Starting phenix.real_space_refine on Sat Jul 4 01:14:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9k_52962/07_2026/9q9k_52962.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9k_52962/07_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_52962/07_2026/9q9k_52962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9k_52962/07_2026/9q9k_52962.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q9k_52962/07_2026/9q9k_52962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9k_52962/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.11, per 1000 atoms: 0.24 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: 1.40 Conformation dependent library (CDL) restraints added in 854.4 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: 2.28 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: 3.36 Time building geometry restraints manager: 1.89 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: 22746 2.46 - 4.92: 641 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.600 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.080 ------------------------------------------------------------------------------- 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 : 0.946 12.312 23519 Z= 0.620 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 0.94554 / 0.62 (23519) hydrogen bonds : bond 0.16224 / 14.69 ( 830) hydrogen bonds : angle 6.69071 / 8.17 ( 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 : 0.662 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: 0.6733 time to fit residues: 193.5357 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 : 0.634 ------------------------------------------------------------------------------- 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: 3.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 443 ASN D 477 GLN E 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.180236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138014 restraints weight = 16597.215| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.06 r_work: 0.3403 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17305 Z= 0.160 Angle : 0.611 7.865 23519 Z= 0.326 Chirality : 0.045 0.230 2601 Planarity : 0.004 0.092 2850 Dihedral : 18.586 80.216 2800 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.10 % Allowed : 23.56 % Favored : 72.34 % 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: 1.85 (0.19), residues: 764 sheet: 0.28 (0.26), residues: 363 loop : -1.14 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 488 TYR 0.024 0.002 TYR B 212 PHE 0.013 0.002 PHE E 54 TRP 0.007 0.001 TRP B 164 HIS 0.007 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (17305) covalent geometry : angle 0.61134 / 0.33 (23519) hydrogen bonds : bond 0.04891 / 4.20 ( 830) hydrogen bonds : angle 4.83693 / 5.86 ( 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 299 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 227 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6348 (tp30) REVERT: K 473 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.6125 (mt0) REVERT: A 1 MET cc_start: 0.6989 (tmm) cc_final: 0.6268 (tmm) REVERT: A 92 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7264 (mm-30) REVERT: A 208 MET cc_start: 0.7110 (mtm) cc_final: 0.6493 (tmt) REVERT: A 1108 MET cc_start: 0.6723 (mmm) cc_final: 0.6175 (tmm) REVERT: A 1239 ARG cc_start: 0.7631 (ttt-90) cc_final: 0.7393 (ptm160) REVERT: A 1243 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7400 (mp0) REVERT: A 1271 GLU cc_start: 0.7905 (tt0) cc_final: 0.7356 (tp30) REVERT: A 1275 GLU cc_start: 0.7252 (tp30) cc_final: 0.7032 (mm-30) REVERT: A 1288 ARG cc_start: 0.8653 (ttp-170) cc_final: 0.7691 (ttp-170) REVERT: A 1290 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7684 (tptp) REVERT: B 92 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7591 (mm-30) REVERT: B 108 LYS cc_start: 0.7365 (mttt) cc_final: 0.7055 (ttpp) REVERT: B 135 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: B 194 GLN cc_start: 0.7554 (tp-100) cc_final: 0.7158 (mt0) REVERT: B 1117 VAL cc_start: 0.7753 (t) cc_final: 0.7448 (p) REVERT: B 1223 LEU cc_start: 0.8120 (tp) cc_final: 0.7557 (mp) REVERT: B 1247 HIS cc_start: 0.7910 (m-70) cc_final: 0.7541 (t70) REVERT: B 1275 GLU cc_start: 0.7197 (tt0) cc_final: 0.6585 (tm-30) REVERT: B 1284 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7381 (mm-30) REVERT: D 161 LYS cc_start: 0.7229 (ptmt) cc_final: 0.6552 (tptt) REVERT: D 200 MET cc_start: 0.7673 (mtt) cc_final: 0.7460 (mtp) REVERT: D 263 ILE cc_start: 0.7290 (mp) cc_final: 0.7017 (mt) REVERT: D 441 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6702 (mt-10) REVERT: D 466 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6744 (tp30) REVERT: D 483 ARG cc_start: 0.6642 (mmm160) cc_final: 0.6299 (mtm180) REVERT: D 499 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7151 (tt0) REVERT: D 503 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6576 (ttt-90) REVERT: E 86 ASP cc_start: 0.7657 (p0) cc_final: 0.7375 (p0) REVERT: E 94 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7055 (pp) REVERT: E 142 ASP cc_start: 0.8104 (m-30) cc_final: 0.7723 (m-30) REVERT: E 205 GLU cc_start: 0.7436 (pm20) cc_final: 0.7181 (pm20) REVERT: E 259 GLN cc_start: 0.6512 (tp-100) cc_final: 0.5534 (mt0) REVERT: E 292 ARG cc_start: 0.7542 (mmm160) cc_final: 0.6814 (mmt180) REVERT: E 310 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6384 (mm-30) REVERT: E 322 ASN cc_start: 0.7231 (t0) cc_final: 0.6817 (t0) REVERT: E 349 ARG cc_start: 0.7089 (mtm110) cc_final: 0.6779 (mtp-110) REVERT: E 488 ARG cc_start: 0.5793 (ttp80) cc_final: 0.5262 (tmt170) outliers start: 72 outliers final: 15 residues processed: 282 average time/residue: 0.5992 time to fit residues: 188.6080 Evaluate side-chains 231 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 473 GLN 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 136 ASP Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain D residue 503 ARG 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: 0.0070 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 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 = 0.4116 r_free = 0.4116 target = 0.178212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136770 restraints weight = 16959.649| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.16 r_work: 0.3366 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1102 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 : 0.611 8.820 23519 Z= 0.323 Chirality : 0.046 0.199 2601 Planarity : 0.004 0.037 2850 Dihedral : 18.205 81.520 2768 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.50 % Allowed : 23.68 % Favored : 71.83 % 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: 0.52 (0.19), residues: 1914 helix: 1.81 (0.18), residues: 765 sheet: 0.32 (0.26), residues: 366 loop : -1.15 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 503 TYR 0.019 0.002 TYR B 212 PHE 0.016 0.002 PHE B 176 TRP 0.008 0.002 TRP B 164 HIS 0.007 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (17305) covalent geometry : angle 0.61113 / 0.32 (23519) hydrogen bonds : bond 0.05192 / 4.34 ( 830) hydrogen bonds : angle 4.63634 / 5.60 ( 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 293 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 214 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6315 (tp30) REVERT: K 473 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.6131 (mt0) REVERT: A 1 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6295 (tmm) REVERT: A 92 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7328 (mm-30) REVERT: A 167 SER cc_start: 0.8006 (OUTLIER) cc_final: 0.7732 (p) REVERT: A 184 ARG cc_start: 0.7563 (mmm160) cc_final: 0.6990 (mtp85) REVERT: A 208 MET cc_start: 0.6970 (mtm) cc_final: 0.6529 (tmt) REVERT: A 1108 MET cc_start: 0.6745 (mmm) cc_final: 0.6143 (tmm) REVERT: A 1235 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8386 (t) REVERT: A 1271 GLU cc_start: 0.7981 (tt0) cc_final: 0.7459 (tp30) REVERT: A 1275 GLU cc_start: 0.7237 (tp30) cc_final: 0.7018 (mm-30) REVERT: A 1288 ARG cc_start: 0.8631 (ttp-170) cc_final: 0.7680 (ttp-170) REVERT: A 1290 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7785 (tptp) REVERT: B 92 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7622 (mm-30) REVERT: B 108 LYS cc_start: 0.7419 (mttt) cc_final: 0.7126 (ttpp) REVERT: B 135 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: B 194 GLN cc_start: 0.7599 (tp-100) cc_final: 0.7210 (mt0) REVERT: B 209 GLU cc_start: 0.7091 (tp30) cc_final: 0.6836 (mm-30) REVERT: B 1117 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7462 (p) REVERT: B 1223 LEU cc_start: 0.8140 (tp) cc_final: 0.7586 (mp) REVERT: B 1247 HIS cc_start: 0.8003 (m-70) cc_final: 0.7590 (t70) REVERT: B 1284 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7424 (mm-30) REVERT: D 161 LYS cc_start: 0.7335 (ptmt) cc_final: 0.6650 (tptt) REVERT: D 205 GLU cc_start: 0.6650 (mp0) cc_final: 0.5804 (pp20) REVERT: D 263 ILE cc_start: 0.7279 (mp) cc_final: 0.6947 (mt) REVERT: D 278 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: D 365 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7907 (tt) REVERT: D 441 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: D 466 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6826 (tp30) REVERT: D 483 ARG cc_start: 0.6706 (mmm160) cc_final: 0.6367 (mtm180) REVERT: D 499 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7058 (mm-30) REVERT: E 86 ASP cc_start: 0.7592 (p0) cc_final: 0.7331 (p0) REVERT: E 142 ASP cc_start: 0.8144 (m-30) cc_final: 0.7761 (m-30) REVERT: E 205 GLU cc_start: 0.7432 (pm20) cc_final: 0.7097 (pp20) REVERT: E 259 GLN cc_start: 0.6485 (tp-100) cc_final: 0.5489 (mt0) REVERT: E 322 ASN cc_start: 0.7313 (t0) cc_final: 0.6775 (t0) REVERT: E 349 ARG cc_start: 0.7126 (mtm110) cc_final: 0.6748 (mtp-110) REVERT: E 488 ARG cc_start: 0.5901 (ttp80) cc_final: 0.5379 (tmt-80) outliers start: 79 outliers final: 30 residues processed: 268 average time/residue: 0.5724 time to fit residues: 171.4430 Evaluate side-chains 244 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 K residue 473 GLN 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 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 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 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 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 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: 10.0000 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 245 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 = 0.4122 r_free = 0.4122 target = 0.178798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137341 restraints weight = 16875.484| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.08 r_work: 0.3386 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17305 Z= 0.164 Angle : 0.582 9.061 23519 Z= 0.308 Chirality : 0.045 0.194 2601 Planarity : 0.004 0.036 2850 Dihedral : 18.141 85.565 2768 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.27 % Allowed : 23.85 % Favored : 71.88 % 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: 0.62 (0.19), residues: 1914 helix: 1.92 (0.18), residues: 765 sheet: 0.33 (0.26), residues: 365 loop : -1.10 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 120 TYR 0.029 0.002 TYR B 212 PHE 0.013 0.001 PHE A 176 TRP 0.008 0.001 TRP B 164 HIS 0.006 0.001 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (17305) covalent geometry : angle 0.58157 / 0.31 (23519) hydrogen bonds : bond 0.04562 / 3.86 ( 830) hydrogen bonds : angle 4.46302 / 5.38 ( 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 289 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 214 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6372 (tp30) REVERT: K 473 GLN cc_start: 0.6408 (OUTLIER) cc_final: 0.6150 (mt0) REVERT: A 1 MET cc_start: 0.6978 (tmm) cc_final: 0.6212 (tmm) REVERT: A 92 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7288 (mm-30) REVERT: A 167 SER cc_start: 0.7934 (OUTLIER) cc_final: 0.7686 (p) REVERT: A 184 ARG cc_start: 0.7535 (mmm160) cc_final: 0.6961 (mtp85) REVERT: A 205 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6865 (tp30) REVERT: A 208 MET cc_start: 0.6999 (mtm) cc_final: 0.6399 (tmt) REVERT: A 1108 MET cc_start: 0.6720 (mmm) cc_final: 0.6138 (tmm) REVERT: A 1235 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8369 (t) REVERT: A 1271 GLU cc_start: 0.7961 (tt0) cc_final: 0.7443 (tp30) REVERT: A 1275 GLU cc_start: 0.7158 (tp30) cc_final: 0.6947 (mm-30) REVERT: A 1288 ARG cc_start: 0.8600 (ttp-170) cc_final: 0.7667 (ttm110) REVERT: A 1290 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7736 (tptp) REVERT: B 92 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7595 (mm-30) REVERT: B 108 LYS cc_start: 0.7432 (mttt) cc_final: 0.7137 (ttpp) REVERT: B 194 GLN cc_start: 0.7545 (tp-100) cc_final: 0.7156 (mt0) REVERT: B 1117 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7446 (p) REVERT: B 1223 LEU cc_start: 0.8141 (tp) cc_final: 0.7570 (mp) REVERT: B 1247 HIS cc_start: 0.7976 (m-70) cc_final: 0.7567 (t70) REVERT: B 1284 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7392 (mm-30) REVERT: D 112 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: D 205 GLU cc_start: 0.6650 (mp0) cc_final: 0.5852 (pp20) REVERT: D 263 ILE cc_start: 0.7261 (mp) cc_final: 0.6934 (mt) REVERT: D 278 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: D 365 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7872 (tt) REVERT: D 441 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6708 (mt-10) REVERT: D 466 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6822 (tp30) REVERT: D 483 ARG cc_start: 0.6703 (mmm160) cc_final: 0.6364 (mtm180) REVERT: D 499 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7113 (tt0) REVERT: E 14 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7601 (mtpp) REVERT: E 86 ASP cc_start: 0.7656 (p0) cc_final: 0.7389 (p0) REVERT: E 142 ASP cc_start: 0.8068 (m-30) cc_final: 0.7669 (m-30) REVERT: E 205 GLU cc_start: 0.7450 (pm20) cc_final: 0.7182 (pm20) REVERT: E 259 GLN cc_start: 0.6529 (tp-100) cc_final: 0.5493 (mt0) REVERT: E 322 ASN cc_start: 0.7325 (t0) cc_final: 0.6793 (t0) outliers start: 75 outliers final: 34 residues processed: 266 average time/residue: 0.5683 time to fit residues: 168.7364 Evaluate side-chains 248 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 461 GLU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 473 GLN 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 205 GLU Chi-restraints excluded: chain A residue 1212 ILE 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 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 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 112 GLN Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 365 LEU 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 14 LYS Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 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 378 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 458 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: 3.9990 chunk 71 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 0.0060 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- 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 245 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 = 0.4125 r_free = 0.4125 target = 0.179158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.136915 restraints weight = 16825.344| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.12 r_work: 0.3394 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17305 Z= 0.154 Angle : 0.570 9.494 23519 Z= 0.302 Chirality : 0.044 0.180 2601 Planarity : 0.003 0.036 2850 Dihedral : 18.006 85.921 2767 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.61 % Allowed : 24.30 % Favored : 71.09 % 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: 0.70 (0.19), residues: 1914 helix: 2.01 (0.18), residues: 765 sheet: 0.33 (0.26), residues: 365 loop : -1.05 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 87 TYR 0.011 0.001 TYR E 111 PHE 0.013 0.001 PHE B 176 TRP 0.008 0.001 TRP B 164 HIS 0.005 0.001 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (17305) covalent geometry : angle 0.56954 / 0.30 (23519) hydrogen bonds : bond 0.04435 / 3.73 ( 830) hydrogen bonds : angle 4.38130 / 5.26 ( 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 288 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 207 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6398 (tp30) REVERT: K 473 GLN cc_start: 0.6362 (OUTLIER) cc_final: 0.6116 (mt0) REVERT: A 1 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6110 (tmm) REVERT: A 92 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7240 (mm-30) REVERT: A 167 SER cc_start: 0.7926 (OUTLIER) cc_final: 0.7691 (p) REVERT: A 184 ARG cc_start: 0.7517 (mmm160) cc_final: 0.6949 (mtp85) REVERT: A 205 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6843 (tp30) REVERT: A 208 MET cc_start: 0.6876 (mtm) cc_final: 0.6460 (tmt) REVERT: A 1108 MET cc_start: 0.6689 (mmm) cc_final: 0.6142 (tmm) REVERT: A 1235 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8345 (t) REVERT: A 1271 GLU cc_start: 0.8003 (tt0) cc_final: 0.7487 (tp30) REVERT: A 1275 GLU cc_start: 0.7156 (tp30) cc_final: 0.6898 (mm-30) REVERT: A 1288 ARG cc_start: 0.8565 (ttp-170) cc_final: 0.7657 (ttm110) REVERT: A 1290 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7745 (tptp) REVERT: B 92 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7601 (mm-30) REVERT: B 108 LYS cc_start: 0.7427 (mttt) cc_final: 0.7107 (ttpp) REVERT: B 194 GLN cc_start: 0.7517 (tp-100) cc_final: 0.7126 (mt0) REVERT: B 1117 VAL cc_start: 0.7771 (OUTLIER) cc_final: 0.7469 (p) REVERT: B 1223 LEU cc_start: 0.8127 (tp) cc_final: 0.7558 (mp) REVERT: B 1247 HIS cc_start: 0.7955 (m-70) cc_final: 0.7542 (t70) REVERT: B 1284 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7372 (mm-30) REVERT: D 112 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: D 205 GLU cc_start: 0.6746 (mp0) cc_final: 0.5838 (pp20) REVERT: D 263 ILE cc_start: 0.7291 (mp) cc_final: 0.6946 (mt) REVERT: D 278 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: D 441 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6680 (mt-10) REVERT: D 466 GLU cc_start: 0.7626 (mt-10) cc_final: 0.6832 (tp30) REVERT: D 483 ARG cc_start: 0.6706 (mmm160) cc_final: 0.6354 (mtm180) REVERT: D 499 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7105 (tt0) REVERT: E 86 ASP cc_start: 0.7628 (p0) cc_final: 0.7370 (p0) REVERT: E 142 ASP cc_start: 0.8098 (m-30) cc_final: 0.7680 (m-30) REVERT: E 205 GLU cc_start: 0.7441 (pm20) cc_final: 0.7167 (pm20) REVERT: E 259 GLN cc_start: 0.6464 (tp-100) cc_final: 0.5393 (mt0) REVERT: E 292 ARG cc_start: 0.7433 (mmt180) cc_final: 0.7202 (mmp-170) REVERT: E 322 ASN cc_start: 0.7280 (t0) cc_final: 0.6743 (t0) outliers start: 81 outliers final: 40 residues processed: 266 average time/residue: 0.5409 time to fit residues: 161.0093 Evaluate side-chains 250 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 K residue 473 GLN 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 167 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1212 ILE 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 154 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 86 optimal weight: 0.0670 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1295 GLN ** A1310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 477 GLN E 170 GLN E 245 HIS E 306 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.174390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132074 restraints weight = 16822.840| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.13 r_work: 0.3321 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 17305 Z= 0.353 Angle : 0.752 13.631 23519 Z= 0.390 Chirality : 0.052 0.247 2601 Planarity : 0.005 0.062 2850 Dihedral : 18.266 94.147 2766 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.41 % Allowed : 23.68 % Favored : 70.92 % 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: 0.16 (0.18), residues: 1914 helix: 1.37 (0.18), residues: 770 sheet: 0.25 (0.26), residues: 368 loop : -1.26 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 13 TYR 0.023 0.003 TYR E 111 PHE 0.023 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 0.00823 / 0.35 (17305) covalent geometry : angle 0.75215 / 0.39 (23519) hydrogen bonds : bond 0.06577 / 5.34 ( 830) hydrogen bonds : angle 4.63649 / 5.61 ( 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 295 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 200 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6320 (tp30) REVERT: A 1 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6268 (tmm) REVERT: A 167 SER cc_start: 0.8047 (OUTLIER) cc_final: 0.7665 (p) REVERT: A 205 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6931 (tp30) REVERT: A 208 MET cc_start: 0.7021 (mtm) cc_final: 0.6382 (tmt) REVERT: A 212 TYR cc_start: 0.6573 (m-80) cc_final: 0.6167 (m-80) REVERT: A 1108 MET cc_start: 0.6895 (mmm) cc_final: 0.6246 (tmm) REVERT: A 1126 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7335 (tttm) REVERT: A 1235 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8517 (t) REVERT: A 1239 ARG cc_start: 0.8036 (ptm-80) cc_final: 0.7796 (ptm-80) REVERT: A 1271 GLU cc_start: 0.8051 (tt0) cc_final: 0.7564 (tp30) REVERT: A 1279 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.5487 (mtp180) REVERT: A 1288 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.7689 (ttm110) REVERT: A 1290 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7835 (tptp) REVERT: B 10 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8710 (tp) REVERT: B 92 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7632 (mm-30) REVERT: B 108 LYS cc_start: 0.7472 (mttt) cc_final: 0.7066 (ttpp) REVERT: B 110 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: B 194 GLN cc_start: 0.7679 (tp-100) cc_final: 0.7260 (mt0) REVERT: B 209 GLU cc_start: 0.7080 (tp30) cc_final: 0.6759 (mm-30) REVERT: B 1117 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7474 (p) REVERT: B 1223 LEU cc_start: 0.8148 (tp) cc_final: 0.7568 (mp) REVERT: B 1247 HIS cc_start: 0.8013 (m-70) cc_final: 0.7618 (t70) REVERT: B 1284 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7476 (mm-30) REVERT: D 112 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: D 263 ILE cc_start: 0.7442 (mp) cc_final: 0.7014 (mt) REVERT: D 278 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7989 (mm-30) REVERT: D 350 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6862 (mt-10) REVERT: D 431 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7716 (t70) REVERT: D 441 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: D 466 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6832 (tp30) REVERT: D 483 ARG cc_start: 0.6768 (mmm160) cc_final: 0.6416 (mtm180) REVERT: D 499 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7068 (mm-30) REVERT: E 86 ASP cc_start: 0.7646 (p0) cc_final: 0.7422 (p0) REVERT: E 142 ASP cc_start: 0.8268 (m-30) cc_final: 0.7927 (m-30) REVERT: E 205 GLU cc_start: 0.7384 (pm20) cc_final: 0.7172 (pp20) REVERT: E 259 GLN cc_start: 0.6588 (tp-100) cc_final: 0.5508 (mt0) REVERT: E 322 ASN cc_start: 0.7327 (t0) cc_final: 0.6820 (t0) REVERT: E 370 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7619 (m) outliers start: 95 outliers final: 43 residues processed: 273 average time/residue: 0.6089 time to fit residues: 185.1634 Evaluate side-chains 250 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 131 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 203 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 1290 LYS Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 110 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 215 GLN 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 112 GLN 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 327 LYS Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 431 ASP 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 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 199 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 370 SER Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 386 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: 3.9990 chunk 110 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 473 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.179066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137318 restraints weight = 16625.221| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.07 r_work: 0.3392 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17305 Z= 0.137 Angle : 0.573 9.466 23519 Z= 0.305 Chirality : 0.044 0.193 2601 Planarity : 0.003 0.036 2850 Dihedral : 18.102 96.746 2766 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.53 % Allowed : 25.73 % 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: 0.57 (0.19), residues: 1914 helix: 1.91 (0.18), residues: 766 sheet: 0.21 (0.26), residues: 365 loop : -1.11 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 349 TYR 0.033 0.002 TYR E 111 PHE 0.012 0.001 PHE B 27 TRP 0.010 0.001 TRP B 164 HIS 0.005 0.001 HIS E 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (17305) covalent geometry : angle 0.57313 / 0.30 (23519) hydrogen bonds : bond 0.04269 / 3.63 ( 830) hydrogen bonds : angle 4.33258 / 5.21 ( 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 266 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 204 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6354 (tp30) REVERT: A 1 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6118 (tmm) REVERT: A 92 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7529 (mm-30) REVERT: A 184 ARG cc_start: 0.7569 (mmm160) cc_final: 0.7009 (mtp85) REVERT: A 205 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6880 (tp30) REVERT: A 208 MET cc_start: 0.7012 (mtm) cc_final: 0.6363 (tmt) REVERT: A 212 TYR cc_start: 0.6659 (m-80) cc_final: 0.6339 (m-80) REVERT: A 1126 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7292 (tttm) REVERT: A 1235 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8391 (t) REVERT: A 1239 ARG cc_start: 0.7892 (ptm-80) cc_final: 0.7652 (ptm-80) REVERT: A 1271 GLU cc_start: 0.8004 (tt0) cc_final: 0.7440 (tp30) REVERT: A 1279 ARG cc_start: 0.5594 (OUTLIER) cc_final: 0.5299 (mtp180) REVERT: A 1288 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.7689 (ttm110) REVERT: A 1290 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7763 (tptp) REVERT: B 92 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7585 (mm-30) REVERT: B 108 LYS cc_start: 0.7450 (mttt) cc_final: 0.7040 (ttpp) REVERT: B 194 GLN cc_start: 0.7497 (tp-100) cc_final: 0.7091 (mt0) REVERT: B 1117 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7498 (p) REVERT: B 1223 LEU cc_start: 0.8095 (tp) cc_final: 0.7529 (mp) REVERT: B 1247 HIS cc_start: 0.7908 (m-70) cc_final: 0.7544 (t70) REVERT: B 1284 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7347 (mm-30) REVERT: D 112 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: D 263 ILE cc_start: 0.7374 (mp) cc_final: 0.6980 (mt) REVERT: D 278 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: D 350 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: D 377 SER cc_start: 0.7523 (OUTLIER) cc_final: 0.6865 (p) REVERT: D 431 ASP cc_start: 0.8042 (t70) cc_final: 0.7704 (t70) REVERT: D 441 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6682 (mt-10) REVERT: D 466 GLU cc_start: 0.7636 (mt-10) cc_final: 0.6834 (tp30) REVERT: D 483 ARG cc_start: 0.6783 (mmm160) cc_final: 0.6449 (mtm180) REVERT: D 499 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7010 (tt0) REVERT: E 14 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7558 (mtpp) REVERT: E 86 ASP cc_start: 0.7663 (p0) cc_final: 0.7438 (p0) REVERT: E 94 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7169 (pp) REVERT: E 142 ASP cc_start: 0.8142 (m-30) cc_final: 0.7723 (m-30) REVERT: E 259 GLN cc_start: 0.6505 (tp-100) cc_final: 0.5419 (mt0) REVERT: E 322 ASN cc_start: 0.7266 (t0) cc_final: 0.6757 (t0) outliers start: 62 outliers final: 30 residues processed: 252 average time/residue: 0.6283 time to fit residues: 176.7987 Evaluate side-chains 241 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 92 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1212 ILE 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 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 112 GLN 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 327 LYS Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 377 SER 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 172 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 169 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1310 ASN B 104 GLN D 73 HIS ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4116 r_free = 0.4116 target = 0.178259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137072 restraints weight = 16940.620| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.06 r_work: 0.3380 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17305 Z= 0.160 Angle : 0.586 9.819 23519 Z= 0.310 Chirality : 0.045 0.240 2601 Planarity : 0.004 0.035 2850 Dihedral : 17.983 97.923 2766 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.47 % Allowed : 26.29 % 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: 0.64 (0.19), residues: 1914 helix: 1.98 (0.18), residues: 765 sheet: 0.22 (0.26), residues: 366 loop : -1.07 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 349 TYR 0.028 0.002 TYR E 111 PHE 0.013 0.001 PHE A 176 TRP 0.008 0.001 TRP B 164 HIS 0.005 0.001 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (17305) covalent geometry : angle 0.58600 / 0.31 (23519) hydrogen bonds : bond 0.04478 / 3.76 ( 830) hydrogen bonds : angle 4.30724 / 5.18 ( 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 259 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 198 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6369 (tp30) REVERT: A 1 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6130 (tmm) REVERT: A 92 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7554 (mm-30) REVERT: A 184 ARG cc_start: 0.7570 (mmm160) cc_final: 0.6990 (mtp85) REVERT: A 205 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6889 (tp30) REVERT: A 208 MET cc_start: 0.6998 (mtm) cc_final: 0.6401 (tmt) REVERT: A 212 TYR cc_start: 0.6661 (m-80) cc_final: 0.6391 (m-80) REVERT: A 1108 MET cc_start: 0.6778 (mmm) cc_final: 0.6168 (tmm) REVERT: A 1235 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8380 (t) REVERT: A 1239 ARG cc_start: 0.7904 (ptm-80) cc_final: 0.7678 (ptm-80) REVERT: A 1271 GLU cc_start: 0.8002 (tt0) cc_final: 0.7459 (tp30) REVERT: A 1288 ARG cc_start: 0.8560 (ttp-110) cc_final: 0.7682 (ttm110) REVERT: A 1290 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7771 (tptp) REVERT: B 92 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7593 (mm-30) REVERT: B 108 LYS cc_start: 0.7421 (mttt) cc_final: 0.7031 (ttpp) REVERT: B 194 GLN cc_start: 0.7493 (tp-100) cc_final: 0.7111 (mt0) REVERT: B 1108 MET cc_start: 0.7575 (ttp) cc_final: 0.7328 (tmt) REVERT: B 1117 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7512 (p) REVERT: B 1168 ASP cc_start: 0.7889 (m-30) cc_final: 0.7681 (m-30) REVERT: B 1223 LEU cc_start: 0.8125 (tp) cc_final: 0.7563 (mp) REVERT: B 1247 HIS cc_start: 0.7955 (m-70) cc_final: 0.7562 (t70) REVERT: B 1270 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8329 (t70) REVERT: B 1284 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7388 (mm-30) REVERT: D 93 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6818 (mt) REVERT: D 112 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: D 263 ILE cc_start: 0.7382 (mp) cc_final: 0.7018 (mt) REVERT: D 278 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: D 377 SER cc_start: 0.7636 (OUTLIER) cc_final: 0.6915 (p) REVERT: D 431 ASP cc_start: 0.8044 (t70) cc_final: 0.7704 (t70) REVERT: D 441 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6706 (mt-10) REVERT: D 466 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6858 (tp30) REVERT: D 483 ARG cc_start: 0.6782 (mmm160) cc_final: 0.6434 (mtm180) REVERT: E 86 ASP cc_start: 0.7683 (p0) cc_final: 0.7472 (p0) REVERT: E 94 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7166 (pp) REVERT: E 142 ASP cc_start: 0.8182 (m-30) cc_final: 0.7747 (m-30) REVERT: E 205 GLU cc_start: 0.7690 (pp20) cc_final: 0.7438 (pm20) REVERT: E 259 GLN cc_start: 0.6563 (tp-100) cc_final: 0.5543 (mt0) REVERT: E 322 ASN cc_start: 0.7288 (t0) cc_final: 0.6787 (t0) REVERT: E 370 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7618 (m) outliers start: 61 outliers final: 32 residues processed: 244 average time/residue: 0.5788 time to fit residues: 157.6386 Evaluate side-chains 243 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 92 GLU 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 1212 ILE 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 B residue 1270 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 VAL 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 186 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 243 TRP Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 377 SER 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 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 370 SER Chi-restraints excluded: chain E residue 378 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 167 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN E 306 GLN E 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.175322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133361 restraints weight = 16917.514| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.11 r_work: 0.3342 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17305 Z= 0.279 Angle : 0.690 12.401 23519 Z= 0.359 Chirality : 0.049 0.281 2601 Planarity : 0.005 0.051 2850 Dihedral : 18.120 101.224 2766 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.98 % Allowed : 25.95 % Favored : 70.06 % 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: 0.31 (0.18), residues: 1914 helix: 1.56 (0.18), residues: 777 sheet: 0.19 (0.26), residues: 366 loop : -1.21 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 13 TYR 0.025 0.002 TYR A 206 PHE 0.021 0.002 PHE A 176 TRP 0.010 0.002 TRP B 164 HIS 0.007 0.002 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.28 (17305) covalent geometry : angle 0.69015 / 0.36 (23519) hydrogen bonds : bond 0.05677 / 4.68 ( 830) hydrogen bonds : angle 4.47534 / 5.40 ( 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 273 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 203 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6277 (tp30) REVERT: A 1 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6214 (tmm) REVERT: A 92 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7648 (mm-30) REVERT: A 184 ARG cc_start: 0.7661 (mmm160) cc_final: 0.7074 (mtp85) REVERT: A 205 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: A 208 MET cc_start: 0.6983 (mtm) cc_final: 0.6354 (tmt) REVERT: A 212 TYR cc_start: 0.6678 (m-80) cc_final: 0.6416 (m-80) REVERT: A 1108 MET cc_start: 0.6901 (mmm) cc_final: 0.6257 (tmm) REVERT: A 1126 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7415 (tttp) REVERT: A 1235 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8485 (t) REVERT: A 1239 ARG cc_start: 0.7950 (ptm-80) cc_final: 0.7730 (ptm-80) REVERT: A 1271 GLU cc_start: 0.8017 (tt0) cc_final: 0.7501 (tp30) REVERT: A 1279 ARG cc_start: 0.5666 (OUTLIER) cc_final: 0.5310 (mtp180) REVERT: A 1288 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.7695 (ttm110) REVERT: A 1290 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7823 (tptp) REVERT: B 92 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7584 (mm-30) REVERT: B 108 LYS cc_start: 0.7465 (mttt) cc_final: 0.6990 (ttpp) REVERT: B 110 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7257 (tp30) REVERT: B 194 GLN cc_start: 0.7599 (tp-100) cc_final: 0.7200 (mt0) REVERT: B 209 GLU cc_start: 0.7065 (tp30) cc_final: 0.6742 (mm-30) REVERT: B 1108 MET cc_start: 0.7578 (ttp) cc_final: 0.7306 (tmt) REVERT: B 1117 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7505 (p) REVERT: B 1168 ASP cc_start: 0.7933 (m-30) cc_final: 0.7700 (m-30) REVERT: B 1189 LEU cc_start: 0.7734 (mp) cc_final: 0.7477 (tt) REVERT: B 1223 LEU cc_start: 0.8140 (tp) cc_final: 0.7561 (mp) REVERT: B 1247 HIS cc_start: 0.7991 (m-70) cc_final: 0.7605 (t70) REVERT: B 1284 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7463 (mm-30) REVERT: D 112 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: D 263 ILE cc_start: 0.7492 (mp) cc_final: 0.7063 (mt) REVERT: D 278 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: D 431 ASP cc_start: 0.8046 (t70) cc_final: 0.7715 (t70) REVERT: D 441 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: D 456 GLU cc_start: 0.7326 (pt0) cc_final: 0.6494 (tp30) REVERT: D 466 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6866 (tp30) REVERT: D 483 ARG cc_start: 0.6798 (mmm160) cc_final: 0.6479 (mtm180) REVERT: E 14 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7598 (mtpp) REVERT: E 94 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7139 (pp) REVERT: E 105 LYS cc_start: 0.6886 (mppt) cc_final: 0.6595 (mmpt) REVERT: E 142 ASP cc_start: 0.8245 (m-30) cc_final: 0.7868 (m-30) REVERT: E 259 GLN cc_start: 0.6517 (tp-100) cc_final: 0.5464 (mt0) REVERT: E 294 MET cc_start: 0.7731 (tpt) cc_final: 0.7389 (tpp) REVERT: E 322 ASN cc_start: 0.7293 (t0) cc_final: 0.6789 (t0) REVERT: E 330 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6704 (mm-40) REVERT: E 370 SER cc_start: 0.7962 (OUTLIER) cc_final: 0.7678 (m) outliers start: 70 outliers final: 35 residues processed: 251 average time/residue: 0.6113 time to fit residues: 171.1739 Evaluate side-chains 245 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J 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 92 GLU 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 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 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 1117 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 112 GLN 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 359 GLU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 441 GLU 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 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 289 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 352 LEU 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 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: 0.8980 chunk 110 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 295 ASN D 438 GLN E 306 GLN E 401 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.178371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136445 restraints weight = 16664.776| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.07 r_work: 0.3385 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17305 Z= 0.148 Angle : 0.601 9.921 23519 Z= 0.317 Chirality : 0.045 0.291 2601 Planarity : 0.003 0.036 2850 Dihedral : 18.052 101.119 2766 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.13 % Allowed : 26.98 % Favored : 69.89 % 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: 0.57 (0.19), residues: 1914 helix: 1.92 (0.18), residues: 766 sheet: 0.19 (0.26), residues: 366 loop : -1.11 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 400 TYR 0.024 0.002 TYR A 206 PHE 0.022 0.001 PHE E 399 TRP 0.010 0.001 TRP B 164 HIS 0.016 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (17305) covalent geometry : angle 0.60114 / 0.32 (23519) hydrogen bonds : bond 0.04368 / 3.69 ( 830) hydrogen bonds : angle 4.32077 / 5.20 ( 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 255 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6349 (tp30) REVERT: A 1 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6127 (tmm) REVERT: A 184 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7023 (mtp85) REVERT: A 205 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6881 (tp30) REVERT: A 208 MET cc_start: 0.7001 (mtm) cc_final: 0.6354 (tmt) REVERT: A 212 TYR cc_start: 0.6650 (m-80) cc_final: 0.6348 (m-80) REVERT: A 1108 MET cc_start: 0.6853 (mmm) cc_final: 0.6219 (tmm) REVERT: A 1126 LYS cc_start: 0.7734 (ttpt) cc_final: 0.7356 (tttp) REVERT: A 1235 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8411 (t) REVERT: A 1239 ARG cc_start: 0.7887 (ptm-80) cc_final: 0.7676 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7963 (tt0) cc_final: 0.7431 (tp30) REVERT: A 1279 ARG cc_start: 0.5584 (OUTLIER) cc_final: 0.5180 (mtp180) REVERT: A 1288 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.7667 (ttm110) REVERT: A 1290 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7751 (tptp) REVERT: B 92 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7582 (mm-30) REVERT: B 108 LYS cc_start: 0.7417 (mttt) cc_final: 0.6973 (ttpp) REVERT: B 194 GLN cc_start: 0.7472 (tp-100) cc_final: 0.7089 (mt0) REVERT: B 1108 MET cc_start: 0.7553 (ttp) cc_final: 0.7264 (tmt) REVERT: B 1117 VAL cc_start: 0.7788 (OUTLIER) cc_final: 0.7483 (p) REVERT: B 1168 ASP cc_start: 0.7884 (m-30) cc_final: 0.7671 (m-30) REVERT: B 1189 LEU cc_start: 0.7679 (mp) cc_final: 0.7394 (tt) REVERT: B 1223 LEU cc_start: 0.8100 (tp) cc_final: 0.7535 (mp) REVERT: B 1247 HIS cc_start: 0.7962 (m-70) cc_final: 0.7545 (t70) REVERT: B 1284 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7315 (mm-30) REVERT: D 112 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: D 260 LEU cc_start: 0.7806 (mp) cc_final: 0.7505 (mt) REVERT: D 263 ILE cc_start: 0.7453 (mp) cc_final: 0.7051 (mt) REVERT: D 278 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: D 377 SER cc_start: 0.7478 (OUTLIER) cc_final: 0.6871 (p) REVERT: D 431 ASP cc_start: 0.8049 (t70) cc_final: 0.7716 (t70) REVERT: D 441 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6744 (mt-10) REVERT: D 456 GLU cc_start: 0.7276 (pt0) cc_final: 0.6472 (tp30) REVERT: D 466 GLU cc_start: 0.7650 (mt-10) cc_final: 0.6821 (tp30) REVERT: D 483 ARG cc_start: 0.6790 (mmm160) cc_final: 0.6463 (mtm180) REVERT: E 14 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7548 (mtpp) REVERT: E 94 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7152 (pp) REVERT: E 105 LYS cc_start: 0.6863 (mppt) cc_final: 0.6570 (mmpt) REVERT: E 142 ASP cc_start: 0.8150 (m-30) cc_final: 0.7730 (m-30) REVERT: E 205 GLU cc_start: 0.7601 (pp20) cc_final: 0.7258 (pt0) REVERT: E 259 GLN cc_start: 0.6533 (tp-100) cc_final: 0.5490 (mt0) REVERT: E 322 ASN cc_start: 0.7258 (t0) cc_final: 0.6756 (t0) REVERT: E 330 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6658 (mm-40) REVERT: E 370 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7613 (m) outliers start: 55 outliers final: 30 residues processed: 241 average time/residue: 0.6133 time to fit residues: 164.5193 Evaluate side-chains 243 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1212 ILE 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 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 1117 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 112 GLN 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 359 GLU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 441 GLU 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 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 330 GLN Chi-restraints excluded: chain E residue 352 LEU 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 401 HIS 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: 4.9990 chunk 154 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN E 306 GLN E 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.177044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.135767 restraints weight = 16862.066| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.06 r_work: 0.3364 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17305 Z= 0.199 Angle : 0.623 10.331 23519 Z= 0.328 Chirality : 0.046 0.314 2601 Planarity : 0.004 0.037 2850 Dihedral : 18.004 100.795 2766 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.30 % Allowed : 26.92 % Favored : 69.78 % 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: 0.51 (0.19), residues: 1914 helix: 1.86 (0.18), residues: 765 sheet: 0.19 (0.26), residues: 367 loop : -1.15 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 349 TYR 0.026 0.002 TYR A 206 PHE 0.016 0.002 PHE A 176 TRP 0.008 0.001 TRP B 164 HIS 0.008 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (17305) covalent geometry : angle 0.62349 / 0.33 (23519) hydrogen bonds : bond 0.04778 / 4.00 ( 830) hydrogen bonds : angle 4.33898 / 5.22 ( 2444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7192.98 seconds wall clock time: 123 minutes 3.99 seconds (7383.99 seconds total)