sheet: 0.26 (0.25), residues: 376 loop : -1.31 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 366 TYR 0.020 0.002 TYR E 369 PHE 0.026 0.002 PHE E 237 TRP 0.008 0.001 TRP D 210 HIS 0.006 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00551 (17762) covalent geometry : angle 0.61452 (24121) hydrogen bonds : bond 0.04591 ( 846) hydrogen bonds : angle 4.67834 ( 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 291 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 204 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6455 (p-80) REVERT: F 703 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.6064 (pp) REVERT: F 707 ASP cc_start: 0.6107 (OUTLIER) cc_final: 0.5322 (t0) REVERT: A 1 MET cc_start: 0.7184 (ttm) cc_final: 0.6839 (mtm) REVERT: A 5 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7260 (mt-10) REVERT: A 20 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7338 (ptmt) REVERT: A 69 ASP cc_start: 0.8451 (t0) cc_final: 0.8141 (t0) REVERT: A 148 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7798 (tttp) REVERT: A 177 ASP cc_start: 0.8041 (p0) cc_final: 0.7757 (p0) REVERT: A 1271 GLU cc_start: 0.6947 (mp0) cc_final: 0.6566 (pm20) REVERT: A 1289 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8344 (mm) REVERT: B 71 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7754 (mtpt) REVERT: B 94 ILE cc_start: 0.7968 (mt) cc_final: 0.7593 (mp) REVERT: B 177 ASP cc_start: 0.7646 (p0) cc_final: 0.7382 (p0) REVERT: B 184 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6395 (mmt180) REVERT: B 1108 MET cc_start: 0.7457 (mmm) cc_final: 0.7022 (mmt) REVERT: B 1189 LEU cc_start: 0.8283 (mp) cc_final: 0.7769 (tt) REVERT: D 374 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7947 (pt0) REVERT: D 438 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6854 (mm-40) REVERT: D 439 THR cc_start: 0.6923 (m) cc_final: 0.6250 (t) REVERT: D 443 ASN cc_start: 0.8740 (m-40) cc_final: 0.8216 (m110) REVERT: D 458 VAL cc_start: 0.8003 (t) cc_final: 0.7788 (m) REVERT: E 64 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7162 (mm-30) REVERT: E 157 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7169 (mmt) REVERT: E 192 MET cc_start: 0.6032 (OUTLIER) cc_final: 0.5366 (mmt) REVERT: E 196 LYS cc_start: 0.8360 (mtmt) cc_final: 0.7754 (tptt) REVERT: E 232 GLN cc_start: 0.8266 (mp10) cc_final: 0.7986 (mm-40) REVERT: E 278 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6911 (mt-10) REVERT: E 281 LYS cc_start: 0.7215 (mttt) cc_final: 0.6745 (mmtm) REVERT: E 294 MET cc_start: 0.7710 (ttp) cc_final: 0.7489 (ttp) REVERT: E 311 ASP cc_start: 0.7533 (m-30) cc_final: 0.7275 (m-30) REVERT: E 330 GLN cc_start: 0.7631 (mt0) cc_final: 0.7213 (mm110) REVERT: E 465 GLU cc_start: 0.7036 (mp0) cc_final: 0.6702 (mp0) REVERT: E 467 LYS cc_start: 0.7403 (ttpt) cc_final: 0.6962 (tppt) REVERT: E 471 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6529 (tt0) outliers start: 87 outliers final: 32 residues processed: 267 average time/residue: 0.5999 time to fit residues: 180.3443 Evaluate side-chains 227 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 661 SER Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 ILE 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 76 THR 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 1089 LYS 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 71 LYS 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 1102 GLU Chi-restraints excluded: chain B residue 1137 SER 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 251 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 464 LYS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 193 PHE 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 278 GLU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 471 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 24 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 154 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1181 ASN D 112 GLN D 317 HIS D 401 HIS D 482 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.175150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130747 restraints weight = 38781.712| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.17 r_work: 0.3488 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17762 Z= 0.129 Angle : 0.551 9.310 24121 Z= 0.290 Chirality : 0.041 0.191 2666 Planarity : 0.003 0.036 2931 Dihedral : 16.603 62.937 2798 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.92 % Allowed : 26.15 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 1972 helix: 2.07 (0.18), residues: 810 sheet: 0.49 (0.26), residues: 365 loop : -1.22 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 745 TYR 0.016 0.002 TYR A1104 PHE 0.012 0.001 PHE E 54 TRP 0.006 0.001 TRP A 164 HIS 0.005 0.001 HIS B1087 Details of bonding type rmsd covalent geometry : bond 0.00288 (17762) covalent geometry : angle 0.55123 (24121) hydrogen bonds : bond 0.03928 ( 846) hydrogen bonds : angle 4.40517 ( 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 262 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 191 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 707 ASP cc_start: 0.6044 (OUTLIER) cc_final: 0.5418 (t0) REVERT: A 1 MET cc_start: 0.7188 (ttm) cc_final: 0.6853 (mtm) REVERT: A 5 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7145 (mt-10) REVERT: A 20 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7334 (ptmt) REVERT: A 69 ASP cc_start: 0.8127 (t0) cc_final: 0.7874 (t0) REVERT: A 148 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7792 (tttp) REVERT: A 177 ASP cc_start: 0.7945 (p0) cc_final: 0.7595 (p0) REVERT: A 1140 MET cc_start: 0.8138 (tpp) cc_final: 0.7740 (mmm) REVERT: A 1271 GLU cc_start: 0.6963 (mp0) cc_final: 0.6625 (pm20) REVERT: B 71 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7513 (mtmt) REVERT: B 94 ILE cc_start: 0.7813 (mt) cc_final: 0.7324 (mp) REVERT: B 119 THR cc_start: 0.7801 (m) cc_final: 0.7378 (p) REVERT: B 184 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6309 (mmt180) REVERT: B 1108 MET cc_start: 0.7503 (mmm) cc_final: 0.7184 (mmm) REVERT: B 1189 LEU cc_start: 0.8224 (mp) cc_final: 0.7692 (tt) REVERT: D 64 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8027 (mm-30) REVERT: D 354 ASN cc_start: 0.7444 (t0) cc_final: 0.6849 (t0) REVERT: D 374 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8097 (mt-10) REVERT: D 438 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6805 (mm-40) REVERT: E 64 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7100 (mm-30) REVERT: E 136 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6424 (t0) REVERT: E 157 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7138 (mmt) REVERT: E 196 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7734 (tptt) REVERT: E 232 GLN cc_start: 0.8253 (mp10) cc_final: 0.8006 (mm-40) REVERT: E 233 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7640 (m-10) REVERT: E 281 LYS cc_start: 0.7118 (mttt) cc_final: 0.6648 (mmtm) REVERT: E 293 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6644 (mtmm) REVERT: E 294 MET cc_start: 0.7648 (ttp) cc_final: 0.7415 (ttp) REVERT: E 311 ASP cc_start: 0.7431 (m-30) cc_final: 0.7116 (m-30) REVERT: E 330 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7118 (mm110) REVERT: E 384 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6699 (mtmm) REVERT: E 467 LYS cc_start: 0.7412 (ttpt) cc_final: 0.6995 (tppt) REVERT: E 468 ASP cc_start: 0.7551 (t0) cc_final: 0.6769 (p0) outliers start: 71 outliers final: 21 residues processed: 241 average time/residue: 0.6369 time to fit residues: 171.1076 Evaluate side-chains 205 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 692 THR 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 76 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 ARG Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain 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 243 TRP Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 297 HIS D 317 HIS D 325 ASN D 401 HIS D 482 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.176234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.133505 restraints weight = 25104.078| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.58 r_work: 0.3531 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17762 Z= 0.118 Angle : 0.537 11.410 24121 Z= 0.283 Chirality : 0.041 0.172 2666 Planarity : 0.003 0.038 2931 Dihedral : 16.380 61.820 2798 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.48 % Allowed : 27.14 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1972 helix: 2.14 (0.18), residues: 815 sheet: 0.50 (0.26), residues: 383 loop : -1.18 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 349 TYR 0.016 0.001 TYR E 476 PHE 0.026 0.001 PHE E 237 TRP 0.006 0.001 TRP B 164 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00261 (17762) covalent geometry : angle 0.53711 (24121) hydrogen bonds : bond 0.03755 ( 846) hydrogen bonds : angle 4.29488 ( 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 250 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 472 PHE cc_start: 0.7362 (m-80) cc_final: 0.6687 (m-80) REVERT: F 703 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.5976 (pp) REVERT: F 707 ASP cc_start: 0.6000 (OUTLIER) cc_final: 0.5542 (t0) REVERT: A 1 MET cc_start: 0.7150 (ttm) cc_final: 0.6810 (mtm) REVERT: A 5 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7258 (mt-10) REVERT: A 20 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7384 (ptmt) REVERT: A 148 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7817 (tttp) REVERT: A 1140 MET cc_start: 0.8192 (tpp) cc_final: 0.7857 (mmm) REVERT: A 1179 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7519 (ttp-170) REVERT: A 1271 GLU cc_start: 0.6945 (mp0) cc_final: 0.6627 (pm20) REVERT: B 71 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7714 (mtpt) REVERT: B 94 ILE cc_start: 0.7812 (mt) cc_final: 0.7331 (mp) REVERT: B 119 THR cc_start: 0.7762 (m) cc_final: 0.7385 (p) REVERT: B 140 MET cc_start: 0.6713 (mmm) cc_final: 0.6364 (mtm) REVERT: B 177 ASP cc_start: 0.7547 (p0) cc_final: 0.7289 (p0) REVERT: B 184 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6306 (mmt180) REVERT: B 1189 LEU cc_start: 0.8185 (mp) cc_final: 0.7659 (tt) REVERT: D 14 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7706 (mtpp) REVERT: D 64 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8010 (mm-30) REVERT: D 187 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6639 (pt0) REVERT: D 354 ASN cc_start: 0.7450 (t0) cc_final: 0.6899 (t0) REVERT: D 374 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8021 (mt-10) REVERT: D 438 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6802 (mm-40) REVERT: D 500 GLU cc_start: 0.6694 (tm-30) cc_final: 0.6428 (tm-30) REVERT: E 64 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7060 (mm-30) REVERT: E 136 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6344 (t0) REVERT: E 157 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7053 (mmt) REVERT: E 196 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7746 (tptt) REVERT: E 232 GLN cc_start: 0.8230 (mp10) cc_final: 0.8004 (mm-40) REVERT: E 233 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7584 (m-10) REVERT: E 281 LYS cc_start: 0.7107 (mttt) cc_final: 0.6663 (mmtm) REVERT: E 293 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6654 (mtmm) REVERT: E 309 MET cc_start: 0.7854 (tpt) cc_final: 0.7610 (tpt) REVERT: E 311 ASP cc_start: 0.7431 (m-30) cc_final: 0.7120 (m-30) REVERT: E 330 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7106 (mm110) REVERT: E 384 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6719 (mttm) REVERT: E 467 LYS cc_start: 0.7465 (ttpt) cc_final: 0.7026 (tppt) REVERT: E 468 ASP cc_start: 0.7483 (t0) cc_final: 0.6805 (p0) outliers start: 63 outliers final: 22 residues processed: 234 average time/residue: 0.6055 time to fit residues: 158.6404 Evaluate side-chains 209 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 703 ILE 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 76 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 ARG Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1159 ASP Chi-restraints excluded: chain D residue 14 LYS 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 286 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 438 GLN 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 233 PHE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 LYS 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: 7.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 22 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 90 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS B 152 ASN D 297 HIS D 317 HIS D 401 HIS D 482 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.176393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.134080 restraints weight = 22467.042| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.44 r_work: 0.3544 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17762 Z= 0.119 Angle : 0.539 10.034 24121 Z= 0.283 Chirality : 0.041 0.150 2666 Planarity : 0.003 0.037 2931 Dihedral : 16.309 61.746 2798 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.04 % Allowed : 27.36 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1972 helix: 2.22 (0.18), residues: 810 sheet: 0.65 (0.27), residues: 363 loop : -1.14 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 349 TYR 0.017 0.001 TYR E 476 PHE 0.012 0.001 PHE E 261 TRP 0.005 0.001 TRP A 164 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00266 (17762) covalent geometry : angle 0.53886 (24121) hydrogen bonds : bond 0.03687 ( 846) hydrogen bonds : angle 4.24860 ( 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: 55 poor density : 189 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 472 PHE cc_start: 0.7241 (m-80) cc_final: 0.6691 (m-80) REVERT: F 701 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6228 (p-80) REVERT: F 707 ASP cc_start: 0.6011 (OUTLIER) cc_final: 0.5591 (t0) REVERT: A 1 MET cc_start: 0.7159 (ttm) cc_final: 0.6831 (mtm) REVERT: A 5 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7248 (mt-10) REVERT: A 20 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7406 (ptmt) REVERT: A 92 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: A 122 LYS cc_start: 0.7677 (tttm) cc_final: 0.7034 (ttpp) REVERT: A 148 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7810 (tttp) REVERT: A 1140 MET cc_start: 0.8185 (tpp) cc_final: 0.7876 (mmm) REVERT: A 1179 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7508 (ttp-170) REVERT: A 1271 GLU cc_start: 0.6920 (mp0) cc_final: 0.6609 (pm20) REVERT: A 1284 GLU cc_start: 0.7219 (mp0) cc_final: 0.6906 (mp0) REVERT: B 71 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7610 (mtmt) REVERT: B 94 ILE cc_start: 0.7817 (mt) cc_final: 0.7334 (mp) REVERT: B 119 THR cc_start: 0.7598 (m) cc_final: 0.7394 (p) REVERT: B 177 ASP cc_start: 0.7515 (p0) cc_final: 0.7261 (p0) REVERT: B 1108 MET cc_start: 0.7443 (mmm) cc_final: 0.7129 (mmm) REVERT: B 1189 LEU cc_start: 0.8180 (mp) cc_final: 0.7643 (tt) REVERT: D 14 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7650 (mtpp) REVERT: D 64 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8029 (mm-30) REVERT: D 290 LYS cc_start: 0.7017 (tttm) cc_final: 0.6554 (ttpt) REVERT: D 354 ASN cc_start: 0.7428 (t0) cc_final: 0.6865 (t0) REVERT: D 374 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7855 (pt0) REVERT: D 438 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6809 (mm-40) REVERT: D 500 GLU cc_start: 0.6619 (tm-30) cc_final: 0.6352 (tm-30) REVERT: E 64 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7007 (mm-30) REVERT: E 136 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6358 (t0) REVERT: E 157 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6982 (mmt) REVERT: E 196 LYS cc_start: 0.8365 (mtmt) cc_final: 0.7751 (tptt) REVERT: E 232 GLN cc_start: 0.8222 (mp10) cc_final: 0.8005 (mm-40) REVERT: E 233 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7542 (m-10) REVERT: E 281 LYS cc_start: 0.7103 (mttt) cc_final: 0.6700 (mmtm) REVERT: E 293 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6721 (mtmm) REVERT: E 306 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: E 309 MET cc_start: 0.7817 (tpt) cc_final: 0.7529 (tpt) REVERT: E 311 ASP cc_start: 0.7336 (m-30) cc_final: 0.7003 (m-30) REVERT: E 330 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7172 (mm110) REVERT: E 384 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6737 (mttm) REVERT: E 467 LYS cc_start: 0.7464 (ttpt) cc_final: 0.7051 (tppt) REVERT: E 468 ASP cc_start: 0.7495 (t0) cc_final: 0.6866 (p0) outliers start: 55 outliers final: 19 residues processed: 228 average time/residue: 0.6438 time to fit residues: 163.2309 Evaluate side-chains 205 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 664 ILE Chi-restraints excluded: chain F residue 692 THR 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 76 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 1159 ASP Chi-restraints excluded: chain D residue 14 LYS 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 341 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 LYS Chi-restraints excluded: chain E residue 306 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 94 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 0.2980 chunk 36 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 701 HIS F 711 HIS B 85 GLN ** B1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS D 317 HIS D 401 HIS D 482 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS E 445 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.170086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125484 restraints weight = 34650.789| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.99 r_work: 0.3424 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4396 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= 0.267 Angle : 0.649 10.421 24121 Z= 0.341 Chirality : 0.046 0.197 2666 Planarity : 0.004 0.057 2931 Dihedral : 16.676 63.027 2798 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.43 % Allowed : 27.31 % 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: 0.51 (0.18), residues: 1972 helix: 1.86 (0.18), residues: 813 sheet: 0.24 (0.25), residues: 389 loop : -1.31 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 502 TYR 0.019 0.002 TYR E 476 PHE 0.027 0.002 PHE E 237 TRP 0.010 0.001 TRP D 210 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00627 (17762) covalent geometry : angle 0.64857 (24121) hydrogen bonds : bond 0.04726 ( 846) hydrogen bonds : angle 4.62967 ( 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 250 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 707 ASP cc_start: 0.6165 (OUTLIER) cc_final: 0.5575 (t0) REVERT: A 1 MET cc_start: 0.7325 (ttm) cc_final: 0.6989 (mtm) REVERT: A 5 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7141 (mt-10) REVERT: A 18 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6222 (mm-30) REVERT: A 92 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: A 122 LYS cc_start: 0.7672 (tttm) cc_final: 0.7070 (ttpp) REVERT: A 148 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7799 (tttp) REVERT: A 1089 LYS cc_start: 0.7724 (ttpt) cc_final: 0.7278 (pttt) REVERT: A 1179 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7636 (ttp80) REVERT: A 1271 GLU cc_start: 0.6944 (mp0) cc_final: 0.6539 (pm20) REVERT: A 1289 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8262 (mm) REVERT: B 71 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7853 (mtpt) REVERT: B 119 THR cc_start: 0.7863 (m) cc_final: 0.7464 (p) REVERT: B 140 MET cc_start: 0.6922 (mmm) cc_final: 0.6437 (mtm) REVERT: D 112 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: D 354 ASN cc_start: 0.7563 (t0) cc_final: 0.6919 (t0) REVERT: D 374 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8018 (pt0) REVERT: D 438 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6835 (mm-40) REVERT: D 479 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7773 (pp20) REVERT: D 496 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7336 (tptp) REVERT: D 500 GLU cc_start: 0.6594 (tm-30) cc_final: 0.6368 (tm-30) REVERT: E 64 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7139 (mm-30) REVERT: E 136 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6533 (t0) REVERT: E 192 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5499 (mmt) REVERT: E 196 LYS cc_start: 0.8426 (mtmt) cc_final: 0.7789 (tptt) REVERT: E 232 GLN cc_start: 0.8269 (mp10) cc_final: 0.7998 (mm-40) REVERT: E 238 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7572 (mt) REVERT: E 239 ASP cc_start: 0.7956 (m-30) cc_final: 0.7728 (m-30) REVERT: E 281 LYS cc_start: 0.7320 (mttt) cc_final: 0.6807 (mmtm) REVERT: E 293 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6788 (mtmm) REVERT: E 306 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6770 (mp10) REVERT: E 309 MET cc_start: 0.8030 (tpt) cc_final: 0.7667 (tpt) REVERT: E 311 ASP cc_start: 0.7389 (m-30) cc_final: 0.7048 (m-30) REVERT: E 330 GLN cc_start: 0.7598 (mt0) cc_final: 0.7209 (mm110) REVERT: E 384 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6579 (mttm) REVERT: E 465 GLU cc_start: 0.7210 (mp0) cc_final: 0.6763 (mp0) REVERT: E 467 LYS cc_start: 0.7511 (ttpt) cc_final: 0.6874 (tppt) outliers start: 62 outliers final: 25 residues processed: 235 average time/residue: 0.6876 time to fit residues: 180.0880 Evaluate side-chains 216 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 664 ILE Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 707 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 92 GLU 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 1179 ARG Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain B residue 147 SER 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 1293 ILE 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 254 THR Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 LYS Chi-restraints excluded: chain E residue 306 GLN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 401 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 297 HIS D 401 HIS D 482 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 ASN E 401 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.173600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130105 restraints weight = 29240.714| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.75 r_work: 0.3488 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17762 Z= 0.137 Angle : 0.577 10.887 24121 Z= 0.303 Chirality : 0.042 0.187 2666 Planarity : 0.003 0.059 2931 Dihedral : 16.533 63.459 2798 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.32 % Allowed : 28.69 % Favored : 68.99 % 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: 2.03 (0.18), residues: 814 sheet: 0.25 (0.26), residues: 385 loop : -1.26 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 488 TYR 0.028 0.002 TYR A 212 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 covalent geometry : bond 0.00307 (17762) covalent geometry : angle 0.57654 (24121) hydrogen bonds : bond 0.04012 ( 846) hydrogen bonds : angle 4.43384 ( 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 225 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7136 (OUTLIER) cc_final: 0.6220 (p-80) REVERT: F 707 ASP cc_start: 0.6052 (OUTLIER) cc_final: 0.5711 (t0) REVERT: A 1 MET cc_start: 0.7273 (ttm) cc_final: 0.6937 (mtm) REVERT: A 5 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7208 (mt-10) REVERT: A 20 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7108 (ptmt) REVERT: A 122 LYS cc_start: 0.7686 (tttm) cc_final: 0.7047 (ttpp) REVERT: A 148 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7849 (tttp) REVERT: A 177 ASP cc_start: 0.8006 (p0) cc_final: 0.7770 (p0) REVERT: A 207 GLN cc_start: 0.8386 (tt0) cc_final: 0.8172 (mt0) REVERT: A 208 MET cc_start: 0.8376 (mmm) cc_final: 0.8104 (tmm) REVERT: A 1089 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7263 (pttt) REVERT: A 1140 MET cc_start: 0.8194 (tpp) cc_final: 0.7982 (mmm) REVERT: A 1179 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7544 (ttp-170) REVERT: A 1271 GLU cc_start: 0.6902 (mp0) cc_final: 0.6557 (pm20) REVERT: A 1284 GLU cc_start: 0.7283 (mp0) cc_final: 0.6959 (mp0) REVERT: A 1289 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8186 (mm) REVERT: B 71 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7533 (mtmt) REVERT: B 119 THR cc_start: 0.7778 (m) cc_final: 0.7470 (p) REVERT: B 140 MET cc_start: 0.6765 (mmm) cc_final: 0.6349 (mtm) REVERT: B 1189 LEU cc_start: 0.8132 (mp) cc_final: 0.7564 (tt) REVERT: D 64 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8046 (mm-30) REVERT: D 112 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: D 354 ASN cc_start: 0.7486 (t0) cc_final: 0.6880 (t0) REVERT: D 374 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8061 (mt-10) REVERT: D 438 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6784 (mm-40) REVERT: D 479 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7811 (pp20) REVERT: D 496 LYS cc_start: 0.7522 (mmmt) cc_final: 0.7310 (tptp) REVERT: D 500 GLU cc_start: 0.6520 (tm-30) cc_final: 0.6233 (tm-30) REVERT: D 502 ARG cc_start: 0.6635 (mtp-110) cc_final: 0.6137 (tpm170) REVERT: E 64 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7080 (mm-30) REVERT: E 136 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6480 (t0) REVERT: E 192 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5487 (mmt) REVERT: E 196 LYS cc_start: 0.8412 (mtmt) cc_final: 0.7798 (tptt) REVERT: E 232 GLN cc_start: 0.8219 (mp10) cc_final: 0.7905 (mm-40) REVERT: E 281 LYS cc_start: 0.7268 (mttt) cc_final: 0.6760 (mmtm) REVERT: E 293 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6634 (mtmm) REVERT: E 306 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: E 309 MET cc_start: 0.7891 (tpt) cc_final: 0.7541 (tpt) REVERT: E 311 ASP cc_start: 0.7337 (m-30) cc_final: 0.6988 (m-30) REVERT: E 330 GLN cc_start: 0.7492 (mt0) cc_final: 0.7091 (mm110) REVERT: E 374 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: E 384 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6813 (mtmm) REVERT: E 465 GLU cc_start: 0.7151 (mp0) cc_final: 0.6721 (mp0) REVERT: E 466 GLU cc_start: 0.7230 (tt0) cc_final: 0.6571 (tt0) REVERT: E 467 LYS cc_start: 0.7477 (ttpt) cc_final: 0.6850 (tppt) REVERT: E 468 ASP cc_start: 0.7419 (t0) cc_final: 0.6818 (p0) outliers start: 42 outliers final: 17 residues processed: 218 average time/residue: 0.6883 time to fit residues: 166.3489 Evaluate side-chains 207 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 664 ILE Chi-restraints excluded: chain F residue 692 THR 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 76 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 148 LYS 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 198 THR Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 192 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 293 LYS Chi-restraints excluded: chain E residue 306 GLN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 384 LYS 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 31 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 182 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 132 optimal weight: 0.0270 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN D 297 HIS D 401 HIS D 482 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** E 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.174002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129865 restraints weight = 34526.600| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.99 r_work: 0.3480 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4512 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= 0.133 Angle : 0.569 11.382 24121 Z= 0.299 Chirality : 0.042 0.164 2666 Planarity : 0.003 0.057 2931 Dihedral : 16.398 63.130 2798 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.43 % Allowed : 28.69 % Favored : 68.88 % 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: 2.13 (0.18), residues: 811 sheet: 0.28 (0.26), residues: 395 loop : -1.24 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 502 TYR 0.028 0.001 TYR A 212 PHE 0.029 0.001 PHE E 237 TRP 0.005 0.001 TRP A 164 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00300 (17762) covalent geometry : angle 0.56943 (24121) hydrogen bonds : bond 0.03879 ( 846) hydrogen bonds : angle 4.36996 ( 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 231 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 701 HIS cc_start: 0.7047 (OUTLIER) cc_final: 0.6139 (p-80) REVERT: F 707 ASP cc_start: 0.5990 (OUTLIER) cc_final: 0.5770 (t0) REVERT: A 1 MET cc_start: 0.7288 (ttm) cc_final: 0.6954 (mtm) REVERT: A 5 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 20 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7103 (ptmt) REVERT: A 92 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: A 122 LYS cc_start: 0.7681 (tttm) cc_final: 0.7057 (ttpp) REVERT: A 148 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7785 (tttp) REVERT: A 177 ASP cc_start: 0.7976 (p0) cc_final: 0.7706 (p0) REVERT: A 208 MET cc_start: 0.8408 (mmm) cc_final: 0.8114 (tmm) REVERT: A 215 GLN cc_start: 0.7858 (mt0) cc_final: 0.7490 (mt0) REVERT: A 1140 MET cc_start: 0.8198 (tpp) cc_final: 0.7941 (mmm) REVERT: A 1179 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7408 (ttp-170) REVERT: A 1271 GLU cc_start: 0.6901 (mp0) cc_final: 0.6544 (pm20) REVERT: A 1284 GLU cc_start: 0.7248 (mp0) cc_final: 0.6929 (mp0) REVERT: A 1289 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8142 (mm) REVERT: B 71 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7648 (mtpt) REVERT: B 94 ILE cc_start: 0.7894 (mt) cc_final: 0.7317 (mp) REVERT: B 119 THR cc_start: 0.7674 (m) cc_final: 0.7395 (p) REVERT: B 140 MET cc_start: 0.6762 (mmm) cc_final: 0.6315 (mtm) REVERT: B 1189 LEU cc_start: 0.8090 (mp) cc_final: 0.7524 (tt) REVERT: D 64 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8036 (mm-30) REVERT: D 112 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: D 354 ASN cc_start: 0.7428 (t0) cc_final: 0.6850 (t0) REVERT: D 374 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8072 (mt-10) REVERT: D 438 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6754 (mm-40) REVERT: D 479 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7808 (pp20) REVERT: D 496 LYS cc_start: 0.7493 (mmmt) cc_final: 0.7285 (tptp) REVERT: D 500 GLU cc_start: 0.6475 (tm-30) cc_final: 0.6241 (tm-30) REVERT: D 502 ARG cc_start: 0.6650 (mtp-110) cc_final: 0.6149 (tpm170) REVERT: E 64 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7067 (mm-30) REVERT: E 136 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6465 (t0) REVERT: E 192 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.5586 (mmt) REVERT: E 196 LYS cc_start: 0.8404 (mtmt) cc_final: 0.7781 (tptt) REVERT: E 232 GLN cc_start: 0.8249 (mp10) cc_final: 0.7902 (mm-40) REVERT: E 281 LYS cc_start: 0.7215 (mttt) cc_final: 0.6708 (mmtm) REVERT: E 293 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6636 (mtmm) REVERT: E 306 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6670 (mp10) REVERT: E 309 MET cc_start: 0.7918 (tpt) cc_final: 0.7554 (tpt) REVERT: E 311 ASP cc_start: 0.7328 (m-30) cc_final: 0.6961 (m-30) REVERT: E 330 GLN cc_start: 0.7512 (mt0) cc_final: 0.7089 (mm110) REVERT: E 374 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: E 384 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6676 (mttm) REVERT: E 459 GLN cc_start: 0.6639 (mm-40) cc_final: 0.6038 (mp10) REVERT: E 465 GLU cc_start: 0.7116 (mp0) cc_final: 0.6689 (mp0) REVERT: E 466 GLU cc_start: 0.7165 (tt0) cc_final: 0.6537 (tt0) REVERT: E 467 LYS cc_start: 0.7509 (ttpt) cc_final: 0.6885 (tppt) REVERT: E 468 ASP cc_start: 0.7312 (t0) cc_final: 0.6761 (p0) outliers start: 44 outliers final: 21 residues processed: 221 average time/residue: 0.6918 time to fit residues: 169.6757 Evaluate side-chains 213 residues out of total 1807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 664 ILE Chi-restraints excluded: chain F residue 692 THR Chi-restraints excluded: chain F residue 701 HIS 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 76 THR Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 192 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 293 LYS Chi-restraints excluded: chain E residue 306 GLN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 374 GLU 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 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 297 HIS D 401 HIS D 482 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128958 restraints weight = 22788.826| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.42 r_work: 0.3483 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17762 Z= 0.191 Angle : 0.607 11.730 24121 Z= 0.318 Chirality : 0.044 0.216 2666 Planarity : 0.004 0.054 2931 Dihedral : 16.485 63.887 2798 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.49 % Allowed : 28.69 % Favored : 68.82 % 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: 0.59 (0.18), residues: 1972 helix: 2.03 (0.18), residues: 813 sheet: 0.14 (0.25), residues: 397 loop : -1.31 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 502 TYR 0.027 0.002 TYR A 212 PHE 0.015 0.002 PHE D 25 TRP 0.007 0.001 TRP D 210 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00448 (17762) covalent geometry : angle 0.60711 (24121) hydrogen bonds : bond 0.04255 ( 846) hydrogen bonds : angle 4.47743 ( 2446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7041.01 seconds wall clock time: 120 minutes 41.72 seconds (7241.72 seconds total)