Starting phenix.real_space_refine on Thu Aug 6 20:58:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9h_52959/08_2026/9q9h_52959.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9h_52959/08_2026/9q9h_52959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q9h_52959/08_2026/9q9h_52959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9h_52959/08_2026/9q9h_52959.map" model { file = "/net/cci-nas-00/data/ceres_data/9q9h_52959/08_2026/9q9h_52959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9h_52959/08_2026/9q9h_52959.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.095 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 54 5.49 5 Mg 2 5.21 5 S 80 5.16 5 Be 2 3.05 5 C 10428 2.51 5 N 2935 2.21 5 O 3275 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 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16786 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3936 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 478} Chain breaks: 1 Chain: "B" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3938 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 478} Chain breaks: 1 Chain: "D" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3908 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 20, 'TRANS': 458} Chain breaks: 1 Chain: "E" Number of atoms: 3906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3906 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 20, 'TRANS': 458} Chain breaks: 1 Chain: "P" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "T" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 525 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "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: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.45, per 1000 atoms: 0.21 Number of scatterers: 16786 At special positions: 0 Unit cell: (93.361, 106.998, 194.065, 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 54 15.00 Mg 2 11.99 F 6 9.00 O 3275 8.00 N 2935 7.00 C 10428 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: 1.03 Conformation dependent library (CDL) restraints added in 793.9 milliseconds 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 21 sheets defined 45.2% alpha, 14.2% beta 14 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.808A pdb=" N ILE A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.557A pdb=" N PHE A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) No H-bonds generated for '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 163 through 167 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 182 through 242 removed outlier: 3.972A pdb=" N MET A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1093 Processing helix chain 'A' and resid 1094 through 1099 removed outlier: 4.809A pdb=" N ASP A1099 " --> pdb=" O PRO A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1155 removed outlier: 3.891A pdb=" N LYS A1103 " --> pdb=" O ASP A1099 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU A1142 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A1149 " --> pdb=" O LYS A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1221 Processing helix chain 'A' and resid 1238 through 1257 Processing helix chain 'A' and resid 1270 through 1280 removed outlier: 3.516A pdb=" N VAL A1274 " --> pdb=" O ASP A1270 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A1279 " --> pdb=" O GLU A1275 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A1280 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1310 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.889A pdb=" N ILE B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.601A 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 163 through 167 Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 182 through 245 removed outlier: 3.579A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1093 Processing helix chain 'B' and resid 1099 through 1155 removed outlier: 3.580A pdb=" N ARG B1105 " --> pdb=" O GLU B1101 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU B1142 " --> pdb=" O MET B1138 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE B1143 " --> pdb=" O LYS B1139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B1146 " --> pdb=" O GLU B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1201 Processing helix chain 'B' and resid 1202 through 1221 Processing helix chain 'B' and resid 1238 through 1257 Processing helix chain 'B' and resid 1272 through 1280 removed outlier: 4.393A pdb=" N SER B1280 " --> pdb=" O LEU B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1305 through 1307 No H-bonds generated for 'chain 'B' and resid 1305 through 1307' Processing helix chain 'D' and resid 35 through 51 Processing helix chain 'D' and resid 68 through 83 Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.669A pdb=" N ASN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 139 through 148 Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'D' and resid 206 through 210 removed outlier: 4.028A pdb=" N TRP D 210 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 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 351 removed outlier: 3.869A pdb=" N ALA D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 386 removed outlier: 3.819A pdb=" N VAL D 386 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 444 Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 468 through 489 Processing helix chain 'D' and resid 493 through 509 removed outlier: 3.696A pdb=" N GLN D 509 " --> pdb=" O ARG D 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 50 removed outlier: 3.760A pdb=" N ASP E 41 " --> pdb=" O PHE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 83 Processing helix chain 'E' and resid 96 through 101 removed outlier: 4.267A pdb=" N ASN E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'E' and resid 185 through 195 Processing helix chain 'E' and resid 275 through 280 removed outlier: 3.761A pdb=" N VAL E 280 " --> pdb=" O GLY E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 352 removed outlier: 3.647A 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 464 removed outlier: 3.653A pdb=" N GLU E 456 " --> pdb=" O ARG E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 488 Processing helix chain 'E' and resid 494 through 507 removed outlier: 3.910A pdb=" N ASP E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.341A pdb=" N ILE A 4 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG A 87 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN A 97 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A 116 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER A 99 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.414A pdb=" N VAL A 35 " --> pdb=" O ILE A1289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1163 through 1166 Processing sheet with id=AA4, first strand: chain 'A' and resid 1227 through 1228 Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 26 removed outlier: 6.570A pdb=" N GLN B 85 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N MET B 7 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 83 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE B 9 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN B 81 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 26 removed outlier: 6.570A pdb=" N GLN B 85 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N MET B 7 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 83 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE B 9 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN B 81 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN B 97 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY B 116 " --> pdb=" O GLN B 97 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER B 99 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1228 through 1231 removed outlier: 3.516A pdb=" N LEU B1265 " --> pdb=" O ILE B1228 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 33 " --> pdb=" O TYR B1287 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE B1289 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 35 " --> pdb=" O ILE B1289 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N LYS B1291 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AA9, first strand: chain 'B' and resid 1164 through 1168 removed outlier: 4.149A pdb=" N ASN B1183 " --> pdb=" O ASP B1168 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 15 through 18 removed outlier: 6.395A pdb=" N VAL D 122 " --> pdb=" O ASN D 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.694A pdb=" N HIS D 217 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN D 212 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE D 242 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE D 214 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY D 244 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE D 216 " --> pdb=" O GLY D 244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 162 through 164 removed outlier: 6.291A pdb=" N ILE D 162 " --> pdb=" O THR D 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 250 through 254 removed outlier: 6.153A pdb=" N ALA D 252 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE D 263 " --> pdb=" O ALA D 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 283 through 284 Processing sheet with id=AB6, first strand: chain 'D' and resid 287 through 290 Processing sheet with id=AB7, first strand: chain 'D' and resid 307 through 313 Processing sheet with id=AB8, first strand: chain 'E' and resid 151 through 152 removed outlier: 6.427A pdb=" N VAL E 122 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE E 55 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE E 54 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.543A pdb=" N THR E 174 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU E 213 " --> pdb=" O LYS E 175 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA E 177 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL E 215 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR E 179 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N HIS E 217 " --> pdb=" O TYR E 179 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU E 181 " --> pdb=" O HIS E 217 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE E 214 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY E 244 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE E 216 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 264 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE E 263 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA E 252 " --> pdb=" O ILE E 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 162 through 164 Processing sheet with id=AC2, first strand: chain 'E' and resid 283 through 284 Processing sheet with id=AC3, first strand: chain 'E' and resid 307 through 312 768 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2765 1.31 - 1.43: 4516 1.43 - 1.56: 9658 1.56 - 1.69: 106 1.69 - 1.81: 126 Bond restraints: 17171 Sorted by residual: bond pdb=" C LYS D 293 " pdb=" N MET D 294 " ideal model delta sigma weight residual 1.330 1.428 -0.098 1.32e-02 5.74e+03 5.50e+01 bond pdb=" C4 ADP A1402 " pdb=" C5 ADP A1402 " ideal model delta sigma weight residual 1.490 1.372 0.118 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C4 ADP B1402 " pdb=" C5 ADP B1402 " ideal model delta sigma weight residual 1.490 1.373 0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" CA TYR A1184 " pdb=" C TYR A1184 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.22e-02 6.72e+03 3.08e+01 bond pdb=" C MET D 294 " pdb=" N ASN D 295 " ideal model delta sigma weight residual 1.331 1.402 -0.071 1.29e-02 6.01e+03 3.02e+01 ... (remaining 17166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 23049 4.04 - 8.09: 231 8.09 - 12.13: 30 12.13 - 16.18: 5 16.18 - 20.22: 2 Bond angle restraints: 23317 Sorted by residual: angle pdb=" C CYS B1222 " pdb=" CA CYS B1222 " pdb=" CB CYS B1222 " ideal model delta sigma weight residual 111.41 91.19 20.22 1.65e+00 3.67e-01 1.50e+02 angle pdb=" N ASP A 177 " pdb=" CA ASP A 177 " pdb=" C ASP A 177 " ideal model delta sigma weight residual 114.39 101.73 12.66 1.45e+00 4.76e-01 7.63e+01 angle pdb=" N VAL E 38 " pdb=" CA VAL E 38 " pdb=" C VAL E 38 " ideal model delta sigma weight residual 111.81 104.31 7.50 8.60e-01 1.35e+00 7.61e+01 angle pdb=" N ILE B1228 " pdb=" CA ILE B1228 " pdb=" C ILE B1228 " ideal model delta sigma weight residual 107.88 95.99 11.89 1.38e+00 5.25e-01 7.42e+01 angle pdb=" CA HIS B1312 " pdb=" CB HIS B1312 " pdb=" CG HIS B1312 " ideal model delta sigma weight residual 113.80 121.79 -7.99 1.00e+00 1.00e+00 6.38e+01 ... (remaining 23312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 9714 34.75 - 69.49: 689 69.49 - 104.24: 33 104.24 - 138.98: 0 138.98 - 173.73: 2 Dihedral angle restraints: 10438 sinusoidal: 4795 harmonic: 5643 Sorted by residual: dihedral pdb=" C CYS B1222 " pdb=" N CYS B1222 " pdb=" CA CYS B1222 " pdb=" CB CYS B1222 " ideal model delta harmonic sigma weight residual -122.60 -101.50 -21.10 0 2.50e+00 1.60e-01 7.12e+01 dihedral pdb=" C ARG A 3 " pdb=" N ARG A 3 " pdb=" CA ARG A 3 " pdb=" CB ARG A 3 " ideal model delta harmonic sigma weight residual -122.60 -106.62 -15.98 0 2.50e+00 1.60e-01 4.09e+01 dihedral pdb=" C GLU A1219 " pdb=" N GLU A1219 " pdb=" CA GLU A1219 " pdb=" CB GLU A1219 " ideal model delta harmonic sigma weight residual -122.60 -111.21 -11.39 0 2.50e+00 1.60e-01 2.08e+01 ... (remaining 10435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2489 0.127 - 0.255: 66 0.255 - 0.382: 12 0.382 - 0.510: 8 0.510 - 0.637: 5 Chirality restraints: 2580 Sorted by residual: chirality pdb=" P DA T 6 " pdb=" OP1 DA T 6 " pdb=" OP2 DA T 6 " pdb=" O5' DA T 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DA T 3 " pdb=" OP1 DA T 3 " pdb=" OP2 DA T 3 " pdb=" O5' DA T 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" P DA T 5 " pdb=" OP1 DA T 5 " pdb=" OP2 DA T 5 " pdb=" O5' DA T 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 8.03e+00 ... (remaining 2577 not shown) Planarity restraints: 2837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 388 " -0.629 9.50e-02 1.11e+02 2.82e-01 4.85e+01 pdb=" NE ARG E 388 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG E 388 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 388 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 388 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1105 " 0.609 9.50e-02 1.11e+02 2.73e-01 4.55e+01 pdb=" NE ARG A1105 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A1105 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A1105 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A1105 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 380 " -0.434 9.50e-02 1.11e+02 1.95e-01 2.32e+01 pdb=" NE ARG E 380 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG E 380 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 380 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 380 " -0.016 2.00e-02 2.50e+03 ... (remaining 2834 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 42 2.43 - 3.05: 10429 3.05 - 3.66: 25678 3.66 - 4.28: 39678 4.28 - 4.90: 65546 Nonbonded interactions: 141373 Sorted by model distance: nonbonded pdb=" OG SER B1202 " pdb=" F2 BEF B1403 " model vdw 1.808 2.990 nonbonded pdb=" NE2 HIS D 247 " pdb="MN MN D 801 " model vdw 1.846 2.400 nonbonded pdb="MG MG B1401 " pdb=" O2B ADP B1402 " model vdw 1.923 2.170 nonbonded pdb="MG MG A1401 " pdb=" O2B ADP A1402 " model vdw 1.943 2.170 nonbonded pdb=" OG1 THR B 43 " pdb="MG MG B1401 " model vdw 1.966 2.170 ... (remaining 141368 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 243 or resid 1071 through 1402)) selection = (chain 'B' and (resid 1 through 243 or resid 1071 through 1402)) } ncs_group { reference = (chain 'D' and (resid 8 through 509 or resid 801 through 802)) selection = (chain 'E' and (resid 8 through 401 or resid 427 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.910 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 16.560 Find NCS groups from input model: 0.240 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 0.118 17171 Z= 0.422 Angle : 0.992 20.221 23317 Z= 0.640 Chirality : 0.066 0.637 2580 Planarity : 0.012 0.282 2837 Dihedral : 20.509 173.727 6766 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.11 % Allowed : 21.63 % Favored : 76.26 % Cbeta Deviations : 0.22 % 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: -0.14 (0.19), residues: 1916 helix: 1.51 (0.18), residues: 783 sheet: -0.98 (0.27), residues: 361 loop : -1.30 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 349 TYR 0.013 0.002 TYR B 206 PHE 0.044 0.001 PHE E 233 TRP 0.008 0.001 TRP E 108 HIS 0.017 0.001 HIS D 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.42 (17171) covalent geometry : angle 0.99250 / 0.64 (23317) hydrogen bonds : bond 0.15635 / 10.09 ( 791) hydrogen bonds : angle 6.64542 / 4.81 ( 2234) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7378 (mtm) cc_final: 0.6349 (ppp) REVERT: A 21 ASP cc_start: 0.7955 (m-30) cc_final: 0.7173 (t0) REVERT: A 126 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7047 (tptp) REVERT: A 140 MET cc_start: 0.8524 (mmm) cc_final: 0.7729 (mmm) REVERT: A 211 LYS cc_start: 0.8602 (tttt) cc_final: 0.8394 (ttmt) REVERT: A 1089 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8046 (mmmt) REVERT: A 1090 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7848 (tttt) REVERT: A 1288 ARG cc_start: 0.8491 (ttm170) cc_final: 0.8190 (ttm170) REVERT: B 211 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8201 (ttpp) REVERT: B 1111 MET cc_start: 0.7873 (tmm) cc_final: 0.7541 (tmm) REVERT: B 1129 ASP cc_start: 0.9047 (t0) cc_final: 0.8844 (t0) REVERT: B 1221 PHE cc_start: 0.7727 (m-10) cc_final: 0.7469 (m-10) REVERT: B 1282 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6056 (m-80) REVERT: D 13 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: D 34 ASN cc_start: 0.7809 (m-40) cc_final: 0.7579 (t0) REVERT: D 161 LYS cc_start: 0.8022 (tttt) cc_final: 0.7747 (tptp) REVERT: D 222 LYS cc_start: 0.6427 (mmtt) cc_final: 0.5976 (tppt) REVERT: D 228 PHE cc_start: 0.5988 (p90) cc_final: 0.5348 (p90) REVERT: D 233 PHE cc_start: 0.8574 (m-80) cc_final: 0.8181 (m-80) REVERT: D 242 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8427 (mp) REVERT: D 483 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7316 (mtm110) REVERT: E 84 MET cc_start: 0.8506 (mtt) cc_final: 0.8203 (mtt) REVERT: E 165 SER cc_start: 0.8748 (t) cc_final: 0.8421 (p) REVERT: E 209 SER cc_start: 0.8323 (m) cc_final: 0.7558 (p) REVERT: E 227 ASN cc_start: 0.6377 (p0) cc_final: 0.6001 (p0) REVERT: E 293 LYS cc_start: 0.8534 (tppt) cc_final: 0.8153 (tttm) REVERT: E 502 ARG cc_start: 0.7911 (ttp-110) cc_final: 0.7199 (ptt90) REVERT: E 506 GLU cc_start: 0.6452 (mm-30) cc_final: 0.5679 (pt0) outliers start: 37 outliers final: 25 residues processed: 283 average time/residue: 0.1192 time to fit residues: 49.2369 Evaluate side-chains 252 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1231 ASP Chi-restraints excluded: chain B residue 1282 TYR Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 484 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A1078 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120184 restraints weight = 22050.270| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.75 r_work: 0.3248 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17171 Z= 0.155 Angle : 0.615 9.800 23317 Z= 0.321 Chirality : 0.045 0.295 2580 Planarity : 0.004 0.055 2837 Dihedral : 18.469 164.192 2757 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.91 % Allowed : 23.06 % Favored : 74.03 % 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: 0.11 (0.19), residues: 1916 helix: 1.78 (0.18), residues: 802 sheet: -1.04 (0.27), residues: 361 loop : -1.21 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1098 TYR 0.012 0.001 TYR B1124 PHE 0.034 0.001 PHE E 233 TRP 0.020 0.001 TRP D 243 HIS 0.008 0.001 HIS B1312 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (17171) covalent geometry : angle 0.61509 / 0.32 (23317) hydrogen bonds : bond 0.04489 / 2.97 ( 791) hydrogen bonds : angle 4.96690 / 3.62 ( 2234) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7929 (m-30) cc_final: 0.7228 (t0) REVERT: A 126 LYS cc_start: 0.7582 (mmmt) cc_final: 0.7096 (tptp) REVERT: A 140 MET cc_start: 0.8533 (mmm) cc_final: 0.7803 (mmm) REVERT: A 211 LYS cc_start: 0.8622 (tttt) cc_final: 0.8406 (ttmt) REVERT: A 1158 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8624 (mp10) REVERT: B 211 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8070 (ttpp) REVERT: B 224 ARG cc_start: 0.7560 (mtm110) cc_final: 0.7187 (ttm110) REVERT: B 1111 MET cc_start: 0.7959 (tmm) cc_final: 0.7638 (tmm) REVERT: B 1129 ASP cc_start: 0.8913 (t0) cc_final: 0.8713 (t0) REVERT: B 1221 PHE cc_start: 0.7919 (m-10) cc_final: 0.7649 (m-10) REVERT: B 1282 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: D 13 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: D 161 LYS cc_start: 0.8066 (tttt) cc_final: 0.7858 (tptp) REVERT: D 222 LYS cc_start: 0.6469 (mmtt) cc_final: 0.6152 (tppt) REVERT: D 228 PHE cc_start: 0.6115 (p90) cc_final: 0.5310 (p90) REVERT: D 233 PHE cc_start: 0.8659 (m-80) cc_final: 0.8059 (m-80) REVERT: D 292 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7632 (mmm160) REVERT: D 355 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7883 (p) REVERT: D 454 MET cc_start: 0.8150 (tpt) cc_final: 0.7926 (tpt) REVERT: D 483 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7398 (mtm110) REVERT: E 20 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: E 84 MET cc_start: 0.8532 (mtt) cc_final: 0.8246 (mtt) REVERT: E 165 SER cc_start: 0.8691 (t) cc_final: 0.8368 (p) REVERT: E 197 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7657 (mmtt) REVERT: E 209 SER cc_start: 0.8227 (m) cc_final: 0.7564 (p) REVERT: E 227 ASN cc_start: 0.6380 (p0) cc_final: 0.5973 (p0) REVERT: E 237 PHE cc_start: 0.7823 (p90) cc_final: 0.7517 (p90) REVERT: E 293 LYS cc_start: 0.8489 (tppt) cc_final: 0.8056 (tttm) REVERT: E 309 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8002 (ttm) outliers start: 51 outliers final: 25 residues processed: 270 average time/residue: 0.1458 time to fit residues: 57.1401 Evaluate side-chains 244 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1282 TYR Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 429 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.152854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118021 restraints weight = 22579.362| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.95 r_work: 0.3250 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17171 Z= 0.208 Angle : 0.626 8.422 23317 Z= 0.326 Chirality : 0.046 0.263 2580 Planarity : 0.004 0.051 2837 Dihedral : 18.142 160.817 2728 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.17 % Allowed : 21.80 % Favored : 74.03 % 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: 0.12 (0.19), residues: 1916 helix: 1.78 (0.18), residues: 803 sheet: -0.97 (0.27), residues: 361 loop : -1.25 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1098 TYR 0.019 0.002 TYR B1124 PHE 0.024 0.002 PHE E 233 TRP 0.014 0.001 TRP D 243 HIS 0.006 0.001 HIS B1312 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (17171) covalent geometry : angle 0.62642 / 0.33 (23317) hydrogen bonds : bond 0.04301 / 2.86 ( 791) hydrogen bonds : angle 4.74021 / 3.44 ( 2234) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 216 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.8110 (m-30) cc_final: 0.7237 (t0) REVERT: A 126 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7104 (tptp) REVERT: A 140 MET cc_start: 0.8668 (mmm) cc_final: 0.7871 (mmm) REVERT: A 211 LYS cc_start: 0.8715 (tttt) cc_final: 0.8408 (ttmt) REVERT: A 1158 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8710 (mp10) REVERT: A 1161 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: A 1288 ARG cc_start: 0.8505 (ttm170) cc_final: 0.8114 (ttm170) REVERT: B 211 LYS cc_start: 0.8355 (ttpp) cc_final: 0.7888 (ttpp) REVERT: B 224 ARG cc_start: 0.7655 (mtm110) cc_final: 0.7298 (ttm110) REVERT: B 1088 PHE cc_start: 0.8449 (m-10) cc_final: 0.8053 (m-80) REVERT: B 1129 ASP cc_start: 0.9027 (t0) cc_final: 0.8807 (t0) REVERT: B 1219 GLU cc_start: 0.7968 (tt0) cc_final: 0.7448 (mt-10) REVERT: B 1282 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: B 1287 TYR cc_start: 0.8955 (m-80) cc_final: 0.8724 (m-80) REVERT: D 161 LYS cc_start: 0.8174 (tttt) cc_final: 0.7876 (tptp) REVERT: D 228 PHE cc_start: 0.6216 (p90) cc_final: 0.5613 (p90) REVERT: D 233 PHE cc_start: 0.8679 (m-80) cc_final: 0.7667 (m-80) REVERT: D 309 MET cc_start: 0.8282 (ttt) cc_final: 0.8042 (ttt) REVERT: D 431 ASP cc_start: 0.8028 (m-30) cc_final: 0.7811 (m-30) REVERT: D 483 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7340 (mtm110) REVERT: E 20 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: E 32 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8022 (mtp180) REVERT: E 84 MET cc_start: 0.8493 (mtt) cc_final: 0.8199 (mtt) REVERT: E 165 SER cc_start: 0.8710 (t) cc_final: 0.8302 (p) REVERT: E 209 SER cc_start: 0.8366 (m) cc_final: 0.7572 (p) REVERT: E 227 ASN cc_start: 0.6388 (p0) cc_final: 0.5988 (p0) REVERT: E 237 PHE cc_start: 0.7863 (p90) cc_final: 0.7577 (p90) REVERT: E 293 LYS cc_start: 0.8467 (tppt) cc_final: 0.7969 (tttm) REVERT: E 309 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7914 (ttm) outliers start: 73 outliers final: 40 residues processed: 273 average time/residue: 0.1385 time to fit residues: 55.1041 Evaluate side-chains 249 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 1097 PHE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 GLN Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain B residue 1202 SER Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1282 TYR Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 429 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 33 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.0030 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.153844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119127 restraints weight = 22403.766| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.97 r_work: 0.3275 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17171 Z= 0.149 Angle : 0.580 10.552 23317 Z= 0.301 Chirality : 0.044 0.236 2580 Planarity : 0.003 0.047 2837 Dihedral : 17.994 161.884 2728 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.17 % Allowed : 21.97 % Favored : 73.86 % 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: 0.21 (0.19), residues: 1916 helix: 1.89 (0.18), residues: 805 sheet: -0.98 (0.27), residues: 360 loop : -1.23 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 380 TYR 0.019 0.001 TYR B1124 PHE 0.020 0.001 PHE E 233 TRP 0.014 0.001 TRP D 243 HIS 0.004 0.001 HIS B1312 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (17171) covalent geometry : angle 0.58025 / 0.30 (23317) hydrogen bonds : bond 0.03918 / 2.63 ( 791) hydrogen bonds : angle 4.58078 / 3.33 ( 2234) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 218 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.8045 (m-30) cc_final: 0.7191 (t0) REVERT: A 126 LYS cc_start: 0.7559 (mmmt) cc_final: 0.7046 (tptp) REVERT: A 140 MET cc_start: 0.8668 (mmm) cc_final: 0.7887 (mmm) REVERT: A 211 LYS cc_start: 0.8709 (tttt) cc_final: 0.8394 (ttmt) REVERT: A 1098 ARG cc_start: 0.7226 (mtp85) cc_final: 0.6892 (mtp180) REVERT: A 1158 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8634 (mp10) REVERT: A 1161 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: B 224 ARG cc_start: 0.7537 (mtm110) cc_final: 0.7152 (ttm110) REVERT: B 1219 GLU cc_start: 0.7981 (tt0) cc_final: 0.7500 (mt-10) REVERT: B 1282 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.5980 (m-80) REVERT: B 1287 TYR cc_start: 0.8956 (m-80) cc_final: 0.8753 (m-80) REVERT: D 23 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7503 (mp) REVERT: D 161 LYS cc_start: 0.8186 (tttt) cc_final: 0.7882 (tptp) REVERT: D 228 PHE cc_start: 0.6241 (p90) cc_final: 0.5643 (p90) REVERT: D 233 PHE cc_start: 0.8693 (m-80) cc_final: 0.7772 (m-80) REVERT: D 242 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7815 (mp) REVERT: D 396 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8617 (tp) REVERT: D 442 LYS cc_start: 0.7702 (mmtm) cc_final: 0.7456 (mmtm) REVERT: D 454 MET cc_start: 0.8167 (tpt) cc_final: 0.7875 (tpt) REVERT: D 483 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.7313 (mtm110) REVERT: E 32 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7969 (mtp180) REVERT: E 84 MET cc_start: 0.8409 (mtt) cc_final: 0.8101 (mtt) REVERT: E 165 SER cc_start: 0.8734 (t) cc_final: 0.8319 (p) REVERT: E 209 SER cc_start: 0.8344 (m) cc_final: 0.7546 (p) REVERT: E 227 ASN cc_start: 0.6364 (p0) cc_final: 0.5986 (p0) REVERT: E 237 PHE cc_start: 0.7837 (p90) cc_final: 0.7581 (p90) REVERT: E 293 LYS cc_start: 0.8450 (tppt) cc_final: 0.7984 (tttm) REVERT: E 309 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7835 (ttm) outliers start: 73 outliers final: 47 residues processed: 271 average time/residue: 0.1390 time to fit residues: 55.3795 Evaluate side-chains 261 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 1097 PHE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 GLN Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1202 SER Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1282 TYR Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 142 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 54 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1269 HIS B 194 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN D 330 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.154317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119809 restraints weight = 22429.698| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.89 r_work: 0.3289 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17171 Z= 0.138 Angle : 0.566 11.733 23317 Z= 0.293 Chirality : 0.043 0.219 2580 Planarity : 0.003 0.044 2837 Dihedral : 17.869 163.532 2728 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.39 % Allowed : 21.86 % Favored : 73.74 % 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: 0.25 (0.19), residues: 1916 helix: 1.95 (0.18), residues: 807 sheet: -0.97 (0.27), residues: 362 loop : -1.23 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 380 TYR 0.010 0.001 TYR B 185 PHE 0.018 0.001 PHE E 237 TRP 0.013 0.001 TRP D 243 HIS 0.003 0.001 HIS B1312 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (17171) covalent geometry : angle 0.56602 / 0.29 (23317) hydrogen bonds : bond 0.03764 / 2.52 ( 791) hydrogen bonds : angle 4.46362 / 3.25 ( 2234) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 222 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8138 (pt) cc_final: 0.7925 (mt) REVERT: A 21 ASP cc_start: 0.7830 (m-30) cc_final: 0.7035 (t0) REVERT: A 126 LYS cc_start: 0.7567 (mmmt) cc_final: 0.7063 (tptp) REVERT: A 140 MET cc_start: 0.8657 (mmm) cc_final: 0.7885 (mmm) REVERT: A 211 LYS cc_start: 0.8734 (tttt) cc_final: 0.8420 (ttmt) REVERT: A 1083 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: A 1098 ARG cc_start: 0.7291 (mtp85) cc_final: 0.7032 (mtp180) REVERT: A 1158 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8606 (mp10) REVERT: A 1161 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7961 (tp30) REVERT: B 224 ARG cc_start: 0.7551 (mtm110) cc_final: 0.7151 (ttm110) REVERT: B 1111 MET cc_start: 0.7584 (tmm) cc_final: 0.7272 (tmm) REVERT: B 1186 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8587 (t) REVERT: B 1219 GLU cc_start: 0.7937 (tt0) cc_final: 0.7428 (mt-10) REVERT: B 1221 PHE cc_start: 0.8417 (m-80) cc_final: 0.8178 (m-80) REVERT: B 1282 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6170 (m-80) REVERT: B 1284 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: D 23 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7751 (mp) REVERT: D 161 LYS cc_start: 0.8202 (tttt) cc_final: 0.7992 (tttm) REVERT: D 228 PHE cc_start: 0.6301 (p90) cc_final: 0.5736 (p90) REVERT: D 233 PHE cc_start: 0.8676 (m-80) cc_final: 0.7943 (m-80) REVERT: D 242 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7807 (mp) REVERT: D 396 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8601 (tp) REVERT: D 454 MET cc_start: 0.8059 (tpt) cc_final: 0.7847 (tpt) REVERT: D 483 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7323 (mtm110) REVERT: E 32 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7973 (mtp180) REVERT: E 84 MET cc_start: 0.8411 (mtt) cc_final: 0.8106 (mtt) REVERT: E 165 SER cc_start: 0.8713 (t) cc_final: 0.8279 (p) REVERT: E 209 SER cc_start: 0.8288 (m) cc_final: 0.7492 (p) REVERT: E 227 ASN cc_start: 0.6499 (p0) cc_final: 0.6113 (p0) REVERT: E 293 LYS cc_start: 0.8460 (tppt) cc_final: 0.7995 (tttm) REVERT: E 309 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7776 (ttm) REVERT: E 313 VAL cc_start: 0.9086 (m) cc_final: 0.8771 (t) outliers start: 77 outliers final: 48 residues processed: 282 average time/residue: 0.1421 time to fit residues: 59.6510 Evaluate side-chains 272 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 GLN Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1202 SER Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1282 TYR Chi-restraints excluded: chain B residue 1284 GLU Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 501 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 100 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 158 optimal weight: 0.0470 chunk 181 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 199 GLN B1096 GLN D 330 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.153962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119323 restraints weight = 22354.722| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.96 r_work: 0.3285 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17171 Z= 0.139 Angle : 0.560 10.121 23317 Z= 0.290 Chirality : 0.043 0.219 2580 Planarity : 0.003 0.044 2837 Dihedral : 17.815 164.960 2728 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.17 % Allowed : 22.03 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 1916 helix: 1.98 (0.18), residues: 808 sheet: -0.94 (0.27), residues: 366 loop : -1.21 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 502 TYR 0.015 0.001 TYR B1124 PHE 0.015 0.001 PHE E 233 TRP 0.012 0.001 TRP D 243 HIS 0.003 0.001 HIS B1312 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (17171) covalent geometry : angle 0.56023 / 0.29 (23317) hydrogen bonds : bond 0.03697 / 2.48 ( 791) hydrogen bonds : angle 4.40914 / 3.21 ( 2234) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 220 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8137 (pt) cc_final: 0.7930 (mt) REVERT: A 21 ASP cc_start: 0.7909 (m-30) cc_final: 0.7099 (t0) REVERT: A 140 MET cc_start: 0.8663 (mmm) cc_final: 0.7875 (mmm) REVERT: A 211 LYS cc_start: 0.8736 (tttt) cc_final: 0.8432 (ttmt) REVERT: A 1083 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: A 1098 ARG cc_start: 0.7381 (mtp85) cc_final: 0.7166 (mtp180) REVERT: A 1158 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8617 (mp10) REVERT: A 1161 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: B 224 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7167 (ttm110) REVERT: B 1111 MET cc_start: 0.7607 (tmm) cc_final: 0.7252 (tmm) REVERT: B 1219 GLU cc_start: 0.7950 (tt0) cc_final: 0.7466 (mt-10) REVERT: B 1221 PHE cc_start: 0.8438 (m-80) cc_final: 0.8195 (m-80) REVERT: B 1282 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6090 (m-80) REVERT: D 23 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7788 (mp) REVERT: D 161 LYS cc_start: 0.8210 (tttt) cc_final: 0.7996 (tttm) REVERT: D 228 PHE cc_start: 0.6318 (p90) cc_final: 0.5713 (p90) REVERT: D 233 PHE cc_start: 0.8689 (m-80) cc_final: 0.7927 (m-80) REVERT: D 242 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7808 (mp) REVERT: D 396 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8600 (tp) REVERT: D 454 MET cc_start: 0.8081 (tpt) cc_final: 0.7786 (tpt) REVERT: D 483 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7307 (mtm110) REVERT: D 503 ARG cc_start: 0.7727 (ptp-170) cc_final: 0.7344 (mtm110) REVERT: E 32 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8022 (mtp180) REVERT: E 84 MET cc_start: 0.8429 (mtt) cc_final: 0.8115 (mtt) REVERT: E 165 SER cc_start: 0.8664 (t) cc_final: 0.8261 (p) REVERT: E 209 SER cc_start: 0.8305 (m) cc_final: 0.7498 (p) REVERT: E 227 ASN cc_start: 0.6481 (p0) cc_final: 0.6122 (p0) REVERT: E 293 LYS cc_start: 0.8454 (tppt) cc_final: 0.7975 (tttm) REVERT: E 309 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7768 (ttm) REVERT: E 313 VAL cc_start: 0.9083 (m) cc_final: 0.8786 (t) REVERT: E 338 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8167 (mm-30) REVERT: E 502 ARG cc_start: 0.7472 (ttp-110) cc_final: 0.6860 (ptt90) outliers start: 73 outliers final: 51 residues processed: 275 average time/residue: 0.1506 time to fit residues: 61.2510 Evaluate side-chains 270 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 136 ILE 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 231 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 GLN Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1282 TYR Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 501 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN B 215 GLN D 330 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118141 restraints weight = 22346.066| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.98 r_work: 0.3269 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17171 Z= 0.158 Angle : 0.577 10.168 23317 Z= 0.297 Chirality : 0.044 0.220 2580 Planarity : 0.004 0.068 2837 Dihedral : 17.797 165.844 2728 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.22 % Allowed : 22.26 % Favored : 73.52 % 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: 0.27 (0.19), residues: 1916 helix: 1.94 (0.18), residues: 809 sheet: -0.90 (0.27), residues: 364 loop : -1.22 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 349 TYR 0.017 0.002 TYR B1124 PHE 0.023 0.001 PHE A1088 TRP 0.011 0.001 TRP D 243 HIS 0.004 0.001 HIS A1087 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (17171) covalent geometry : angle 0.57692 / 0.30 (23317) hydrogen bonds : bond 0.03751 / 2.52 ( 791) hydrogen bonds : angle 4.41201 / 3.21 ( 2234) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 216 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8178 (pt) cc_final: 0.7967 (mt) REVERT: A 120 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.6772 (ttm-80) REVERT: A 126 LYS cc_start: 0.7599 (mmmt) cc_final: 0.7067 (tptp) REVERT: A 140 MET cc_start: 0.8671 (mmm) cc_final: 0.7874 (mmm) REVERT: A 211 LYS cc_start: 0.8746 (tttt) cc_final: 0.8436 (ttmt) REVERT: A 1083 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: A 1103 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7500 (mtmt) REVERT: A 1158 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8628 (mp10) REVERT: A 1161 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: B 224 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7164 (ttm110) REVERT: B 1111 MET cc_start: 0.7678 (tmm) cc_final: 0.7318 (tmm) REVERT: B 1219 GLU cc_start: 0.7983 (tt0) cc_final: 0.7456 (mt-10) REVERT: B 1221 PHE cc_start: 0.8570 (m-80) cc_final: 0.8347 (m-80) REVERT: B 1282 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6080 (m-80) REVERT: B 1284 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: D 23 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7943 (mp) REVERT: D 161 LYS cc_start: 0.8244 (tttt) cc_final: 0.8030 (tttm) REVERT: D 233 PHE cc_start: 0.8708 (m-80) cc_final: 0.7942 (m-80) REVERT: D 242 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7825 (mp) REVERT: D 396 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8610 (tp) REVERT: D 454 MET cc_start: 0.8153 (tpt) cc_final: 0.7934 (tpt) REVERT: D 483 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7329 (mtm110) REVERT: D 503 ARG cc_start: 0.7746 (ptp-170) cc_final: 0.7354 (mtm110) REVERT: E 32 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8032 (mtp180) REVERT: E 84 MET cc_start: 0.8488 (mtt) cc_final: 0.8172 (mtt) REVERT: E 165 SER cc_start: 0.8732 (t) cc_final: 0.8272 (p) REVERT: E 209 SER cc_start: 0.8318 (m) cc_final: 0.7508 (p) REVERT: E 227 ASN cc_start: 0.6499 (p0) cc_final: 0.6140 (p0) REVERT: E 293 LYS cc_start: 0.8450 (tppt) cc_final: 0.7988 (tttm) REVERT: E 309 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7753 (ttm) REVERT: E 313 VAL cc_start: 0.9088 (m) cc_final: 0.8806 (t) outliers start: 74 outliers final: 52 residues processed: 272 average time/residue: 0.1594 time to fit residues: 63.6852 Evaluate side-chains 271 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 133 CYS 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 231 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 GLN Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1202 SER Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1282 TYR Chi-restraints excluded: chain B residue 1284 GLU Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 501 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 131 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 162 optimal weight: 0.0980 chunk 82 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1130 GLN D 330 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118757 restraints weight = 22451.089| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.95 r_work: 0.3287 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17171 Z= 0.145 Angle : 0.577 10.274 23317 Z= 0.298 Chirality : 0.044 0.258 2580 Planarity : 0.003 0.051 2837 Dihedral : 17.728 166.848 2724 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.28 % Allowed : 22.20 % Favored : 73.52 % 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: 0.29 (0.19), residues: 1916 helix: 1.92 (0.18), residues: 811 sheet: -0.86 (0.27), residues: 366 loop : -1.20 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 349 TYR 0.023 0.002 TYR B1124 PHE 0.027 0.001 PHE E 484 TRP 0.012 0.001 TRP D 243 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (17171) covalent geometry : angle 0.57742 / 0.30 (23317) hydrogen bonds : bond 0.03685 / 2.48 ( 791) hydrogen bonds : angle 4.37735 / 3.19 ( 2234) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 214 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8152 (pt) cc_final: 0.7951 (mt) REVERT: A 21 ASP cc_start: 0.7876 (m-30) cc_final: 0.7182 (t0) REVERT: A 120 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7834 (ptm160) REVERT: A 126 LYS cc_start: 0.7567 (mmmt) cc_final: 0.7048 (tptp) REVERT: A 140 MET cc_start: 0.8609 (mmm) cc_final: 0.7888 (mmm) REVERT: A 211 LYS cc_start: 0.8734 (tttt) cc_final: 0.8457 (ttmt) REVERT: A 1083 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6844 (tm-30) REVERT: A 1103 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7478 (mtmt) REVERT: A 1158 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8621 (mp10) REVERT: A 1161 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: B 224 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7148 (ttm110) REVERT: B 1111 MET cc_start: 0.7704 (tmm) cc_final: 0.7348 (tmm) REVERT: B 1219 GLU cc_start: 0.7975 (tt0) cc_final: 0.7501 (mt-10) REVERT: B 1221 PHE cc_start: 0.8601 (m-80) cc_final: 0.8399 (m-80) REVERT: B 1282 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6032 (m-80) REVERT: B 1284 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: D 23 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7865 (mp) REVERT: D 161 LYS cc_start: 0.8232 (tttt) cc_final: 0.8022 (tttm) REVERT: D 233 PHE cc_start: 0.8714 (m-80) cc_final: 0.7949 (m-80) REVERT: D 242 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7802 (mp) REVERT: D 396 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8597 (tp) REVERT: D 454 MET cc_start: 0.8179 (tpt) cc_final: 0.7719 (tpt) REVERT: D 483 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7303 (mtm110) REVERT: D 503 ARG cc_start: 0.7789 (ptp-170) cc_final: 0.7385 (mtm110) REVERT: E 32 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8136 (mtp180) REVERT: E 84 MET cc_start: 0.8470 (mtt) cc_final: 0.8146 (mtt) REVERT: E 165 SER cc_start: 0.8666 (t) cc_final: 0.8241 (p) REVERT: E 189 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7826 (tm) REVERT: E 209 SER cc_start: 0.8316 (m) cc_final: 0.7513 (p) REVERT: E 227 ASN cc_start: 0.6590 (p0) cc_final: 0.6240 (p0) REVERT: E 293 LYS cc_start: 0.8452 (tppt) cc_final: 0.7982 (tttm) REVERT: E 309 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7671 (ttm) REVERT: E 313 VAL cc_start: 0.9097 (m) cc_final: 0.8837 (t) REVERT: E 338 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8173 (mm-30) REVERT: E 502 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.6953 (ptt90) outliers start: 75 outliers final: 54 residues processed: 270 average time/residue: 0.1459 time to fit residues: 58.1995 Evaluate side-chains 274 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 133 CYS 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 234 LEU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 GLN Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1202 SER Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1282 TYR Chi-restraints excluded: chain B residue 1284 GLU Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 501 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 172 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1078 GLN B 194 GLN D 330 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117999 restraints weight = 22315.202| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.92 r_work: 0.3267 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17171 Z= 0.183 Angle : 0.606 10.934 23317 Z= 0.311 Chirality : 0.045 0.231 2580 Planarity : 0.003 0.045 2837 Dihedral : 17.737 167.244 2724 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.05 % Allowed : 22.72 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 1916 helix: 1.85 (0.18), residues: 812 sheet: -0.76 (0.27), residues: 356 loop : -1.29 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 349 TYR 0.015 0.002 TYR B 212 PHE 0.027 0.002 PHE D 261 TRP 0.009 0.001 TRP D 243 HIS 0.004 0.001 HIS B1312 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (17171) covalent geometry : angle 0.60646 / 0.31 (23317) hydrogen bonds : bond 0.03842 / 2.59 ( 791) hydrogen bonds : angle 4.41214 / 3.22 ( 2234) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 210 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8190 (pt) cc_final: 0.7979 (mt) REVERT: A 120 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7869 (ptm160) REVERT: A 140 MET cc_start: 0.8688 (mmm) cc_final: 0.7798 (mmm) REVERT: A 211 LYS cc_start: 0.8726 (tttt) cc_final: 0.8501 (ttmt) REVERT: A 1083 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: A 1103 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7436 (mtmt) REVERT: A 1158 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8651 (mp10) REVERT: A 1161 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: B 224 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7243 (ttm110) REVERT: B 1219 GLU cc_start: 0.7943 (tt0) cc_final: 0.7476 (mt-10) REVERT: B 1282 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.5920 (m-80) REVERT: D 23 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7985 (mp) REVERT: D 233 PHE cc_start: 0.8743 (m-80) cc_final: 0.7962 (m-80) REVERT: D 242 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7831 (mp) REVERT: D 396 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8604 (tp) REVERT: D 454 MET cc_start: 0.8171 (tpt) cc_final: 0.7740 (tpt) REVERT: D 483 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7306 (mtm110) REVERT: D 503 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.7398 (mtm110) REVERT: E 32 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8151 (mtp180) REVERT: E 35 ASP cc_start: 0.8259 (t0) cc_final: 0.7878 (m-30) REVERT: E 84 MET cc_start: 0.8493 (mtt) cc_final: 0.8143 (mtt) REVERT: E 165 SER cc_start: 0.8734 (t) cc_final: 0.8273 (p) REVERT: E 189 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7835 (tm) REVERT: E 209 SER cc_start: 0.8306 (m) cc_final: 0.7508 (p) REVERT: E 227 ASN cc_start: 0.6549 (p0) cc_final: 0.6188 (p0) REVERT: E 293 LYS cc_start: 0.8463 (tppt) cc_final: 0.7955 (tttm) REVERT: E 309 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7654 (ttm) REVERT: E 313 VAL cc_start: 0.9103 (m) cc_final: 0.8843 (t) REVERT: E 502 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.6818 (ptt90) outliers start: 71 outliers final: 57 residues processed: 266 average time/residue: 0.1590 time to fit residues: 61.8927 Evaluate side-chains 273 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 205 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 133 CYS 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 234 LEU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 GLN Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1202 SER Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1282 TYR Chi-restraints excluded: chain B residue 1284 GLU Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 501 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 185 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1078 GLN D 330 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.153047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118069 restraints weight = 22374.756| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.94 r_work: 0.3271 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17171 Z= 0.154 Angle : 0.597 11.191 23317 Z= 0.307 Chirality : 0.044 0.235 2580 Planarity : 0.003 0.054 2837 Dihedral : 17.678 167.718 2724 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.00 % Allowed : 22.89 % Favored : 73.12 % 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: 0.25 (0.19), residues: 1916 helix: 1.88 (0.18), residues: 812 sheet: -0.83 (0.27), residues: 366 loop : -1.24 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 349 TYR 0.033 0.002 TYR B 212 PHE 0.023 0.001 PHE E 484 TRP 0.011 0.001 TRP D 243 HIS 0.003 0.001 HIS B1312 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (17171) covalent geometry : angle 0.59737 / 0.31 (23317) hydrogen bonds : bond 0.03735 / 2.52 ( 791) hydrogen bonds : angle 4.39053 / 3.21 ( 2234) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 217 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8177 (pt) cc_final: 0.7974 (mt) REVERT: A 120 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7955 (ptm160) REVERT: A 140 MET cc_start: 0.8636 (mmm) cc_final: 0.7900 (mmm) REVERT: A 219 LYS cc_start: 0.8293 (tppt) cc_final: 0.8011 (tppt) REVERT: A 1083 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: A 1103 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7451 (mtmt) REVERT: A 1161 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: B 224 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7307 (ttm110) REVERT: B 1111 MET cc_start: 0.8129 (tmm) cc_final: 0.7426 (tmm) REVERT: B 1219 GLU cc_start: 0.8013 (tt0) cc_final: 0.7520 (mt-10) REVERT: B 1282 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.5886 (m-80) REVERT: D 23 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8072 (mp) REVERT: D 161 LYS cc_start: 0.8172 (tttm) cc_final: 0.7862 (tptp) REVERT: D 233 PHE cc_start: 0.8725 (m-80) cc_final: 0.7955 (m-80) REVERT: D 242 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7831 (mp) REVERT: D 396 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8593 (tp) REVERT: D 454 MET cc_start: 0.8171 (tpt) cc_final: 0.7783 (tpt) REVERT: D 483 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7302 (mtm110) REVERT: D 503 ARG cc_start: 0.7855 (ptp-170) cc_final: 0.7470 (mtm110) REVERT: E 35 ASP cc_start: 0.8233 (t0) cc_final: 0.7931 (m-30) REVERT: E 84 MET cc_start: 0.8535 (mtt) cc_final: 0.8190 (mtt) REVERT: E 165 SER cc_start: 0.8722 (t) cc_final: 0.8257 (p) REVERT: E 189 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7869 (tm) REVERT: E 209 SER cc_start: 0.8239 (m) cc_final: 0.7445 (p) REVERT: E 227 ASN cc_start: 0.6520 (p0) cc_final: 0.6194 (p0) REVERT: E 293 LYS cc_start: 0.8475 (tppt) cc_final: 0.7909 (tttm) REVERT: E 309 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7698 (ttm) REVERT: E 313 VAL cc_start: 0.9093 (m) cc_final: 0.8838 (t) REVERT: E 502 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.6868 (ptt90) outliers start: 70 outliers final: 53 residues processed: 271 average time/residue: 0.1591 time to fit residues: 62.9437 Evaluate side-chains 265 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 133 CYS 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 234 LEU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1202 SER Chi-restraints excluded: chain B residue 1244 SER Chi-restraints excluded: chain B residue 1282 TYR Chi-restraints excluded: chain B residue 1284 GLU Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 501 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 159 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 173 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1078 GLN A1158 GLN B 194 GLN B 207 GLN D 330 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118336 restraints weight = 22235.648| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.94 r_work: 0.3281 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17171 Z= 0.145 Angle : 0.598 10.840 23317 Z= 0.306 Chirality : 0.044 0.225 2580 Planarity : 0.004 0.060 2837 Dihedral : 17.607 168.159 2724 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.48 % Allowed : 23.40 % Favored : 73.12 % 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: 0.30 (0.19), residues: 1916 helix: 1.90 (0.18), residues: 811 sheet: -0.78 (0.27), residues: 364 loop : -1.20 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 349 TYR 0.045 0.002 TYR B 212 PHE 0.023 0.001 PHE E 484 TRP 0.011 0.001 TRP D 243 HIS 0.003 0.001 HIS B1312 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (17171) covalent geometry : angle 0.59850 / 0.31 (23317) hydrogen bonds : bond 0.03685 / 2.49 ( 791) hydrogen bonds : angle 4.36961 / 3.19 ( 2234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4703.52 seconds wall clock time: 81 minutes 19.29 seconds (4879.29 seconds total)