Starting phenix.real_space_refine on Thu Feb 5 12:00:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9k_52962/02_2026/9q9k_52962.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9k_52962/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9q9k_52962/02_2026/9q9k_52962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9k_52962/02_2026/9q9k_52962.map" model { file = "/net/cci-nas-00/data/ceres_data/9q9k_52962/02_2026/9q9k_52962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9k_52962/02_2026/9q9k_52962.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16910 Number of models: 1 Model: "" Number of chains: 16 Chain: "J" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 141 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "K" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 145 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "P" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3820 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 463} Chain breaks: 1 Chain: "B" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3815 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 463} Chain breaks: 1 Chain: "D" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3909 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 20, 'TRANS': 458} Chain breaks: 1 Chain: "E" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3899 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 20, 'TRANS': 457} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.39, per 1000 atoms: 0.20 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: 1.52 Conformation dependent library (CDL) restraints added in 641.2 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: 1.76 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: 2.56 Time building geometry restraints manager: 1.96 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: 22798 2.46 - 4.92: 590 4.92 - 7.39: 103 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 - 0.126: 2502 0.126 - 0.252: 78 0.252 - 0.378: 3 0.378 - 0.504: 13 0.504 - 0.630: 5 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 2.35 -2.98 -0.63 2.00e-01 2.50e+01 9.91e+00 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 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.45e+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 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.90e+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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.410 Find NCS groups from input model: 0.310 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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= 0.355 Angle : 0.931 12.312 23519 Z= 0.572 Chirality : 0.068 0.630 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 covalent geometry : bond 0.00571 (17305) covalent geometry : angle 0.93131 (23519) hydrogen bonds : bond 0.16224 ( 830) hydrogen bonds : angle 6.69071 ( 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 : 0.646 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: 0.6262 time to fit residues: 179.3586 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 : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1268 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 458 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B1172 ASN D 245 HIS ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 443 ASN E 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.179022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138267 restraints weight = 16781.023| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.04 r_work: 0.3398 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17305 Z= 0.164 Angle : 0.574 7.414 23519 Z= 0.311 Chirality : 0.043 0.167 2601 Planarity : 0.004 0.046 2850 Dihedral : 18.358 81.919 2800 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.93 % Allowed : 23.51 % Favored : 72.57 % 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: 0.55 (0.19), residues: 1914 helix: 1.86 (0.19), residues: 765 sheet: 0.29 (0.27), residues: 364 loop : -1.12 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 502 TYR 0.021 0.002 TYR B 212 PHE 0.012 0.001 PHE E 54 TRP 0.009 0.001 TRP D 210 HIS 0.006 0.001 HIS E 283 Details of bonding type rmsd covalent geometry : bond 0.00369 (17305) covalent geometry : angle 0.57355 (23519) hydrogen bonds : bond 0.04719 ( 830) hydrogen bonds : angle 4.75996 ( 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 298 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 229 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6333 (tp30) REVERT: K 473 GLN cc_start: 0.6368 (OUTLIER) cc_final: 0.6160 (mt0) REVERT: A 1 MET cc_start: 0.6962 (tmm) cc_final: 0.6251 (tmm) REVERT: A 92 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7264 (mm-30) REVERT: A 208 MET cc_start: 0.7076 (mtm) cc_final: 0.6730 (tmt) REVERT: A 1108 MET cc_start: 0.6761 (mmm) cc_final: 0.6244 (tmm) REVERT: A 1239 ARG cc_start: 0.7638 (ttt-90) cc_final: 0.7407 (ptm160) REVERT: A 1243 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7380 (mp0) REVERT: A 1271 GLU cc_start: 0.7968 (tt0) cc_final: 0.7449 (tp30) REVERT: A 1275 GLU cc_start: 0.7216 (tp30) cc_final: 0.6995 (mm-30) REVERT: A 1288 ARG cc_start: 0.8638 (ttp-170) cc_final: 0.7696 (ttp-170) REVERT: A 1290 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7699 (tptp) REVERT: B 92 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7592 (mm-30) REVERT: B 108 LYS cc_start: 0.7410 (mttt) cc_final: 0.7145 (ttpp) REVERT: B 110 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7594 (tp30) REVERT: B 135 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: B 194 GLN cc_start: 0.7558 (tp-100) cc_final: 0.7175 (mt0) REVERT: B 1117 VAL cc_start: 0.7761 (t) cc_final: 0.7456 (p) REVERT: B 1223 LEU cc_start: 0.8156 (tp) cc_final: 0.7589 (mp) REVERT: B 1247 HIS cc_start: 0.7916 (m-70) cc_final: 0.7555 (t70) REVERT: B 1270 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8335 (t70) REVERT: B 1275 GLU cc_start: 0.7232 (tt0) cc_final: 0.6632 (tm-30) REVERT: B 1284 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7351 (mm-30) REVERT: D 161 LYS cc_start: 0.7281 (ptmt) cc_final: 0.6612 (tptt) REVERT: D 263 ILE cc_start: 0.7298 (mp) cc_final: 0.7021 (mt) REVERT: D 434 LYS cc_start: 0.7644 (mtmm) cc_final: 0.7431 (ttmt) REVERT: D 441 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: D 466 GLU cc_start: 0.7594 (mt-10) cc_final: 0.6830 (tp30) REVERT: D 483 ARG cc_start: 0.6657 (mmm160) cc_final: 0.6349 (mtm180) REVERT: D 499 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7142 (tt0) REVERT: E 86 ASP cc_start: 0.7638 (p0) cc_final: 0.7367 (p0) REVERT: E 94 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7162 (pp) REVERT: E 142 ASP cc_start: 0.8078 (m-30) cc_final: 0.7697 (m-30) REVERT: E 205 GLU cc_start: 0.7444 (pm20) cc_final: 0.7205 (pm20) REVERT: E 259 GLN cc_start: 0.6498 (tp-100) cc_final: 0.5528 (mt0) REVERT: E 322 ASN cc_start: 0.7224 (t0) cc_final: 0.6816 (t0) outliers start: 69 outliers final: 13 residues processed: 282 average time/residue: 0.5756 time to fit residues: 180.8486 Evaluate side-chains 230 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 1270 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 441 GLU 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 199 THR 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: 0.9990 chunk 157 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN D 477 GLN E 306 GLN E 325 ASN E 438 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.176786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134639 restraints weight = 16865.076| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.09 r_work: 0.3356 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17305 Z= 0.236 Angle : 0.623 9.483 23519 Z= 0.333 Chirality : 0.045 0.222 2601 Planarity : 0.004 0.038 2850 Dihedral : 17.960 78.446 2762 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.89 % Allowed : 23.39 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 1914 helix: 1.76 (0.18), residues: 765 sheet: 0.28 (0.26), residues: 365 loop : -1.16 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 488 TYR 0.018 0.002 TYR B 212 PHE 0.019 0.002 PHE A 176 TRP 0.009 0.002 TRP B 164 HIS 0.007 0.001 HIS E 283 Details of bonding type rmsd covalent geometry : bond 0.00547 (17305) covalent geometry : angle 0.62278 (23519) hydrogen bonds : bond 0.05340 ( 830) hydrogen bonds : angle 4.62119 ( 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 298 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 212 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6289 (tp30) REVERT: K 473 GLN cc_start: 0.6412 (OUTLIER) cc_final: 0.6173 (mt0) REVERT: A 1 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6335 (tmm) REVERT: A 167 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7734 (p) REVERT: A 205 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6892 (tp30) REVERT: A 208 MET cc_start: 0.7080 (mtm) cc_final: 0.6475 (tmt) REVERT: A 1108 MET cc_start: 0.6805 (mmm) cc_final: 0.6175 (tmm) REVERT: A 1126 LYS cc_start: 0.7711 (ttpt) cc_final: 0.7267 (tttm) REVERT: A 1235 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8468 (t) REVERT: A 1271 GLU cc_start: 0.7969 (tt0) cc_final: 0.7503 (tp30) REVERT: A 1288 ARG cc_start: 0.8623 (ttp-170) cc_final: 0.7713 (ttm110) REVERT: A 1290 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7819 (tptp) REVERT: B 92 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7578 (mm-30) REVERT: B 108 LYS cc_start: 0.7399 (mttt) cc_final: 0.6993 (ttpp) REVERT: B 135 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: B 194 GLN cc_start: 0.7647 (tp-100) cc_final: 0.7261 (mt0) REVERT: B 209 GLU cc_start: 0.7049 (tp30) cc_final: 0.6765 (mm-30) REVERT: B 1117 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7532 (p) REVERT: B 1223 LEU cc_start: 0.8141 (tp) cc_final: 0.7567 (mp) REVERT: B 1247 HIS cc_start: 0.8011 (m-70) cc_final: 0.7569 (t70) REVERT: B 1270 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8371 (t70) REVERT: B 1284 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7417 (mm-30) REVERT: D 205 GLU cc_start: 0.6640 (mp0) cc_final: 0.5935 (pp20) REVERT: D 263 ILE cc_start: 0.7399 (mp) cc_final: 0.7036 (mt) REVERT: D 278 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: D 431 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7693 (t70) REVERT: D 441 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: D 466 GLU cc_start: 0.7692 (mt-10) cc_final: 0.6858 (tp30) REVERT: D 483 ARG cc_start: 0.6778 (mmm160) cc_final: 0.6401 (mtm180) REVERT: D 499 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7068 (mm-30) REVERT: E 86 ASP cc_start: 0.7578 (p0) cc_final: 0.7348 (p0) REVERT: E 142 ASP cc_start: 0.8166 (m-30) cc_final: 0.7822 (m-30) REVERT: E 205 GLU cc_start: 0.7403 (pm20) cc_final: 0.7189 (pp20) REVERT: E 259 GLN cc_start: 0.6508 (tp-100) cc_final: 0.5509 (mt0) REVERT: E 310 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: E 322 ASN cc_start: 0.7294 (t0) cc_final: 0.6767 (t0) REVERT: E 488 ARG cc_start: 0.6039 (ttt-90) cc_final: 0.5600 (tmt-80) outliers start: 86 outliers final: 31 residues processed: 271 average time/residue: 0.5985 time to fit residues: 179.9181 Evaluate side-chains 242 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 459 VAL 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 183 THR 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 1284 GLU Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 76 THR 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 1117 VAL Chi-restraints excluded: chain B residue 1270 ASP 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 431 ASP Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain E residue 12 THR 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 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 458 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 170 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 112 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1310 ASN B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.178540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137427 restraints weight = 16923.540| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.06 r_work: 0.3377 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17305 Z= 0.169 Angle : 0.564 9.184 23519 Z= 0.304 Chirality : 0.043 0.200 2601 Planarity : 0.004 0.035 2850 Dihedral : 17.822 78.132 2762 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.38 % Allowed : 24.19 % Favored : 71.43 % 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: 1.95 (0.18), residues: 765 sheet: 0.31 (0.26), residues: 365 loop : -1.08 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 87 TYR 0.022 0.002 TYR B 212 PHE 0.014 0.001 PHE D 484 TRP 0.008 0.001 TRP B 164 HIS 0.005 0.001 HIS D 283 Details of bonding type rmsd covalent geometry : bond 0.00387 (17305) covalent geometry : angle 0.56416 (23519) hydrogen bonds : bond 0.04446 ( 830) hydrogen bonds : angle 4.40435 ( 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 283 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 206 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6387 (tp30) REVERT: K 473 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.6180 (mt0) REVERT: A 1 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6154 (tmm) REVERT: A 92 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7526 (mm-30) REVERT: A 167 SER cc_start: 0.7953 (OUTLIER) cc_final: 0.7710 (p) REVERT: A 205 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6898 (tp30) REVERT: A 208 MET cc_start: 0.6912 (mtm) cc_final: 0.6327 (tmt) REVERT: A 1108 MET cc_start: 0.6739 (mmm) cc_final: 0.6154 (tmm) REVERT: A 1235 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8383 (t) REVERT: A 1239 ARG cc_start: 0.7916 (ptm-80) cc_final: 0.7619 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7998 (tt0) cc_final: 0.7467 (tp30) REVERT: A 1288 ARG cc_start: 0.8564 (ttp-170) cc_final: 0.7666 (ttm110) REVERT: A 1290 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7735 (tptp) REVERT: B 92 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7606 (mm-30) REVERT: B 108 LYS cc_start: 0.7394 (mttt) cc_final: 0.7003 (ttpp) REVERT: B 110 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: B 194 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7141 (mt0) REVERT: B 212 TYR cc_start: 0.5927 (m-10) cc_final: 0.5721 (m-10) REVERT: B 1117 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7497 (p) REVERT: B 1223 LEU cc_start: 0.8141 (tp) cc_final: 0.7571 (mp) REVERT: B 1247 HIS cc_start: 0.7965 (m-70) cc_final: 0.7545 (t70) REVERT: B 1270 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8354 (t70) REVERT: B 1284 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7412 (mm-30) REVERT: D 205 GLU cc_start: 0.6764 (mp0) cc_final: 0.5929 (pp20) REVERT: D 263 ILE cc_start: 0.7364 (mp) cc_final: 0.7005 (mt) REVERT: D 278 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: D 441 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6734 (mt-10) REVERT: D 466 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6880 (tp30) REVERT: D 483 ARG cc_start: 0.6752 (mmm160) cc_final: 0.6419 (mtm180) REVERT: D 499 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7033 (mm-30) REVERT: E 14 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7554 (mtpp) REVERT: E 86 ASP cc_start: 0.7625 (p0) cc_final: 0.7410 (p0) REVERT: E 142 ASP cc_start: 0.8126 (m-30) cc_final: 0.7711 (m-30) REVERT: E 205 GLU cc_start: 0.7448 (pm20) cc_final: 0.7171 (pm20) REVERT: E 259 GLN cc_start: 0.6535 (tp-100) cc_final: 0.5527 (mt0) REVERT: E 310 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: E 322 ASN cc_start: 0.7207 (t0) cc_final: 0.6708 (t0) REVERT: E 488 ARG cc_start: 0.6027 (ttt-90) cc_final: 0.5756 (tmt-80) outliers start: 77 outliers final: 30 residues processed: 263 average time/residue: 0.5951 time to fit residues: 173.6752 Evaluate side-chains 235 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 459 VAL 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 92 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 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 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 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 136 ASP 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 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 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 386 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: 10.0000 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1310 ASN B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.179876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137795 restraints weight = 16805.757| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.04 r_work: 0.3406 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17305 Z= 0.138 Angle : 0.533 8.250 23519 Z= 0.287 Chirality : 0.042 0.183 2601 Planarity : 0.003 0.036 2850 Dihedral : 17.567 74.254 2761 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.15 % Allowed : 24.82 % Favored : 71.03 % 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: 0.83 (0.19), residues: 1914 helix: 2.14 (0.18), residues: 766 sheet: 0.37 (0.26), residues: 363 loop : -0.99 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 87 TYR 0.015 0.001 TYR A 206 PHE 0.011 0.001 PHE A1135 TRP 0.009 0.001 TRP B 164 HIS 0.005 0.001 HIS D 283 Details of bonding type rmsd covalent geometry : bond 0.00310 (17305) covalent geometry : angle 0.53262 (23519) hydrogen bonds : bond 0.04062 ( 830) hydrogen bonds : angle 4.25938 ( 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 280 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 207 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6427 (tp30) REVERT: A 1 MET cc_start: 0.6740 (tmm) cc_final: 0.6045 (tmm) REVERT: A 92 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7475 (mm-30) REVERT: A 205 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6878 (tp30) REVERT: A 208 MET cc_start: 0.6821 (mtm) cc_final: 0.6477 (tmt) REVERT: A 1108 MET cc_start: 0.6668 (mmm) cc_final: 0.6208 (tmm) REVERT: A 1235 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8333 (t) REVERT: A 1271 GLU cc_start: 0.7985 (tt0) cc_final: 0.7454 (tp30) REVERT: A 1279 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.5369 (mtp180) REVERT: A 1288 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.7703 (ttm110) REVERT: A 1290 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7713 (tptp) REVERT: B 92 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7614 (mm-30) REVERT: B 108 LYS cc_start: 0.7436 (mttt) cc_final: 0.7074 (ttpp) REVERT: B 110 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7332 (tp30) REVERT: B 194 GLN cc_start: 0.7484 (tp-100) cc_final: 0.7112 (mt0) REVERT: B 1117 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7496 (p) REVERT: B 1223 LEU cc_start: 0.8165 (tp) cc_final: 0.7615 (mp) REVERT: B 1247 HIS cc_start: 0.7935 (m-70) cc_final: 0.7577 (t70) REVERT: B 1284 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7345 (mm-30) REVERT: D 205 GLU cc_start: 0.6766 (mp0) cc_final: 0.5987 (pp20) REVERT: D 263 ILE cc_start: 0.7321 (mp) cc_final: 0.6982 (mt) REVERT: D 278 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: D 441 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6719 (mt-10) REVERT: D 456 GLU cc_start: 0.7301 (pt0) cc_final: 0.6490 (tp30) REVERT: D 466 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6880 (tp30) REVERT: D 483 ARG cc_start: 0.6762 (mmm160) cc_final: 0.6396 (mtm180) REVERT: E 27 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8362 (pt0) REVERT: E 86 ASP cc_start: 0.7667 (p0) cc_final: 0.7462 (p0) REVERT: E 142 ASP cc_start: 0.8060 (m-30) cc_final: 0.7624 (m-30) REVERT: E 205 GLU cc_start: 0.7500 (pm20) cc_final: 0.7258 (pm20) REVERT: E 259 GLN cc_start: 0.6472 (tp-100) cc_final: 0.5460 (mt0) REVERT: E 310 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: E 322 ASN cc_start: 0.7248 (t0) cc_final: 0.6764 (t0) REVERT: E 488 ARG cc_start: 0.6055 (ttt-90) cc_final: 0.5802 (tmt-80) outliers start: 73 outliers final: 34 residues processed: 264 average time/residue: 0.5655 time to fit residues: 166.3351 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 : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 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 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 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 1092 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1290 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 228 PHE 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 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 154 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 86 optimal weight: 0.0370 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1310 ASN B 104 GLN D 73 HIS ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS E 438 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.175719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133805 restraints weight = 16800.424| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.09 r_work: 0.3343 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17305 Z= 0.275 Angle : 0.653 10.337 23519 Z= 0.347 Chirality : 0.046 0.234 2601 Planarity : 0.004 0.047 2850 Dihedral : 17.778 78.248 2761 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.89 % Allowed : 24.53 % Favored : 70.57 % 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: 0.46 (0.19), residues: 1914 helix: 1.66 (0.18), residues: 777 sheet: 0.33 (0.26), residues: 368 loop : -1.12 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 364 TYR 0.015 0.002 TYR E 111 PHE 0.021 0.002 PHE A 176 TRP 0.010 0.002 TRP B 164 HIS 0.007 0.001 HIS E 283 Details of bonding type rmsd covalent geometry : bond 0.00641 (17305) covalent geometry : angle 0.65257 (23519) hydrogen bonds : bond 0.05492 ( 830) hydrogen bonds : angle 4.49634 ( 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 293 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 207 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6265 (tp30) REVERT: A 1 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6224 (tmm) REVERT: A 92 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: A 205 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6896 (tp30) REVERT: A 208 MET cc_start: 0.6974 (mtm) cc_final: 0.6484 (tmt) REVERT: A 1126 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7370 (tttm) REVERT: A 1235 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8489 (t) REVERT: A 1239 ARG cc_start: 0.7950 (ptm-80) cc_final: 0.7700 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7995 (tt0) cc_final: 0.7489 (tp30) REVERT: A 1279 ARG cc_start: 0.5679 (OUTLIER) cc_final: 0.5385 (mtp180) REVERT: A 1288 ARG cc_start: 0.8584 (ttp-110) cc_final: 0.7686 (ttm110) REVERT: A 1290 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7848 (tptp) REVERT: B 92 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7576 (mm-30) REVERT: B 108 LYS cc_start: 0.7377 (mttt) cc_final: 0.7019 (ttpt) REVERT: B 110 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: B 194 GLN cc_start: 0.7614 (tp-100) cc_final: 0.7197 (mt0) REVERT: B 1108 MET cc_start: 0.7553 (ttp) cc_final: 0.7269 (tmt) REVERT: B 1117 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7525 (p) REVERT: B 1223 LEU cc_start: 0.8129 (tp) cc_final: 0.7547 (mp) REVERT: B 1247 HIS cc_start: 0.7992 (m-70) cc_final: 0.7593 (t70) REVERT: B 1284 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7443 (mm-30) REVERT: D 112 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: D 205 GLU cc_start: 0.6815 (mp0) cc_final: 0.6048 (pp20) REVERT: D 263 ILE cc_start: 0.7483 (mp) cc_final: 0.7060 (mt) REVERT: D 278 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: D 431 ASP cc_start: 0.8043 (t70) cc_final: 0.7713 (t70) REVERT: D 441 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: D 456 GLU cc_start: 0.7364 (pt0) cc_final: 0.6520 (tp30) REVERT: D 463 ASP cc_start: 0.7848 (m-30) cc_final: 0.7513 (m-30) REVERT: D 466 GLU cc_start: 0.7666 (mt-10) cc_final: 0.6859 (tp30) REVERT: D 483 ARG cc_start: 0.6845 (mmm160) cc_final: 0.6506 (mtm180) REVERT: E 14 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7593 (mtpp) REVERT: E 142 ASP cc_start: 0.8223 (m-30) cc_final: 0.7821 (m-30) REVERT: E 259 GLN cc_start: 0.6541 (tp-100) cc_final: 0.5503 (mt0) REVERT: E 310 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: E 322 ASN cc_start: 0.7286 (t0) cc_final: 0.6784 (t0) REVERT: E 343 MET cc_start: 0.7434 (mtm) cc_final: 0.6771 (mtm) REVERT: E 464 LYS cc_start: 0.7563 (mmtt) cc_final: 0.6998 (mttm) REVERT: E 488 ARG cc_start: 0.5989 (ttt-90) cc_final: 0.5617 (tmt-80) outliers start: 86 outliers final: 39 residues processed: 270 average time/residue: 0.6273 time to fit residues: 188.2923 Evaluate side-chains 247 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 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 1117 VAL Chi-restraints excluded: chain B residue 1290 LYS 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 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 441 GLU Chi-restraints excluded: chain E residue 12 THR 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 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 228 PHE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 310 GLU 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 401 HIS 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: 6.9990 chunk 110 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1310 ASN B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN E 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.178084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137020 restraints weight = 16813.457| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.05 r_work: 0.3379 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1771 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= 0.165 Angle : 0.570 9.388 23519 Z= 0.306 Chirality : 0.043 0.218 2601 Planarity : 0.003 0.035 2850 Dihedral : 17.651 78.201 2761 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.21 % Allowed : 25.67 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1914 helix: 1.97 (0.18), residues: 766 sheet: 0.32 (0.26), residues: 365 loop : -1.07 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 400 TYR 0.022 0.002 TYR A 206 PHE 0.012 0.001 PHE A1135 TRP 0.008 0.001 TRP B 164 HIS 0.009 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00378 (17305) covalent geometry : angle 0.56970 (23519) hydrogen bonds : bond 0.04337 ( 830) hydrogen bonds : angle 4.31866 ( 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 280 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 206 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6374 (tp30) REVERT: A 1 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6123 (tmm) REVERT: A 92 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: A 205 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6876 (tp30) REVERT: A 208 MET cc_start: 0.6898 (mtm) cc_final: 0.6343 (tmt) REVERT: A 212 TYR cc_start: 0.6789 (m-80) cc_final: 0.6446 (m-80) REVERT: A 1235 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8386 (t) REVERT: A 1239 ARG cc_start: 0.7893 (ptm-80) cc_final: 0.7666 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7982 (tt0) cc_final: 0.7442 (tp30) REVERT: A 1279 ARG cc_start: 0.5603 (OUTLIER) cc_final: 0.5260 (mtp180) REVERT: A 1288 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.7674 (ttm110) REVERT: A 1290 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7737 (tptp) REVERT: B 92 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7597 (mm-30) REVERT: B 108 LYS cc_start: 0.7274 (mttt) cc_final: 0.7037 (ttpp) REVERT: B 110 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7084 (tp30) REVERT: B 194 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7139 (mt0) REVERT: B 1108 MET cc_start: 0.7564 (ttp) cc_final: 0.7243 (tmt) REVERT: B 1117 VAL cc_start: 0.7827 (OUTLIER) cc_final: 0.7522 (p) REVERT: B 1223 LEU cc_start: 0.8121 (tp) cc_final: 0.7557 (mp) REVERT: B 1247 HIS cc_start: 0.7964 (m-70) cc_final: 0.7553 (t70) REVERT: B 1270 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8357 (t70) REVERT: B 1284 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7330 (mm-30) REVERT: D 112 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: D 205 GLU cc_start: 0.6779 (mp0) cc_final: 0.6103 (pp20) REVERT: D 263 ILE cc_start: 0.7466 (mp) cc_final: 0.7070 (mt) REVERT: D 278 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: D 431 ASP cc_start: 0.8011 (t70) cc_final: 0.7705 (t70) REVERT: D 441 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6734 (mt-10) REVERT: D 456 GLU cc_start: 0.7274 (pt0) cc_final: 0.6504 (tp30) REVERT: D 463 ASP cc_start: 0.7889 (m-30) cc_final: 0.7602 (m-30) REVERT: D 466 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6875 (tp30) REVERT: D 483 ARG cc_start: 0.6828 (mmm160) cc_final: 0.6497 (mtm180) REVERT: E 14 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7545 (mtpp) REVERT: E 105 LYS cc_start: 0.6766 (mppt) cc_final: 0.6457 (mmtm) REVERT: E 142 ASP cc_start: 0.8176 (m-30) cc_final: 0.7731 (m-30) REVERT: E 205 GLU cc_start: 0.7787 (pp20) cc_final: 0.7515 (pm20) REVERT: E 259 GLN cc_start: 0.6506 (tp-100) cc_final: 0.5441 (mt0) REVERT: E 310 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: E 322 ASN cc_start: 0.7258 (t0) cc_final: 0.6752 (t0) REVERT: E 330 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6705 (mm-40) REVERT: E 488 ARG cc_start: 0.5975 (ttt-90) cc_final: 0.5608 (tmt-80) outliers start: 74 outliers final: 38 residues processed: 257 average time/residue: 0.6265 time to fit residues: 179.2035 Evaluate side-chains 254 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 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 1172 ASN 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 76 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1270 ASP Chi-restraints excluded: chain B residue 1290 LYS 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 186 ASP 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 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 84 MET Chi-restraints excluded: chain E residue 90 GLN 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 228 PHE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 330 GLN 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 401 HIS Chi-restraints excluded: chain E residue 458 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: 0.7980 chunk 129 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.177216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135911 restraints weight = 17031.333| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.09 r_work: 0.3370 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17305 Z= 0.190 Angle : 0.592 10.094 23519 Z= 0.316 Chirality : 0.044 0.251 2601 Planarity : 0.004 0.036 2850 Dihedral : 17.637 77.501 2761 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.81 % Allowed : 26.41 % 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: 0.65 (0.19), residues: 1914 helix: 1.96 (0.18), residues: 765 sheet: 0.33 (0.26), residues: 365 loop : -1.09 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 400 TYR 0.027 0.002 TYR E 111 PHE 0.015 0.002 PHE B 176 TRP 0.007 0.001 TRP B 164 HIS 0.011 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00440 (17305) covalent geometry : angle 0.59165 (23519) hydrogen bonds : bond 0.04614 ( 830) hydrogen bonds : angle 4.33428 ( 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 270 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 203 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6367 (tp30) REVERT: A 1 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6144 (tmm) REVERT: A 92 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: A 205 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6870 (tp30) REVERT: A 208 MET cc_start: 0.6895 (mtm) cc_final: 0.6333 (tmt) REVERT: A 212 TYR cc_start: 0.6765 (m-80) cc_final: 0.6407 (m-80) REVERT: A 1235 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8395 (t) REVERT: A 1239 ARG cc_start: 0.7894 (ptm-80) cc_final: 0.7671 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7985 (tt0) cc_final: 0.7445 (tp30) REVERT: A 1279 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.5225 (mtp180) REVERT: A 1288 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.7671 (ttm110) REVERT: A 1290 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7782 (tptp) REVERT: B 71 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7538 (mtpt) REVERT: B 92 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7585 (mm-30) REVERT: B 108 LYS cc_start: 0.7249 (mttt) cc_final: 0.6997 (ttpp) REVERT: B 110 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: B 194 GLN cc_start: 0.7518 (tp-100) cc_final: 0.7131 (mt0) REVERT: B 1108 MET cc_start: 0.7555 (ttp) cc_final: 0.7227 (tmt) REVERT: B 1117 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7491 (p) REVERT: B 1223 LEU cc_start: 0.8132 (tp) cc_final: 0.7557 (mp) REVERT: B 1247 HIS cc_start: 0.7971 (m-70) cc_final: 0.7568 (t70) REVERT: B 1284 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7357 (mm-30) REVERT: D 112 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7308 (tt0) REVERT: D 205 GLU cc_start: 0.6798 (mp0) cc_final: 0.6100 (pp20) REVERT: D 260 LEU cc_start: 0.7790 (mp) cc_final: 0.7506 (mt) REVERT: D 263 ILE cc_start: 0.7476 (mp) cc_final: 0.7077 (mt) REVERT: D 278 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: D 431 ASP cc_start: 0.8021 (t70) cc_final: 0.7716 (t70) REVERT: D 441 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: D 456 GLU cc_start: 0.7262 (pt0) cc_final: 0.6493 (tp30) REVERT: D 463 ASP cc_start: 0.7860 (m-30) cc_final: 0.7535 (m-30) REVERT: D 466 GLU cc_start: 0.7718 (mt-10) cc_final: 0.6872 (tp30) REVERT: D 483 ARG cc_start: 0.6831 (mmm160) cc_final: 0.6499 (mtm180) REVERT: E 14 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7570 (mtpp) REVERT: E 105 LYS cc_start: 0.6777 (mppt) cc_final: 0.6474 (mmtm) REVERT: E 142 ASP cc_start: 0.8182 (m-30) cc_final: 0.7760 (m-30) REVERT: E 205 GLU cc_start: 0.7734 (pp20) cc_final: 0.7382 (pm20) REVERT: E 259 GLN cc_start: 0.6497 (tp-100) cc_final: 0.5456 (mt0) REVERT: E 294 MET cc_start: 0.7689 (tpt) cc_final: 0.7327 (tpp) REVERT: E 310 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: E 322 ASN cc_start: 0.7276 (t0) cc_final: 0.6779 (t0) REVERT: E 330 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6714 (mm-40) REVERT: E 464 LYS cc_start: 0.7511 (mmtt) cc_final: 0.6928 (mttm) REVERT: E 488 ARG cc_start: 0.5944 (ttt-90) cc_final: 0.5557 (tmt-80) outliers start: 67 outliers final: 38 residues processed: 250 average time/residue: 0.6475 time to fit residues: 180.5786 Evaluate side-chains 251 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 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 A residue 1303 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1290 LYS 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 186 ASP 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 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 84 MET Chi-restraints excluded: chain E residue 90 GLN 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 228 PHE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 330 GLN 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 401 HIS Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 458 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 167 optimal weight: 4.9990 chunk 117 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.179570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139290 restraints weight = 16934.661| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.08 r_work: 0.3401 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1876 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 : 0.545 8.620 23519 Z= 0.293 Chirality : 0.042 0.244 2601 Planarity : 0.003 0.035 2850 Dihedral : 17.464 73.482 2761 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.30 % Allowed : 27.03 % Favored : 69.66 % 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: 0.84 (0.19), residues: 1914 helix: 2.19 (0.18), residues: 765 sheet: 0.32 (0.26), residues: 367 loop : -1.01 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 400 TYR 0.022 0.002 TYR E 111 PHE 0.012 0.001 PHE A1135 TRP 0.010 0.001 TRP B 164 HIS 0.013 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00307 (17305) covalent geometry : angle 0.54463 (23519) hydrogen bonds : bond 0.03972 ( 830) hydrogen bonds : angle 4.21383 ( 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 268 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6394 (tp30) REVERT: A 1 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6051 (tmm) REVERT: A 92 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7481 (mm-30) REVERT: A 205 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: A 208 MET cc_start: 0.6881 (mtm) cc_final: 0.6335 (tmt) REVERT: A 212 TYR cc_start: 0.6734 (m-80) cc_final: 0.6397 (m-80) REVERT: A 1235 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8312 (t) REVERT: A 1239 ARG cc_start: 0.7835 (ptm-80) cc_final: 0.7611 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7971 (tt0) cc_final: 0.7417 (tp30) REVERT: A 1288 ARG cc_start: 0.8534 (ttp-110) cc_final: 0.7676 (ttm110) REVERT: A 1290 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7679 (tptp) REVERT: B 92 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7614 (mm-30) REVERT: B 110 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7126 (tp30) REVERT: B 194 GLN cc_start: 0.7450 (tp-100) cc_final: 0.7098 (mt0) REVERT: B 1108 MET cc_start: 0.7528 (ttp) cc_final: 0.6424 (tmt) REVERT: B 1117 VAL cc_start: 0.7817 (t) cc_final: 0.7519 (p) REVERT: B 1189 LEU cc_start: 0.7665 (mp) cc_final: 0.7342 (tt) REVERT: B 1223 LEU cc_start: 0.8132 (tp) cc_final: 0.7566 (mp) REVERT: B 1247 HIS cc_start: 0.7952 (m-70) cc_final: 0.7540 (t70) REVERT: B 1284 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7363 (mm-30) REVERT: D 205 GLU cc_start: 0.6772 (mp0) cc_final: 0.6117 (pp20) REVERT: D 260 LEU cc_start: 0.7749 (mp) cc_final: 0.7486 (mt) REVERT: D 263 ILE cc_start: 0.7407 (mp) cc_final: 0.7060 (mt) REVERT: D 278 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: D 431 ASP cc_start: 0.8050 (t70) cc_final: 0.7734 (t70) REVERT: D 441 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6821 (mt-10) REVERT: D 456 GLU cc_start: 0.7237 (pt0) cc_final: 0.6523 (tp30) REVERT: D 463 ASP cc_start: 0.7888 (m-30) cc_final: 0.7545 (m-30) REVERT: D 466 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6851 (tp30) REVERT: D 483 ARG cc_start: 0.6845 (mmm160) cc_final: 0.6515 (mtm180) REVERT: E 14 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7551 (mtpp) REVERT: E 105 LYS cc_start: 0.6739 (mppt) cc_final: 0.6522 (mmtm) REVERT: E 142 ASP cc_start: 0.8072 (m-30) cc_final: 0.7612 (m-30) REVERT: E 205 GLU cc_start: 0.7763 (pp20) cc_final: 0.7441 (pm20) REVERT: E 259 GLN cc_start: 0.6459 (tp-100) cc_final: 0.5428 (mt0) REVERT: E 310 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: E 322 ASN cc_start: 0.7268 (t0) cc_final: 0.6782 (t0) REVERT: E 464 LYS cc_start: 0.7514 (mmtt) cc_final: 0.6901 (mttm) REVERT: E 488 ARG cc_start: 0.5972 (ttt-90) cc_final: 0.5592 (tmt-80) outliers start: 58 outliers final: 36 residues processed: 255 average time/residue: 0.5739 time to fit residues: 163.5745 Evaluate side-chains 244 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1290 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 243 TRP 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 D residue 452 ARG 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 84 MET Chi-restraints excluded: chain E residue 90 GLN 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 272 THR Chi-restraints excluded: chain E residue 310 GLU 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 401 HIS Chi-restraints excluded: chain E residue 429 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: 0.7980 chunk 6 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.179787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.140268 restraints weight = 16884.977| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.11 r_work: 0.3396 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17305 Z= 0.134 Angle : 0.546 8.984 23519 Z= 0.292 Chirality : 0.042 0.273 2601 Planarity : 0.003 0.035 2850 Dihedral : 17.393 72.507 2761 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.02 % Allowed : 27.77 % Favored : 69.21 % 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: 0.91 (0.19), residues: 1914 helix: 2.27 (0.18), residues: 765 sheet: 0.33 (0.26), residues: 365 loop : -0.97 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 184 TYR 0.019 0.001 TYR A 206 PHE 0.011 0.001 PHE A1135 TRP 0.010 0.001 TRP B 164 HIS 0.014 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00304 (17305) covalent geometry : angle 0.54569 (23519) hydrogen bonds : bond 0.03963 ( 830) hydrogen bonds : angle 4.17770 ( 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 261 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 208 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: K 470 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6344 (tp30) REVERT: A 1 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6027 (tmm) REVERT: A 92 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: A 205 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6895 (tp30) REVERT: A 208 MET cc_start: 0.6896 (mtm) cc_final: 0.6368 (tmt) REVERT: A 212 TYR cc_start: 0.6661 (m-80) cc_final: 0.6316 (m-80) REVERT: A 1235 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8304 (t) REVERT: A 1239 ARG cc_start: 0.7828 (ptm-80) cc_final: 0.7618 (ptm-80) REVERT: A 1271 GLU cc_start: 0.7987 (tt0) cc_final: 0.7441 (tp30) REVERT: A 1288 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.7689 (ttm110) REVERT: A 1290 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7716 (tptp) REVERT: B 92 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7605 (mm-30) REVERT: B 110 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7154 (tp30) REVERT: B 194 GLN cc_start: 0.7496 (tp-100) cc_final: 0.7140 (mt0) REVERT: B 1103 LYS cc_start: 0.7136 (mmmt) cc_final: 0.6920 (mtmm) REVERT: B 1108 MET cc_start: 0.7478 (ttp) cc_final: 0.6391 (tmt) REVERT: B 1117 VAL cc_start: 0.7800 (t) cc_final: 0.7496 (p) REVERT: B 1189 LEU cc_start: 0.7634 (mp) cc_final: 0.7274 (tt) REVERT: B 1223 LEU cc_start: 0.8174 (tp) cc_final: 0.7617 (mp) REVERT: B 1247 HIS cc_start: 0.7972 (m-70) cc_final: 0.7573 (t70) REVERT: B 1284 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7372 (mm-30) REVERT: D 205 GLU cc_start: 0.6731 (mp0) cc_final: 0.6061 (pp20) REVERT: D 260 LEU cc_start: 0.7720 (mp) cc_final: 0.7466 (mt) REVERT: D 263 ILE cc_start: 0.7426 (mp) cc_final: 0.7080 (mt) REVERT: D 278 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: D 431 ASP cc_start: 0.8068 (t70) cc_final: 0.7751 (t70) REVERT: D 441 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: D 456 GLU cc_start: 0.7200 (pt0) cc_final: 0.6526 (tp30) REVERT: D 463 ASP cc_start: 0.7894 (m-30) cc_final: 0.7524 (m-30) REVERT: D 466 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6885 (tp30) REVERT: D 483 ARG cc_start: 0.6856 (mmm160) cc_final: 0.6523 (mtm180) REVERT: E 14 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7582 (mtpp) REVERT: E 105 LYS cc_start: 0.6764 (mppt) cc_final: 0.6545 (mmtm) REVERT: E 111 TYR cc_start: 0.8000 (p90) cc_final: 0.7705 (p90) REVERT: E 142 ASP cc_start: 0.8082 (m-30) cc_final: 0.7633 (m-30) REVERT: E 205 GLU cc_start: 0.7767 (pp20) cc_final: 0.7495 (pm20) REVERT: E 239 ASP cc_start: 0.7831 (m-30) cc_final: 0.6866 (t0) REVERT: E 259 GLN cc_start: 0.6398 (tp-100) cc_final: 0.5413 (mt0) REVERT: E 310 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: E 322 ASN cc_start: 0.7265 (t0) cc_final: 0.6776 (t0) REVERT: E 464 LYS cc_start: 0.7499 (mmtt) cc_final: 0.6881 (mttm) REVERT: E 488 ARG cc_start: 0.5934 (ttt-90) cc_final: 0.5528 (tmt170) outliers start: 53 outliers final: 32 residues processed: 248 average time/residue: 0.6269 time to fit residues: 173.6257 Evaluate side-chains 246 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 459 VAL 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 92 GLU Chi-restraints excluded: chain A residue 119 THR 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 1235 THR 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 110 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 243 TRP 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 D residue 452 ARG 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 84 MET Chi-restraints excluded: chain E residue 90 GLN 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 272 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 386 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 4 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.179481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138189 restraints weight = 16877.242| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.05 r_work: 0.3407 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17305 Z= 0.146 Angle : 0.561 12.894 23519 Z= 0.297 Chirality : 0.042 0.257 2601 Planarity : 0.003 0.036 2850 Dihedral : 17.349 73.439 2761 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.73 % Allowed : 27.83 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.19), residues: 1914 helix: 2.28 (0.18), residues: 764 sheet: 0.35 (0.26), residues: 365 loop : -0.98 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 184 TYR 0.019 0.001 TYR A 206 PHE 0.012 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 covalent geometry : bond 0.00332 (17305) covalent geometry : angle 0.56076 (23519) hydrogen bonds : bond 0.04085 ( 830) hydrogen bonds : angle 4.17546 ( 2444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7545.81 seconds wall clock time: 128 minutes 53.57 seconds (7733.57 seconds total)