Starting phenix.real_space_refine on Thu Aug 6 21:10:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9k_52962/08_2026/9q9k_52962.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9k_52962/08_2026/9q9k_52962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q9k_52962/08_2026/9q9k_52962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9k_52962/08_2026/9q9k_52962.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q9k_52962/08_2026/9q9k_52962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9k_52962/08_2026/9q9k_52962.map" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.083 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 58 5.49 5 Mg 2 5.21 5 S 80 5.16 5 Be 2 3.05 5 C 10497 2.51 5 N 2940 2.21 5 O 3321 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 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16910 Number of models: 1 Model: "" Number of chains: 16 Chain: "J" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 141 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "K" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 145 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "P" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3820 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 463} Chain breaks: 1 Chain: "B" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3815 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 463} Chain breaks: 1 Chain: "D" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3909 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 20, 'TRANS': 458} Chain breaks: 1 Chain: "E" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3899 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 20, 'TRANS': 457} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 3.96, per 1000 atoms: 0.23 Number of scatterers: 16910 At special positions: 0 Unit cell: (97.418, 106.142, 179.569, 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 80 16.00 P 58 15.00 Mg 2 11.99 F 6 9.00 O 3321 8.00 N 2940 7.00 C 10497 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: 1.34 Conformation dependent library (CDL) restraints added in 937.6 milliseconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3678 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 16 sheets defined 45.3% alpha, 19.2% beta 26 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'K' and resid 467 through 472 removed outlier: 3.531A pdb=" N PHE K 472 " --> pdb=" O GLU K 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.737A 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 69 through 74 Processing helix chain 'A' and resid 132 through 145 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 182 through 236 removed outlier: 3.847A pdb=" N LYS A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1093 removed outlier: 3.603A pdb=" N GLU A1091 " --> pdb=" O HIS A1087 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A1092 " --> pdb=" O PHE A1088 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1099 removed outlier: 3.822A pdb=" N ASP A1099 " --> pdb=" O PRO A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1155 removed outlier: 4.188A pdb=" N GLU A1142 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 3.670A 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 1257 Processing helix chain 'A' and resid 1270 through 1278 Processing helix chain 'A' and resid 1279 through 1281 No H-bonds generated for 'chain 'A' and resid 1279 through 1281' Processing helix chain 'A' and resid 1306 through 1311 removed outlier: 3.540A pdb=" N PHE A1309 " --> pdb=" O SER A1306 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A1310 " --> pdb=" O LEU A1307 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1311 " --> pdb=" O GLY A1308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1306 through 1311' Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 41 through 55 removed outlier: 3.836A pdb=" N ILE B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.511A pdb=" N VAL B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 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: 3.610A pdb=" N SER B 162 " --> pdb=" O GLN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 182 through 237 removed outlier: 4.236A pdb=" N TYR B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1093 removed outlier: 3.689A pdb=" N ILE B1086 " --> pdb=" O GLU B1082 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS B1087 " --> pdb=" O GLU B1083 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B1093 " --> pdb=" O LYS B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1099 removed outlier: 4.537A pdb=" N ASP B1099 " --> pdb=" O PRO B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1155 removed outlier: 4.406A pdb=" N GLU B1142 " --> pdb=" O MET B1138 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B1143 " --> pdb=" O LYS B1139 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B1146 " --> pdb=" O GLU B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1222 Processing helix chain 'B' and resid 1238 through 1257 Processing helix chain 'B' and resid 1270 through 1281 removed outlier: 4.352A pdb=" N SER B1280 " --> pdb=" O LEU B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1305 through 1310 removed outlier: 5.162A pdb=" N GLY B1308 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 51 Processing helix chain 'D' and resid 68 through 84 removed outlier: 3.764A pdb=" N MET D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.536A pdb=" N ASN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 148 removed outlier: 3.527A pdb=" N ILE D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'D' and resid 230 through 234 removed outlier: 3.518A pdb=" N LEU D 234 " --> pdb=" O GLU D 231 " (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 349 removed outlier: 3.947A pdb=" N GLN D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 382 Processing helix chain 'D' and resid 383 through 386 removed outlier: 3.625A pdb=" N VAL D 386 " --> pdb=" O GLN D 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 383 through 386' Processing helix chain 'D' and resid 428 through 444 Processing helix chain 'D' and resid 452 through 464 removed outlier: 4.167A pdb=" N GLN D 459 " --> pdb=" O GLY D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 489 removed outlier: 3.663A pdb=" N LEU D 473 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 506 removed outlier: 3.767A pdb=" N ASP D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) 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 removed outlier: 3.645A pdb=" N ASN E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.675A pdb=" N ASP E 113 " --> pdb=" O ASN E 110 " (cutoff:3.500A) 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: 3.673A pdb=" N VAL E 280 " --> pdb=" O GLY E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 317 No H-bonds generated for 'chain 'E' and resid 315 through 317' Processing helix chain 'E' and resid 327 through 352 removed outlier: 3.611A pdb=" N ALA E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN E 333 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 382 Processing helix chain 'E' and resid 428 through 444 Processing helix chain 'E' and resid 452 through 465 removed outlier: 3.541A pdb=" N GLU E 456 " --> pdb=" O ARG E 452 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 465 " --> pdb=" O PHE E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 488 removed outlier: 3.543A pdb=" N LEU E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 507 Processing sheet with id=AA1, first strand: chain 'K' and resid 460 through 461 removed outlier: 8.064A pdb=" N LEU A 31 " --> pdb=" O LYS A1285 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N TYR A1287 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 33 " --> pdb=" O TYR A1287 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A1289 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 35 " --> pdb=" O ILE A1289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.488A pdb=" N ILE A 4 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A 87 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.488A pdb=" N ILE A 4 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A 87 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU A 93 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR A 121 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1163 through 1168 removed outlier: 3.891A pdb=" N ASN A1183 " --> pdb=" O ASP A1168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 26 removed outlier: 5.351A pdb=" N ILE B 4 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG B 87 " --> pdb=" O ILE B 4 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 26 removed outlier: 5.351A pdb=" N ILE B 4 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG B 87 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 93 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR B 121 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1230 through 1231 removed outlier: 6.577A pdb=" N LEU B1230 " --> pdb=" O ILE B1267 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 33 " --> pdb=" O TYR B1287 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE B1289 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 35 " --> pdb=" O ILE B1289 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N LYS B1291 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B1300 " --> pdb=" O ARG B1288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1163 through 1168 removed outlier: 4.021A pdb=" N ASN B1183 " --> pdb=" O ASP B1168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 151 through 152 removed outlier: 6.520A pdb=" N VAL D 122 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N PHE D 54 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS D 14 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU D 56 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 16 " --> pdb=" O LEU D 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.944A pdb=" N LYS D 175 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU D 213 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA D 177 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL D 215 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR D 179 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN D 212 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE D 242 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE D 214 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL D 241 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE D 263 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA D 252 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 265 " --> pdb=" O LYS D 250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 162 through 164 Processing sheet with id=AB3, first strand: chain 'D' and resid 307 through 313 removed outlier: 3.660A pdb=" N GLU D 310 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 151 through 152 removed outlier: 6.547A pdb=" N VAL E 122 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE E 55 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE E 54 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.786A pdb=" N HIS E 217 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE E 214 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY E 244 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE E 216 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL E 241 " --> pdb=" O SER E 264 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE E 263 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA E 252 " --> pdb=" O ILE E 263 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 162 through 163 removed outlier: 6.085A pdb=" N ILE E 162 " --> pdb=" O THR E 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 307 through 313 removed outlier: 6.108A pdb=" N PHE E 308 " --> pdb=" O ARG E 364 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ARG E 366 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU E 310 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASP E 368 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE E 312 " --> pdb=" O ASP E 368 " (cutoff:3.500A) 818 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2770 1.30 - 1.43: 4501 1.43 - 1.56: 9794 1.56 - 1.68: 114 1.68 - 1.81: 126 Bond restraints: 17305 Sorted by residual: bond pdb=" C ASP D 463 " pdb=" N LYS D 464 " ideal model delta sigma weight residual 1.330 1.434 -0.104 1.38e-02 5.25e+03 5.69e+01 bond pdb=" C PRO A 58 " pdb=" O PRO A 58 " ideal model delta sigma weight residual 1.240 1.175 0.066 1.12e-02 7.97e+03 3.45e+01 bond pdb=" C VAL B 96 " pdb=" O VAL B 96 " ideal model delta sigma weight residual 1.236 1.186 0.050 9.90e-03 1.02e+04 2.51e+01 bond pdb=" C PHE A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.18e-02 7.18e+03 2.33e+01 bond pdb=" C GLU D 460 " pdb=" O GLU D 460 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.16e-02 7.43e+03 2.31e+01 ... (remaining 17300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 22744 2.46 - 4.92: 643 4.92 - 7.39: 104 7.39 - 9.85: 19 9.85 - 12.31: 9 Bond angle restraints: 23519 Sorted by residual: angle pdb=" CA PHE A 57 " pdb=" C PHE A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 117.51 107.14 10.37 1.13e+00 7.83e-01 8.42e+01 angle pdb=" N PRO D 326 " pdb=" CA PRO D 326 " pdb=" C PRO D 326 " ideal model delta sigma weight residual 114.68 105.17 9.51 1.04e+00 9.25e-01 8.37e+01 angle pdb=" N ARG D 351 " pdb=" CA ARG D 351 " pdb=" C ARG D 351 " ideal model delta sigma weight residual 112.94 101.67 11.27 1.41e+00 5.03e-01 6.38e+01 angle pdb=" O PHE A 57 " pdb=" C PHE A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 121.12 132.16 -11.04 1.42e+00 4.96e-01 6.04e+01 angle pdb=" N HIS B1269 " pdb=" CA HIS B1269 " pdb=" C HIS B1269 " ideal model delta sigma weight residual 113.89 101.91 11.98 1.58e+00 4.01e-01 5.75e+01 ... (remaining 23514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8512 17.97 - 35.93: 1226 35.93 - 53.90: 562 53.90 - 71.87: 179 71.87 - 89.83: 21 Dihedral angle restraints: 10500 sinusoidal: 4852 harmonic: 5648 Sorted by residual: dihedral pdb=" CD ARG E 488 " pdb=" NE ARG E 488 " pdb=" CZ ARG E 488 " pdb=" NH1 ARG E 488 " ideal model delta sinusoidal sigma weight residual 0.00 89.12 -89.12 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CD ARG D 503 " pdb=" NE ARG D 503 " pdb=" CZ ARG D 503 " pdb=" NH1 ARG D 503 " ideal model delta sinusoidal sigma weight residual 0.00 -87.81 87.81 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CD ARG B1105 " pdb=" NE ARG B1105 " pdb=" CZ ARG B1105 " pdb=" NH1 ARG B1105 " ideal model delta sinusoidal sigma weight residual 0.00 72.90 -72.90 1 1.00e+01 1.00e-02 6.78e+01 ... (remaining 10497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2506 0.128 - 0.256: 74 0.256 - 0.384: 3 0.384 - 0.512: 12 0.512 - 0.640: 6 Chirality restraints: 2601 Sorted by residual: chirality pdb=" P DA T 6 " pdb=" OP1 DA T 6 " pdb=" OP2 DA T 6 " pdb=" O5' DA T 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DA T 13 " pdb=" OP1 DA T 13 " pdb=" OP2 DA T 13 " pdb=" O5' DA T 13 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" P DA T 31 " pdb=" OP1 DA T 31 " pdb=" OP2 DA T 31 " pdb=" O5' DA T 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.17e+00 ... (remaining 2598 not shown) Planarity restraints: 2850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 488 " 1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG E 488 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 488 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 488 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG E 488 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 503 " -1.086 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG D 503 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 503 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 503 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 503 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1105 " 1.039 9.50e-02 1.11e+02 4.66e-01 1.31e+02 pdb=" NE ARG B1105 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG B1105 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B1105 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B1105 " 0.020 2.00e-02 2.50e+03 ... (remaining 2847 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 41 2.46 - 3.07: 10719 3.07 - 3.68: 26281 3.68 - 4.29: 41189 4.29 - 4.90: 65410 Nonbonded interactions: 143640 Sorted by model distance: nonbonded pdb="MG MG B1402 " pdb=" F3 BEF B1403 " model vdw 1.845 2.120 nonbonded pdb="MG MG A1402 " pdb=" O HOH A1502 " model vdw 1.913 2.170 nonbonded pdb="MG MG A1402 " pdb=" F3 BEF A1403 " model vdw 1.926 2.120 nonbonded pdb=" OG1 THR B 43 " pdb="MG MG B1402 " model vdw 1.971 2.170 nonbonded pdb="MG MG B1402 " pdb=" O HOH B1501 " model vdw 1.987 2.170 ... (remaining 143635 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 236 or resid 1078 through 1403)) selection = (chain 'B' and (resid 1 through 236 or resid 1078 through 1403)) } ncs_group { reference = (chain 'D' and (resid 8 through 401 or resid 427 through 802)) selection = (chain 'E' and (resid 8 through 508 or resid 801 through 802)) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 459 through 474) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.140 Find NCS groups from input model: 0.400 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:8.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 0.104 17305 Z= 0.402 Angle : 0.947 12.312 23519 Z= 0.621 Chirality : 0.069 0.640 2601 Planarity : 0.026 0.490 2850 Dihedral : 20.879 89.833 6822 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.82 % Allowed : 24.13 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.18 (0.18), residues: 1914 helix: 1.43 (0.19), residues: 752 sheet: 0.14 (0.27), residues: 353 loop : -1.15 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 349 TYR 0.026 0.002 TYR E 111 PHE 0.018 0.002 PHE D 321 TRP 0.016 0.002 TRP D 210 HIS 0.009 0.001 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.40 (17305) covalent geometry : angle 0.94739 / 0.62 (23519) hydrogen bonds : bond 0.16224 / 14.74 ( 830) hydrogen bonds : angle 6.69071 / 8.18 ( 2444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6743 (tmm) cc_final: 0.5940 (tmm) REVERT: A 92 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7032 (mm-30) REVERT: A 135 GLU cc_start: 0.7050 (tp30) cc_final: 0.6836 (tp30) REVERT: A 208 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6754 (tmt) REVERT: A 1239 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6919 (ptm-80) REVERT: A 1243 GLU cc_start: 0.7561 (mt-10) cc_final: 0.6951 (mp0) REVERT: A 1256 ARG cc_start: 0.7278 (tpp80) cc_final: 0.6937 (tpp80) REVERT: A 1271 GLU cc_start: 0.7721 (tt0) cc_final: 0.7088 (tp30) REVERT: A 1275 GLU cc_start: 0.7240 (tp30) cc_final: 0.7011 (mm-30) REVERT: A 1288 ARG cc_start: 0.8452 (ttp-170) cc_final: 0.7441 (ttp-170) REVERT: A 1290 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7563 (tptp) REVERT: B 92 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7436 (mm-30) REVERT: B 108 LYS cc_start: 0.7144 (mttt) cc_final: 0.6841 (ttpt) REVERT: B 110 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: B 194 GLN cc_start: 0.7528 (tp-100) cc_final: 0.7088 (mt0) REVERT: B 1117 VAL cc_start: 0.7922 (t) cc_final: 0.7614 (p) REVERT: B 1223 LEU cc_start: 0.8136 (tp) cc_final: 0.7541 (mp) REVERT: B 1247 HIS cc_start: 0.7885 (m-70) cc_final: 0.7468 (t70) REVERT: B 1270 ASP cc_start: 0.8833 (t70) cc_final: 0.8559 (t70) REVERT: B 1275 GLU cc_start: 0.7154 (tt0) cc_final: 0.6791 (mt-10) REVERT: B 1284 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7446 (mm-30) REVERT: D 161 LYS cc_start: 0.7253 (ptmt) cc_final: 0.6781 (tptt) REVERT: D 239 ASP cc_start: 0.6827 (m-30) cc_final: 0.6556 (m-30) REVERT: D 263 ILE cc_start: 0.7508 (mp) cc_final: 0.7236 (mt) REVERT: D 278 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: D 435 GLN cc_start: 0.7801 (pt0) cc_final: 0.7594 (pt0) REVERT: D 466 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7166 (tp30) REVERT: D 468 ASP cc_start: 0.7448 (m-30) cc_final: 0.7060 (p0) REVERT: D 483 ARG cc_start: 0.7019 (mmm160) cc_final: 0.6725 (mtm180) REVERT: D 499 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7362 (mm-30) REVERT: E 259 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.5641 (mt0) REVERT: E 292 ARG cc_start: 0.7642 (mmm160) cc_final: 0.7020 (mmt180) REVERT: E 310 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6254 (mm-30) REVERT: E 322 ASN cc_start: 0.7516 (t0) cc_final: 0.7128 (t0) REVERT: E 349 ARG cc_start: 0.7449 (mtm110) cc_final: 0.7191 (mtp-110) REVERT: E 483 ARG cc_start: 0.6933 (ttp80) cc_final: 0.6695 (ttp-170) REVERT: E 496 LYS cc_start: 0.7686 (mptt) cc_final: 0.7397 (mtpt) outliers start: 32 outliers final: 15 residues processed: 260 average time/residue: 0.6972 time to fit residues: 200.4434 Evaluate side-chains 239 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1268 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 458 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B1172 ASN D 245 HIS ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 443 ASN E 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.179716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139150 restraints weight = 16771.424| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.07 r_work: 0.3390 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17305 Z= 0.159 Angle : 0.617 8.496 23519 Z= 0.327 Chirality : 0.045 0.253 2601 Planarity : 0.004 0.083 2850 Dihedral : 18.543 80.249 2800 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.87 % Allowed : 23.73 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 1914 helix: 1.86 (0.19), residues: 764 sheet: 0.29 (0.27), residues: 362 loop : -1.13 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 488 TYR 0.026 0.002 TYR B 212 PHE 0.013 0.001 PHE E 54 TRP 0.008 0.001 TRP B 164 HIS 0.007 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (17305) covalent geometry : angle 0.61743 / 0.33 (23519) hydrogen bonds : bond 0.04874 / 4.21 ( 830) hydrogen bonds : angle 4.83089 / 5.85 ( 2444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 225 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6343 (tp30) REVERT: A 1 MET cc_start: 0.7020 (tmm) cc_final: 0.6303 (tmm) REVERT: A 92 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7307 (mm-30) REVERT: A 208 MET cc_start: 0.7138 (mtm) cc_final: 0.6514 (tmt) REVERT: A 1108 MET cc_start: 0.6757 (mmm) cc_final: 0.6210 (tmm) REVERT: A 1239 ARG cc_start: 0.7648 (ttt-90) cc_final: 0.7411 (ptm160) REVERT: A 1243 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7422 (mp0) REVERT: A 1271 GLU cc_start: 0.7919 (tt0) cc_final: 0.7402 (tp30) REVERT: A 1275 GLU cc_start: 0.7262 (tp30) cc_final: 0.7044 (mm-30) REVERT: A 1288 ARG cc_start: 0.8669 (ttp-170) cc_final: 0.7718 (ttp-170) REVERT: A 1290 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7711 (tptp) REVERT: B 92 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7619 (mm-30) REVERT: B 108 LYS cc_start: 0.7393 (mttt) cc_final: 0.7096 (ttpp) REVERT: B 135 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: B 194 GLN cc_start: 0.7573 (tp-100) cc_final: 0.7189 (mt0) REVERT: B 1117 VAL cc_start: 0.7779 (t) cc_final: 0.7474 (p) REVERT: B 1223 LEU cc_start: 0.8137 (tp) cc_final: 0.7578 (mp) REVERT: B 1247 HIS cc_start: 0.7944 (m-70) cc_final: 0.7567 (t70) REVERT: B 1275 GLU cc_start: 0.7208 (tt0) cc_final: 0.6604 (tm-30) REVERT: B 1284 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7383 (mm-30) REVERT: D 161 LYS cc_start: 0.7242 (ptmt) cc_final: 0.6575 (tptt) REVERT: D 200 MET cc_start: 0.7694 (mtt) cc_final: 0.7491 (mtp) REVERT: D 263 ILE cc_start: 0.7320 (mp) cc_final: 0.7047 (mt) REVERT: D 441 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6724 (mt-10) REVERT: D 466 GLU cc_start: 0.7558 (mt-10) cc_final: 0.6765 (tp30) REVERT: D 483 ARG cc_start: 0.6662 (mmm160) cc_final: 0.6321 (mtm180) REVERT: D 499 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7151 (tt0) REVERT: E 86 ASP cc_start: 0.7655 (p0) cc_final: 0.7373 (p0) REVERT: E 94 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7083 (pp) REVERT: E 142 ASP cc_start: 0.8125 (m-30) cc_final: 0.7752 (m-30) REVERT: E 205 GLU cc_start: 0.7431 (pm20) cc_final: 0.7184 (pm20) REVERT: E 259 GLN cc_start: 0.6530 (tp-100) cc_final: 0.5509 (mt0) REVERT: E 292 ARG cc_start: 0.7555 (mmm160) cc_final: 0.6836 (mmt180) REVERT: E 310 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6402 (mm-30) REVERT: E 322 ASN cc_start: 0.7258 (t0) cc_final: 0.6859 (t0) REVERT: E 349 ARG cc_start: 0.7108 (mtm110) cc_final: 0.6797 (mtp-110) REVERT: E 488 ARG cc_start: 0.5795 (ttp80) cc_final: 0.5283 (tmt-80) outliers start: 68 outliers final: 16 residues processed: 277 average time/residue: 0.6483 time to fit residues: 200.0660 Evaluate side-chains 229 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 365 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 157 optimal weight: 0.0030 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 438 GLN E 306 GLN E 325 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.178114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136526 restraints weight = 16941.573| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.17 r_work: 0.3364 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17305 Z= 0.195 Angle : 0.616 8.750 23519 Z= 0.325 Chirality : 0.046 0.203 2601 Planarity : 0.004 0.037 2850 Dihedral : 18.149 81.344 2768 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.55 % Allowed : 23.45 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 1914 helix: 1.81 (0.18), residues: 765 sheet: 0.33 (0.26), residues: 366 loop : -1.13 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 488 TYR 0.018 0.002 TYR B 212 PHE 0.016 0.002 PHE B 176 TRP 0.008 0.001 TRP B 164 HIS 0.007 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (17305) covalent geometry : angle 0.61643 / 0.32 (23519) hydrogen bonds : bond 0.05201 / 4.36 ( 830) hydrogen bonds : angle 4.63629 / 5.61 ( 2444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 219 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6246 (tp30) REVERT: A 1 MET cc_start: 0.7045 (tmm) cc_final: 0.6290 (tmm) REVERT: A 92 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7308 (mm-30) REVERT: A 167 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7730 (p) REVERT: A 184 ARG cc_start: 0.7541 (mmm160) cc_final: 0.6976 (mtp85) REVERT: A 208 MET cc_start: 0.6971 (mtm) cc_final: 0.6527 (tmt) REVERT: A 1108 MET cc_start: 0.6755 (mmm) cc_final: 0.6136 (tmm) REVERT: A 1235 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8371 (t) REVERT: A 1271 GLU cc_start: 0.7974 (tt0) cc_final: 0.7448 (tp30) REVERT: A 1275 GLU cc_start: 0.7215 (tp30) cc_final: 0.6997 (mm-30) REVERT: A 1288 ARG cc_start: 0.8642 (ttp-170) cc_final: 0.7682 (ttp-170) REVERT: A 1290 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7781 (tptp) REVERT: A 1310 ASN cc_start: 0.6015 (OUTLIER) cc_final: 0.5793 (m-40) REVERT: B 92 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7635 (mm-30) REVERT: B 108 LYS cc_start: 0.7422 (mttt) cc_final: 0.7134 (ttpp) REVERT: B 135 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: B 194 GLN cc_start: 0.7591 (tp-100) cc_final: 0.7210 (mt0) REVERT: B 209 GLU cc_start: 0.7093 (tp30) cc_final: 0.6838 (mm-30) REVERT: B 1117 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7462 (p) REVERT: B 1223 LEU cc_start: 0.8151 (tp) cc_final: 0.7590 (mp) REVERT: B 1247 HIS cc_start: 0.8006 (m-70) cc_final: 0.7570 (t70) REVERT: B 1284 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7438 (mm-30) REVERT: D 161 LYS cc_start: 0.7312 (ptmt) cc_final: 0.6619 (tptt) REVERT: D 263 ILE cc_start: 0.7281 (mp) cc_final: 0.6950 (mt) REVERT: D 278 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: D 365 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7892 (tt) REVERT: D 441 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6722 (mt-10) REVERT: D 466 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6812 (tp30) REVERT: D 483 ARG cc_start: 0.6703 (mmm160) cc_final: 0.6384 (mtm180) REVERT: D 499 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7124 (tt0) REVERT: E 86 ASP cc_start: 0.7599 (p0) cc_final: 0.7336 (p0) REVERT: E 142 ASP cc_start: 0.8150 (m-30) cc_final: 0.7784 (m-30) REVERT: E 205 GLU cc_start: 0.7426 (pm20) cc_final: 0.7089 (pp20) REVERT: E 259 GLN cc_start: 0.6481 (tp-100) cc_final: 0.5477 (mt0) REVERT: E 322 ASN cc_start: 0.7303 (t0) cc_final: 0.6761 (t0) REVERT: E 488 ARG cc_start: 0.5904 (ttp80) cc_final: 0.5392 (tmt-80) outliers start: 80 outliers final: 31 residues processed: 276 average time/residue: 0.6254 time to fit residues: 192.7425 Evaluate side-chains 242 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1284 GLU Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain A residue 1310 ASN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 458 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 170 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN E 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.180157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139402 restraints weight = 16894.374| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.11 r_work: 0.3395 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17305 Z= 0.128 Angle : 0.558 8.279 23519 Z= 0.296 Chirality : 0.043 0.195 2601 Planarity : 0.003 0.036 2850 Dihedral : 18.011 82.334 2768 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.47 % Allowed : 24.82 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.19), residues: 1914 helix: 2.05 (0.18), residues: 765 sheet: 0.33 (0.26), residues: 361 loop : -1.02 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 349 TYR 0.027 0.002 TYR B 212 PHE 0.012 0.001 PHE A1135 TRP 0.009 0.001 TRP B 164 HIS 0.005 0.001 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (17305) covalent geometry : angle 0.55751 / 0.30 (23519) hydrogen bonds : bond 0.04202 / 3.59 ( 830) hydrogen bonds : angle 4.40707 / 5.30 ( 2444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6285 (tp30) REVERT: A 1 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6166 (tmm) REVERT: A 92 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7237 (mm-30) REVERT: A 184 ARG cc_start: 0.7518 (mmm160) cc_final: 0.6944 (mtp85) REVERT: A 208 MET cc_start: 0.6985 (mtm) cc_final: 0.6376 (tmt) REVERT: A 1108 MET cc_start: 0.6688 (mmm) cc_final: 0.6134 (tmm) REVERT: A 1235 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8313 (t) REVERT: A 1271 GLU cc_start: 0.7993 (tt0) cc_final: 0.7468 (tp30) REVERT: A 1275 GLU cc_start: 0.7151 (tp30) cc_final: 0.6927 (mm-30) REVERT: A 1288 ARG cc_start: 0.8605 (ttp-170) cc_final: 0.7681 (ttp-170) REVERT: A 1290 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7704 (tptp) REVERT: B 92 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7613 (mm-30) REVERT: B 108 LYS cc_start: 0.7426 (mttt) cc_final: 0.7172 (ttpp) REVERT: B 194 GLN cc_start: 0.7507 (tp-100) cc_final: 0.7120 (mt0) REVERT: B 1117 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7453 (p) REVERT: B 1159 ASP cc_start: 0.7254 (m-30) cc_final: 0.7049 (m-30) REVERT: B 1223 LEU cc_start: 0.8158 (tp) cc_final: 0.7587 (mp) REVERT: B 1247 HIS cc_start: 0.7934 (m-70) cc_final: 0.7556 (t70) REVERT: B 1275 GLU cc_start: 0.7299 (tt0) cc_final: 0.6756 (tm-30) REVERT: B 1284 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7356 (mm-30) REVERT: D 161 LYS cc_start: 0.7257 (ptmt) cc_final: 0.6497 (tptt) REVERT: D 263 ILE cc_start: 0.7226 (mp) cc_final: 0.6917 (mt) REVERT: D 278 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: D 441 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6723 (mt-10) REVERT: D 466 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6804 (tp30) REVERT: D 483 ARG cc_start: 0.6700 (mmm160) cc_final: 0.6366 (mtm180) REVERT: D 499 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7122 (tt0) REVERT: E 13 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.6128 (t80) REVERT: E 14 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7593 (mtpp) REVERT: E 86 ASP cc_start: 0.7658 (p0) cc_final: 0.7385 (p0) REVERT: E 142 ASP cc_start: 0.8037 (m-30) cc_final: 0.7596 (m-30) REVERT: E 205 GLU cc_start: 0.7453 (pm20) cc_final: 0.7191 (pm20) REVERT: E 259 GLN cc_start: 0.6529 (tp-100) cc_final: 0.5473 (mt0) REVERT: E 322 ASN cc_start: 0.7308 (t0) cc_final: 0.6793 (t0) outliers start: 61 outliers final: 20 residues processed: 251 average time/residue: 0.5917 time to fit residues: 166.1676 Evaluate side-chains 230 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 378 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 79 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1310 ASN B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN E 306 GLN E 438 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.179365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138422 restraints weight = 16889.746| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.13 r_work: 0.3381 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17305 Z= 0.147 Angle : 0.564 8.370 23519 Z= 0.299 Chirality : 0.044 0.182 2601 Planarity : 0.003 0.036 2850 Dihedral : 17.884 83.236 2766 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.21 % Allowed : 24.99 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.78 (0.19), residues: 1914 helix: 2.08 (0.18), residues: 765 sheet: 0.35 (0.26), residues: 363 loop : -1.00 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 349 TYR 0.013 0.001 TYR E 111 PHE 0.013 0.001 PHE A 176 TRP 0.007 0.001 TRP B 164 HIS 0.005 0.001 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (17305) covalent geometry : angle 0.56367 / 0.30 (23519) hydrogen bonds : bond 0.04400 / 3.71 ( 830) hydrogen bonds : angle 4.35729 / 5.22 ( 2444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 205 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6397 (tp30) REVERT: A 1 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6102 (tmm) REVERT: A 92 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7245 (mm-30) REVERT: A 184 ARG cc_start: 0.7511 (mmm160) cc_final: 0.6940 (mtp85) REVERT: A 205 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: A 208 MET cc_start: 0.6882 (mtm) cc_final: 0.6489 (tmt) REVERT: A 1108 MET cc_start: 0.6674 (mmm) cc_final: 0.6145 (tmm) REVERT: A 1235 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8335 (t) REVERT: A 1239 ARG cc_start: 0.7906 (ptm-80) cc_final: 0.7586 (ptm-80) REVERT: A 1271 GLU cc_start: 0.8012 (tt0) cc_final: 0.7482 (tp30) REVERT: A 1275 GLU cc_start: 0.7155 (tp30) cc_final: 0.6903 (mm-30) REVERT: A 1288 ARG cc_start: 0.8595 (ttp-170) cc_final: 0.7692 (ttm110) REVERT: A 1290 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7754 (tptp) REVERT: B 92 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7617 (mm-30) REVERT: B 108 LYS cc_start: 0.7429 (mttt) cc_final: 0.7139 (ttpp) REVERT: B 194 GLN cc_start: 0.7520 (tp-100) cc_final: 0.7150 (mt0) REVERT: B 1117 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7473 (p) REVERT: B 1159 ASP cc_start: 0.7255 (m-30) cc_final: 0.7025 (m-30) REVERT: B 1223 LEU cc_start: 0.8155 (tp) cc_final: 0.7588 (mp) REVERT: B 1247 HIS cc_start: 0.7984 (m-70) cc_final: 0.7570 (t70) REVERT: B 1284 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7411 (mm-30) REVERT: D 112 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: D 263 ILE cc_start: 0.7294 (mp) cc_final: 0.6968 (mt) REVERT: D 278 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: D 441 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: D 466 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6840 (tp30) REVERT: D 483 ARG cc_start: 0.6755 (mmm160) cc_final: 0.6399 (mtm180) REVERT: D 499 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7041 (tt0) REVERT: E 13 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.6104 (t80) REVERT: E 86 ASP cc_start: 0.7644 (p0) cc_final: 0.7374 (p0) REVERT: E 142 ASP cc_start: 0.8097 (m-30) cc_final: 0.7650 (m-30) REVERT: E 205 GLU cc_start: 0.7457 (pm20) cc_final: 0.7190 (pm20) REVERT: E 259 GLN cc_start: 0.6491 (tp-100) cc_final: 0.5443 (mt0) REVERT: E 322 ASN cc_start: 0.7308 (t0) cc_final: 0.6770 (t0) outliers start: 74 outliers final: 33 residues processed: 257 average time/residue: 0.6214 time to fit residues: 178.3228 Evaluate side-chains 242 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 154 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 177 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1295 GLN ** A1310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN E 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.176835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134850 restraints weight = 16750.241| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.07 r_work: 0.3355 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17305 Z= 0.223 Angle : 0.645 11.120 23519 Z= 0.336 Chirality : 0.047 0.213 2601 Planarity : 0.004 0.041 2850 Dihedral : 17.992 89.143 2766 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.50 % Allowed : 24.82 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.56 (0.19), residues: 1914 helix: 1.85 (0.18), residues: 765 sheet: 0.31 (0.26), residues: 365 loop : -1.11 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 87 TYR 0.031 0.002 TYR E 111 PHE 0.020 0.002 PHE A 176 TRP 0.009 0.002 TRP B 164 HIS 0.006 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (17305) covalent geometry : angle 0.64545 / 0.34 (23519) hydrogen bonds : bond 0.05307 / 4.41 ( 830) hydrogen bonds : angle 4.47094 / 5.38 ( 2444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 204 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6257 (tp30) REVERT: A 1 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6196 (tmm) REVERT: A 184 ARG cc_start: 0.7564 (mmm160) cc_final: 0.6988 (mtp85) REVERT: A 205 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6886 (tp30) REVERT: A 208 MET cc_start: 0.6990 (mtm) cc_final: 0.6378 (tmt) REVERT: A 212 TYR cc_start: 0.6514 (m-80) cc_final: 0.6118 (m-80) REVERT: A 1108 MET cc_start: 0.6786 (mmm) cc_final: 0.6202 (tmm) REVERT: A 1235 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8461 (t) REVERT: A 1239 ARG cc_start: 0.7956 (ptm-80) cc_final: 0.7669 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7991 (tt0) cc_final: 0.7496 (tp30) REVERT: A 1279 ARG cc_start: 0.5657 (OUTLIER) cc_final: 0.5397 (mtp180) REVERT: A 1288 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.7669 (ttm110) REVERT: A 1290 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7783 (tptp) REVERT: B 92 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7593 (mm-30) REVERT: B 108 LYS cc_start: 0.7462 (mttt) cc_final: 0.7079 (ttpp) REVERT: B 194 GLN cc_start: 0.7588 (tp-100) cc_final: 0.7194 (mt0) REVERT: B 209 GLU cc_start: 0.7084 (tp30) cc_final: 0.6708 (mm-30) REVERT: B 1117 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7520 (p) REVERT: B 1223 LEU cc_start: 0.8118 (tp) cc_final: 0.7542 (mp) REVERT: B 1247 HIS cc_start: 0.7982 (m-70) cc_final: 0.7579 (t70) REVERT: B 1284 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7453 (mm-30) REVERT: D 112 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: D 263 ILE cc_start: 0.7405 (mp) cc_final: 0.7035 (mt) REVERT: D 278 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: D 441 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: D 466 GLU cc_start: 0.7632 (mt-10) cc_final: 0.6829 (tp30) REVERT: D 483 ARG cc_start: 0.6752 (mmm160) cc_final: 0.6378 (mtm180) REVERT: D 499 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7109 (tt0) REVERT: E 86 ASP cc_start: 0.7663 (p0) cc_final: 0.7407 (p0) REVERT: E 94 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7109 (pp) REVERT: E 142 ASP cc_start: 0.8248 (m-30) cc_final: 0.7859 (m-30) REVERT: E 205 GLU cc_start: 0.7441 (pm20) cc_final: 0.7192 (pm20) REVERT: E 259 GLN cc_start: 0.6577 (tp-100) cc_final: 0.5527 (mt0) REVERT: E 292 ARG cc_start: 0.7423 (mmp-170) cc_final: 0.7195 (mmp-170) REVERT: E 322 ASN cc_start: 0.7300 (t0) cc_final: 0.6790 (t0) outliers start: 79 outliers final: 43 residues processed: 260 average time/residue: 0.6367 time to fit residues: 184.6602 Evaluate side-chains 249 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1284 GLU Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 243 TRP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 47 optimal weight: 0.0270 chunk 110 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1310 ASN B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN E 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.180302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138060 restraints weight = 16653.048| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.98 r_work: 0.3399 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17305 Z= 0.122 Angle : 0.553 8.784 23519 Z= 0.293 Chirality : 0.043 0.175 2601 Planarity : 0.003 0.036 2850 Dihedral : 17.861 92.657 2766 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.13 % Allowed : 26.12 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.80 (0.19), residues: 1914 helix: 2.13 (0.18), residues: 766 sheet: 0.32 (0.26), residues: 365 loop : -1.00 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 349 TYR 0.029 0.002 TYR E 111 PHE 0.014 0.001 PHE D 484 TRP 0.010 0.001 TRP B 164 HIS 0.005 0.001 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17305) covalent geometry : angle 0.55282 / 0.29 (23519) hydrogen bonds : bond 0.04041 / 3.44 ( 830) hydrogen bonds : angle 4.28021 / 5.12 ( 2444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 205 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6398 (tp30) REVERT: A 1 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6092 (tmm) REVERT: A 92 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7501 (mm-30) REVERT: A 184 ARG cc_start: 0.7550 (mmm160) cc_final: 0.6987 (mtp85) REVERT: A 205 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6861 (tp30) REVERT: A 208 MET cc_start: 0.6984 (mtm) cc_final: 0.6417 (tmt) REVERT: A 212 TYR cc_start: 0.6641 (m-80) cc_final: 0.6335 (m-80) REVERT: A 1108 MET cc_start: 0.6695 (mmm) cc_final: 0.6148 (tmm) REVERT: A 1235 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8356 (t) REVERT: A 1239 ARG cc_start: 0.7864 (ptm-80) cc_final: 0.7584 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7978 (tt0) cc_final: 0.7450 (tp30) REVERT: A 1288 ARG cc_start: 0.8567 (ttp-110) cc_final: 0.7697 (ttm110) REVERT: A 1290 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7712 (tptp) REVERT: B 92 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7632 (mm-30) REVERT: B 108 LYS cc_start: 0.7445 (mttt) cc_final: 0.7120 (ttpp) REVERT: B 194 GLN cc_start: 0.7509 (tp-100) cc_final: 0.7155 (mt0) REVERT: B 1108 MET cc_start: 0.7524 (ttp) cc_final: 0.7227 (tmt) REVERT: B 1117 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7525 (p) REVERT: B 1223 LEU cc_start: 0.8132 (tp) cc_final: 0.7578 (mp) REVERT: B 1247 HIS cc_start: 0.7911 (m-70) cc_final: 0.7582 (t70) REVERT: B 1284 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7365 (mm-30) REVERT: D 205 GLU cc_start: 0.6620 (mp0) cc_final: 0.5786 (pp20) REVERT: D 263 ILE cc_start: 0.7319 (mp) cc_final: 0.6966 (mt) REVERT: D 278 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7214 (mt-10) REVERT: D 431 ASP cc_start: 0.8076 (t70) cc_final: 0.7730 (t70) REVERT: D 441 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6675 (mt-10) REVERT: D 466 GLU cc_start: 0.7627 (mt-10) cc_final: 0.6823 (tp30) REVERT: D 483 ARG cc_start: 0.6750 (mmm160) cc_final: 0.6391 (mtm180) REVERT: D 499 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7066 (tt0) REVERT: E 13 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.6047 (t80) REVERT: E 14 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7564 (mtpp) REVERT: E 27 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: E 86 ASP cc_start: 0.7691 (p0) cc_final: 0.7460 (p0) REVERT: E 94 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7163 (pp) REVERT: E 105 LYS cc_start: 0.6891 (mppt) cc_final: 0.6577 (mmtm) REVERT: E 142 ASP cc_start: 0.8124 (m-30) cc_final: 0.7684 (m-30) REVERT: E 205 GLU cc_start: 0.7457 (pm20) cc_final: 0.7203 (pm20) REVERT: E 259 GLN cc_start: 0.6485 (tp-100) cc_final: 0.5436 (mt0) REVERT: E 322 ASN cc_start: 0.7289 (t0) cc_final: 0.6770 (t0) REVERT: E 370 SER cc_start: 0.7772 (OUTLIER) cc_final: 0.7534 (m) outliers start: 55 outliers final: 23 residues processed: 247 average time/residue: 0.6747 time to fit residues: 185.4508 Evaluate side-chains 229 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 370 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 172 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1310 ASN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN E 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.180312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.140143 restraints weight = 16982.324| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.11 r_work: 0.3400 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17305 Z= 0.126 Angle : 0.547 8.206 23519 Z= 0.290 Chirality : 0.043 0.215 2601 Planarity : 0.003 0.051 2850 Dihedral : 17.653 91.845 2766 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.19 % Allowed : 26.35 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.92 (0.19), residues: 1914 helix: 2.25 (0.18), residues: 765 sheet: 0.37 (0.26), residues: 361 loop : -0.96 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 349 TYR 0.025 0.001 TYR E 111 PHE 0.012 0.001 PHE A1135 TRP 0.009 0.001 TRP B 164 HIS 0.005 0.001 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (17305) covalent geometry : angle 0.54737 / 0.29 (23519) hydrogen bonds : bond 0.04050 / 3.43 ( 830) hydrogen bonds : angle 4.20424 / 5.01 ( 2444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6397 (tp30) REVERT: A 1 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6009 (tmm) REVERT: A 92 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7391 (mm-30) REVERT: A 184 ARG cc_start: 0.7523 (mmm160) cc_final: 0.6939 (mtp85) REVERT: A 205 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6842 (tp30) REVERT: A 208 MET cc_start: 0.6934 (mtm) cc_final: 0.6410 (tmt) REVERT: A 212 TYR cc_start: 0.6626 (m-80) cc_final: 0.6352 (m-80) REVERT: A 1107 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.6227 (mtt) REVERT: A 1239 ARG cc_start: 0.7858 (ptm-80) cc_final: 0.7585 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7981 (tt0) cc_final: 0.7427 (tp30) REVERT: A 1288 ARG cc_start: 0.8563 (ttp-110) cc_final: 0.7684 (ttm110) REVERT: A 1290 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7685 (tptp) REVERT: B 92 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7640 (mm-30) REVERT: B 108 LYS cc_start: 0.7413 (mttt) cc_final: 0.7050 (ttpt) REVERT: B 194 GLN cc_start: 0.7501 (tp-100) cc_final: 0.7143 (mt0) REVERT: B 1108 MET cc_start: 0.7505 (ttp) cc_final: 0.7176 (tmt) REVERT: B 1117 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7504 (p) REVERT: B 1223 LEU cc_start: 0.8144 (tp) cc_final: 0.7591 (mp) REVERT: B 1247 HIS cc_start: 0.7947 (m-70) cc_final: 0.7552 (t70) REVERT: B 1270 ASP cc_start: 0.8796 (t70) cc_final: 0.8561 (t0) REVERT: B 1284 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7361 (mm-30) REVERT: D 205 GLU cc_start: 0.6711 (mp0) cc_final: 0.5825 (pp20) REVERT: D 263 ILE cc_start: 0.7300 (mp) cc_final: 0.6965 (mt) REVERT: D 278 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: D 431 ASP cc_start: 0.8061 (t70) cc_final: 0.7704 (t70) REVERT: D 441 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: D 456 GLU cc_start: 0.7284 (pt0) cc_final: 0.6519 (tp30) REVERT: D 466 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6839 (tp30) REVERT: D 483 ARG cc_start: 0.6729 (mmm160) cc_final: 0.6391 (mtm180) REVERT: D 499 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7038 (tt0) REVERT: E 13 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.6011 (t80) REVERT: E 14 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7509 (mtpp) REVERT: E 86 ASP cc_start: 0.7687 (p0) cc_final: 0.7466 (p0) REVERT: E 94 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7254 (pp) REVERT: E 105 LYS cc_start: 0.6815 (mppt) cc_final: 0.6544 (mmtm) REVERT: E 142 ASP cc_start: 0.8093 (m-30) cc_final: 0.7615 (m-30) REVERT: E 157 MET cc_start: 0.7789 (mpp) cc_final: 0.7456 (mpp) REVERT: E 205 GLU cc_start: 0.7492 (pm20) cc_final: 0.7258 (pm20) REVERT: E 259 GLN cc_start: 0.6572 (tp-100) cc_final: 0.5496 (mt0) REVERT: E 322 ASN cc_start: 0.7266 (t0) cc_final: 0.6763 (t0) REVERT: E 370 SER cc_start: 0.7732 (OUTLIER) cc_final: 0.7522 (m) outliers start: 56 outliers final: 26 residues processed: 251 average time/residue: 0.6412 time to fit residues: 179.7986 Evaluate side-chains 239 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1107 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 386 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 167 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 477 GLN E 306 GLN E 401 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.174756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132477 restraints weight = 16883.000| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.12 r_work: 0.3323 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 17305 Z= 0.335 Angle : 0.763 13.339 23519 Z= 0.390 Chirality : 0.052 0.293 2601 Planarity : 0.005 0.067 2850 Dihedral : 17.976 99.194 2766 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.93 % Allowed : 25.84 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.30 (0.18), residues: 1914 helix: 1.49 (0.18), residues: 776 sheet: 0.28 (0.26), residues: 368 loop : -1.20 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1198 TYR 0.020 0.003 TYR A 206 PHE 0.027 0.003 PHE A 176 TRP 0.012 0.002 TRP B 164 HIS 0.008 0.002 HIS E 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.34 (17305) covalent geometry : angle 0.76253 / 0.39 (23519) hydrogen bonds : bond 0.06400 / 5.22 ( 830) hydrogen bonds : angle 4.57779 / 5.51 ( 2444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 206 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6286 (tp30) REVERT: A 1 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6281 (tmm) REVERT: A 184 ARG cc_start: 0.7651 (mmm160) cc_final: 0.7064 (mtp85) REVERT: A 205 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: A 208 MET cc_start: 0.7024 (mtm) cc_final: 0.6436 (tmt) REVERT: A 212 TYR cc_start: 0.6713 (m-80) cc_final: 0.6416 (m-80) REVERT: A 1126 LYS cc_start: 0.7785 (ttpt) cc_final: 0.7404 (tttp) REVERT: A 1235 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8514 (t) REVERT: A 1239 ARG cc_start: 0.8005 (ptm-80) cc_final: 0.7764 (ptm-80) REVERT: A 1271 GLU cc_start: 0.8034 (tt0) cc_final: 0.7524 (tp30) REVERT: A 1279 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.5353 (mtp180) REVERT: A 1288 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.7672 (ttm110) REVERT: A 1290 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7851 (tptp) REVERT: B 92 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7621 (mm-30) REVERT: B 110 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: B 194 GLN cc_start: 0.7648 (tp-100) cc_final: 0.7220 (mt0) REVERT: B 209 GLU cc_start: 0.7082 (tp30) cc_final: 0.6692 (mm-30) REVERT: B 1117 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7476 (p) REVERT: B 1223 LEU cc_start: 0.8106 (tp) cc_final: 0.7527 (mp) REVERT: B 1247 HIS cc_start: 0.8008 (m-70) cc_final: 0.7597 (t70) REVERT: B 1284 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7474 (mm-30) REVERT: D 205 GLU cc_start: 0.6648 (mp0) cc_final: 0.5890 (pp20) REVERT: D 263 ILE cc_start: 0.7510 (mp) cc_final: 0.7093 (mt) REVERT: D 278 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: D 431 ASP cc_start: 0.8067 (t70) cc_final: 0.7734 (t70) REVERT: D 441 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: D 456 GLU cc_start: 0.7337 (pt0) cc_final: 0.6549 (tp30) REVERT: D 466 GLU cc_start: 0.7693 (mt-10) cc_final: 0.6891 (tp30) REVERT: D 483 ARG cc_start: 0.6820 (mmm160) cc_final: 0.6487 (mtm180) REVERT: D 499 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7065 (tt0) REVERT: E 94 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7166 (pp) REVERT: E 105 LYS cc_start: 0.6851 (mppt) cc_final: 0.6638 (mmtm) REVERT: E 142 ASP cc_start: 0.8272 (m-30) cc_final: 0.7902 (m-30) REVERT: E 259 GLN cc_start: 0.6494 (tp-100) cc_final: 0.5426 (mt0) REVERT: E 322 ASN cc_start: 0.7324 (t0) cc_final: 0.6809 (t0) REVERT: E 370 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7635 (m) REVERT: E 464 LYS cc_start: 0.7598 (mmtt) cc_final: 0.7051 (mttm) outliers start: 69 outliers final: 33 residues processed: 253 average time/residue: 0.6348 time to fit residues: 179.2222 Evaluate side-chains 242 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 58 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1310 ASN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 438 GLN E 306 GLN E 401 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.178627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137908 restraints weight = 16790.251| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.08 r_work: 0.3381 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17305 Z= 0.137 Angle : 0.595 10.134 23519 Z= 0.313 Chirality : 0.044 0.295 2601 Planarity : 0.003 0.036 2850 Dihedral : 17.904 99.883 2766 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.22 % Allowed : 27.83 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.67 (0.19), residues: 1914 helix: 1.99 (0.18), residues: 766 sheet: 0.28 (0.26), residues: 367 loop : -1.06 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 400 TYR 0.024 0.002 TYR A 206 PHE 0.027 0.001 PHE E 399 TRP 0.009 0.001 TRP B 164 HIS 0.013 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (17305) covalent geometry : angle 0.59538 / 0.31 (23519) hydrogen bonds : bond 0.04247 / 3.61 ( 830) hydrogen bonds : angle 4.31675 / 5.19 ( 2444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6372 (tp30) REVERT: A 1 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6105 (tmm) REVERT: A 92 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7490 (mm-30) REVERT: A 184 ARG cc_start: 0.7572 (mmm160) cc_final: 0.6984 (mtp85) REVERT: A 205 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6868 (tp30) REVERT: A 208 MET cc_start: 0.7030 (mtm) cc_final: 0.6429 (tmt) REVERT: A 212 TYR cc_start: 0.6627 (m-80) cc_final: 0.6341 (m-80) REVERT: A 1108 MET cc_start: 0.6830 (mmm) cc_final: 0.6258 (tmm) REVERT: A 1235 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8377 (t) REVERT: A 1239 ARG cc_start: 0.7903 (ptm-80) cc_final: 0.7663 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7979 (tt0) cc_final: 0.7445 (tp30) REVERT: A 1279 ARG cc_start: 0.5607 (OUTLIER) cc_final: 0.5207 (mtp180) REVERT: A 1288 ARG cc_start: 0.8561 (ttp-110) cc_final: 0.7682 (ttm110) REVERT: A 1290 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7759 (tptp) REVERT: B 92 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7631 (mm-30) REVERT: B 108 LYS cc_start: 0.7420 (mttt) cc_final: 0.7141 (ttpt) REVERT: B 194 GLN cc_start: 0.7508 (tp-100) cc_final: 0.7122 (mt0) REVERT: B 1108 MET cc_start: 0.7560 (ttp) cc_final: 0.6537 (tmt) REVERT: B 1117 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7495 (p) REVERT: B 1189 LEU cc_start: 0.7670 (mp) cc_final: 0.7373 (tt) REVERT: B 1223 LEU cc_start: 0.8085 (tp) cc_final: 0.7527 (mp) REVERT: B 1247 HIS cc_start: 0.7953 (m-70) cc_final: 0.7510 (t70) REVERT: B 1284 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7356 (mm-30) REVERT: D 205 GLU cc_start: 0.6596 (mp0) cc_final: 0.5846 (pp20) REVERT: D 263 ILE cc_start: 0.7375 (mp) cc_final: 0.6979 (mt) REVERT: D 278 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7923 (mm-30) REVERT: D 377 SER cc_start: 0.7631 (OUTLIER) cc_final: 0.6969 (p) REVERT: D 431 ASP cc_start: 0.8068 (t70) cc_final: 0.7741 (t70) REVERT: D 441 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6691 (mt-10) REVERT: D 456 GLU cc_start: 0.7244 (pt0) cc_final: 0.6504 (tp30) REVERT: D 466 GLU cc_start: 0.7692 (mt-10) cc_final: 0.6827 (tp30) REVERT: D 483 ARG cc_start: 0.6770 (mmm160) cc_final: 0.6411 (mtm180) REVERT: D 499 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7035 (tt0) REVERT: E 94 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7228 (pp) REVERT: E 105 LYS cc_start: 0.6811 (mppt) cc_final: 0.6587 (mmtm) REVERT: E 142 ASP cc_start: 0.8148 (m-30) cc_final: 0.7704 (m-30) REVERT: E 157 MET cc_start: 0.7782 (mpp) cc_final: 0.7440 (mpp) REVERT: E 205 GLU cc_start: 0.7685 (pp20) cc_final: 0.7204 (pt0) REVERT: E 259 GLN cc_start: 0.6539 (tp-100) cc_final: 0.5464 (mt0) REVERT: E 322 ASN cc_start: 0.7271 (t0) cc_final: 0.6764 (t0) REVERT: E 370 SER cc_start: 0.7794 (OUTLIER) cc_final: 0.7535 (m) outliers start: 39 outliers final: 19 residues processed: 237 average time/residue: 0.6547 time to fit residues: 172.7171 Evaluate side-chains 231 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 386 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 4 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 125 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 ASN B 104 GLN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 438 GLN E 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.177254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135951 restraints weight = 16855.202| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.09 r_work: 0.3361 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17305 Z= 0.191 Angle : 0.623 10.362 23519 Z= 0.325 Chirality : 0.046 0.305 2601 Planarity : 0.004 0.036 2850 Dihedral : 17.803 99.574 2766 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.39 % Allowed : 27.89 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.64 (0.19), residues: 1914 helix: 1.96 (0.18), residues: 765 sheet: 0.29 (0.26), residues: 367 loop : -1.09 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 349 TYR 0.023 0.002 TYR A 206 PHE 0.017 0.002 PHE A 176 TRP 0.009 0.001 TRP B1151 HIS 0.005 0.001 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (17305) covalent geometry : angle 0.62250 / 0.33 (23519) hydrogen bonds : bond 0.04741 / 3.98 ( 830) hydrogen bonds : angle 4.32728 / 5.20 ( 2444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7896.39 seconds wall clock time: 135 minutes 3.13 seconds (8103.13 seconds total)