Starting phenix.real_space_refine on Thu Feb 5 11:46:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9h_52959/02_2026/9q9h_52959.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9h_52959/02_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_52959/02_2026/9q9h_52959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9h_52959/02_2026/9q9h_52959.map" model { file = "/net/cci-nas-00/data/ceres_data/9q9h_52959/02_2026/9q9h_52959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9h_52959/02_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.77, per 1000 atoms: 0.22 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: 1.12 Conformation dependent library (CDL) restraints added in 674.7 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: 1.79 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: 3.17 Time building geometry restraints manager: 1.51 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: 23051 4.04 - 8.09: 229 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 - 0.125: 2484 0.125 - 0.251: 71 0.251 - 0.376: 11 0.376 - 0.501: 9 0.501 - 0.627: 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 2.35 -2.97 -0.63 2.00e-01 2.50e+01 9.82e+00 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 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.33e+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 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.74e+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: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.980 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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= 0.380 Angle : 0.977 20.221 23317 Z= 0.595 Chirality : 0.064 0.627 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 covalent geometry : bond 0.00612 (17171) covalent geometry : angle 0.97651 (23317) hydrogen bonds : bond 0.15635 ( 791) hydrogen bonds : angle 6.64542 ( 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 : 0.565 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: 0.1344 time to fit residues: 54.7959 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 : 0.596 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A1078 GLN A1269 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120610 restraints weight = 22077.253| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.65 r_work: 0.3255 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17171 Z= 0.156 Angle : 0.573 8.519 23317 Z= 0.307 Chirality : 0.042 0.167 2580 Planarity : 0.004 0.050 2837 Dihedral : 18.357 171.613 2757 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.25 % Allowed : 22.43 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 1916 helix: 1.82 (0.18), residues: 801 sheet: -0.93 (0.28), residues: 346 loop : -1.24 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1098 TYR 0.015 0.001 TYR B1124 PHE 0.033 0.001 PHE E 233 TRP 0.018 0.001 TRP D 243 HIS 0.005 0.001 HIS B1312 Details of bonding type rmsd covalent geometry : bond 0.00353 (17171) covalent geometry : angle 0.57317 (23317) hydrogen bonds : bond 0.04248 ( 791) hydrogen bonds : angle 4.87154 ( 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 288 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7890 (m-30) cc_final: 0.7235 (t0) REVERT: A 88 ASP cc_start: 0.8309 (p0) cc_final: 0.8106 (p0) REVERT: A 126 LYS cc_start: 0.7542 (mmmt) cc_final: 0.7109 (tptp) REVERT: A 140 MET cc_start: 0.8548 (mmm) cc_final: 0.7839 (mmm) REVERT: A 211 LYS cc_start: 0.8621 (tttt) cc_final: 0.8398 (ttmt) REVERT: A 1158 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8549 (mp10) REVERT: B 211 LYS cc_start: 0.8357 (ttpp) cc_final: 0.8057 (ttpp) REVERT: B 224 ARG cc_start: 0.7547 (mtm110) cc_final: 0.7147 (ttm110) REVERT: B 1111 MET cc_start: 0.7979 (tmm) cc_final: 0.7632 (tmm) REVERT: B 1219 GLU cc_start: 0.7777 (tt0) cc_final: 0.7378 (mt-10) REVERT: B 1282 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6212 (m-80) REVERT: D 161 LYS cc_start: 0.8084 (tttt) cc_final: 0.7883 (tptp) REVERT: D 222 LYS cc_start: 0.6471 (mmtt) cc_final: 0.6145 (tppt) REVERT: D 228 PHE cc_start: 0.6250 (p90) cc_final: 0.5452 (p90) REVERT: D 233 PHE cc_start: 0.8641 (m-80) cc_final: 0.7978 (m-80) REVERT: D 292 ARG cc_start: 0.7924 (mmm160) cc_final: 0.7646 (mmm160) REVERT: D 309 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7854 (ttt) REVERT: D 355 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7901 (p) REVERT: D 483 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7347 (mtm110) REVERT: E 84 MET cc_start: 0.8549 (mtt) cc_final: 0.8271 (mtt) REVERT: E 165 SER cc_start: 0.8682 (t) cc_final: 0.8360 (p) REVERT: E 197 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7602 (mmtt) REVERT: E 209 SER cc_start: 0.8198 (m) cc_final: 0.7550 (p) REVERT: E 227 ASN cc_start: 0.6370 (p0) cc_final: 0.5973 (p0) REVERT: E 237 PHE cc_start: 0.7834 (p90) cc_final: 0.7535 (p90) REVERT: E 293 LYS cc_start: 0.8453 (tppt) cc_final: 0.8040 (tttm) REVERT: E 309 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7934 (ttm) outliers start: 57 outliers final: 27 residues processed: 275 average time/residue: 0.1456 time to fit residues: 57.7009 Evaluate side-chains 240 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 118 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1189 LEU 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 309 MET 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 D residue 432 LEU 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 312 ILE Chi-restraints excluded: chain E residue 367 VAL 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: 0.6980 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 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 = 0.3886 r_free = 0.3886 target = 0.153518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118268 restraints weight = 22553.847| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.93 r_work: 0.3270 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17171 Z= 0.182 Angle : 0.574 9.202 23317 Z= 0.303 Chirality : 0.043 0.148 2580 Planarity : 0.004 0.049 2837 Dihedral : 17.970 170.702 2728 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.00 % Allowed : 21.35 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1916 helix: 1.85 (0.18), residues: 807 sheet: -0.98 (0.27), residues: 362 loop : -1.25 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 349 TYR 0.011 0.002 TYR B 206 PHE 0.023 0.001 PHE E 233 TRP 0.014 0.001 TRP D 243 HIS 0.005 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00423 (17171) covalent geometry : angle 0.57363 (23317) hydrogen bonds : bond 0.04052 ( 791) hydrogen bonds : angle 4.62537 ( 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: 70 poor density : 219 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.8065 (m-30) cc_final: 0.7204 (t0) REVERT: A 126 LYS cc_start: 0.7585 (mmmt) cc_final: 0.7088 (tptp) REVERT: A 140 MET cc_start: 0.8654 (mmm) cc_final: 0.7877 (mmm) REVERT: A 211 LYS cc_start: 0.8707 (tttt) cc_final: 0.8388 (ttmt) REVERT: A 1158 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8617 (mp10) REVERT: A 1161 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: B 224 ARG cc_start: 0.7597 (mtm110) cc_final: 0.7205 (ttm110) REVERT: B 1088 PHE cc_start: 0.8456 (m-10) cc_final: 0.8089 (m-80) REVERT: B 1219 GLU cc_start: 0.7995 (tt0) cc_final: 0.7509 (mt-10) REVERT: B 1282 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6003 (m-80) REVERT: D 23 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7788 (mp) REVERT: D 161 LYS cc_start: 0.8184 (tttt) cc_final: 0.7886 (tptp) REVERT: D 228 PHE cc_start: 0.6226 (p90) cc_final: 0.5606 (p90) REVERT: D 233 PHE cc_start: 0.8702 (m-80) cc_final: 0.7743 (m-80) REVERT: D 396 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8645 (tp) REVERT: D 483 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7295 (mtm110) REVERT: E 32 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.7931 (mtp180) REVERT: E 84 MET cc_start: 0.8474 (mtt) cc_final: 0.8175 (mtt) REVERT: E 165 SER cc_start: 0.8736 (t) cc_final: 0.8333 (p) REVERT: E 209 SER cc_start: 0.8382 (m) cc_final: 0.7583 (p) REVERT: E 227 ASN cc_start: 0.6402 (p0) cc_final: 0.6026 (p0) REVERT: E 237 PHE cc_start: 0.7846 (p90) cc_final: 0.7587 (p90) REVERT: E 293 LYS cc_start: 0.8455 (tppt) cc_final: 0.7987 (tttm) REVERT: E 309 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7781 (ttm) outliers start: 70 outliers final: 38 residues processed: 270 average time/residue: 0.1273 time to fit residues: 50.0898 Evaluate side-chains 250 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU 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 205 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 1071 HIS 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 204 LYS 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 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 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 429 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 33 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 187 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 137 optimal weight: 0.0770 chunk 72 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120724 restraints weight = 22359.188| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.78 r_work: 0.3299 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17171 Z= 0.133 Angle : 0.541 9.784 23317 Z= 0.286 Chirality : 0.041 0.143 2580 Planarity : 0.003 0.045 2837 Dihedral : 17.765 170.772 2728 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.71 % Allowed : 22.26 % 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: 0.29 (0.19), residues: 1916 helix: 1.99 (0.18), residues: 808 sheet: -0.95 (0.27), residues: 361 loop : -1.22 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 502 TYR 0.010 0.001 TYR B1104 PHE 0.026 0.001 PHE E 484 TRP 0.013 0.001 TRP D 243 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00300 (17171) covalent geometry : angle 0.54059 (23317) hydrogen bonds : bond 0.03680 ( 791) hydrogen bonds : angle 4.46175 ( 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 299 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 234 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7991 (m-30) cc_final: 0.7091 (t0) REVERT: A 126 LYS cc_start: 0.7546 (mmmt) cc_final: 0.7060 (tptp) REVERT: A 140 MET cc_start: 0.8658 (mmm) cc_final: 0.7902 (mmm) REVERT: A 211 LYS cc_start: 0.8719 (tttt) cc_final: 0.8416 (ttmt) REVERT: A 1098 ARG cc_start: 0.7094 (mtp85) cc_final: 0.6878 (mtp180) REVERT: A 1161 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: A 1275 GLU cc_start: 0.7864 (pt0) cc_final: 0.7647 (pt0) REVERT: B 224 ARG cc_start: 0.7522 (mtm110) cc_final: 0.7115 (ttm110) REVERT: B 1219 GLU cc_start: 0.7975 (tt0) cc_final: 0.7486 (mt-10) REVERT: B 1221 PHE cc_start: 0.8407 (m-80) cc_final: 0.8138 (m-80) REVERT: B 1282 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: D 161 LYS cc_start: 0.8160 (tttt) cc_final: 0.7866 (tptp) REVERT: D 228 PHE cc_start: 0.6265 (p90) cc_final: 0.5710 (p90) REVERT: D 233 PHE cc_start: 0.8684 (m-80) cc_final: 0.7966 (m-80) REVERT: D 309 MET cc_start: 0.8352 (ttt) cc_final: 0.8107 (ttt) REVERT: D 396 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8633 (tp) REVERT: D 483 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7285 (mtm110) REVERT: D 500 GLU cc_start: 0.7837 (tp30) cc_final: 0.7617 (tp30) REVERT: E 32 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7950 (mtp180) REVERT: E 84 MET cc_start: 0.8396 (mtt) cc_final: 0.8073 (mtt) REVERT: E 165 SER cc_start: 0.8629 (t) cc_final: 0.8201 (p) REVERT: E 209 SER cc_start: 0.8316 (m) cc_final: 0.7516 (p) REVERT: E 227 ASN cc_start: 0.6432 (p0) cc_final: 0.6073 (p0) REVERT: E 293 LYS cc_start: 0.8455 (tppt) cc_final: 0.7989 (tttm) REVERT: E 309 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7783 (ttm) REVERT: E 338 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8087 (mm-30) REVERT: E 502 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.6994 (ptt90) outliers start: 65 outliers final: 40 residues processed: 282 average time/residue: 0.1297 time to fit residues: 53.7673 Evaluate side-chains 251 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 133 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 1071 HIS 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 B residue 61 THR 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 1172 ASN 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 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 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 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 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 429 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 142 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 0.0170 chunk 54 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 GLN B 215 GLN B1130 GLN D 330 GLN E 317 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.157157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122700 restraints weight = 22496.136| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.84 r_work: 0.3285 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17171 Z= 0.139 Angle : 0.536 9.391 23317 Z= 0.283 Chirality : 0.041 0.142 2580 Planarity : 0.003 0.043 2837 Dihedral : 17.636 171.580 2728 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.54 % Allowed : 22.66 % 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: 0.34 (0.19), residues: 1916 helix: 2.02 (0.18), residues: 809 sheet: -0.89 (0.27), residues: 366 loop : -1.20 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 380 TYR 0.013 0.001 TYR B1287 PHE 0.031 0.001 PHE A1088 TRP 0.012 0.001 TRP D 243 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00319 (17171) covalent geometry : angle 0.53624 (23317) hydrogen bonds : bond 0.03614 ( 791) hydrogen bonds : angle 4.38178 ( 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 287 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7985 (m-30) cc_final: 0.7114 (t0) REVERT: A 140 MET cc_start: 0.8661 (mmm) cc_final: 0.7897 (mmm) REVERT: A 211 LYS cc_start: 0.8739 (tttt) cc_final: 0.8449 (ttmt) REVERT: A 1161 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8058 (tp30) REVERT: A 1275 GLU cc_start: 0.7928 (pt0) cc_final: 0.7723 (pt0) REVERT: B 224 ARG cc_start: 0.7562 (mtm110) cc_final: 0.7156 (ttm110) REVERT: B 1111 MET cc_start: 0.7711 (tmm) cc_final: 0.7322 (tmm) REVERT: B 1219 GLU cc_start: 0.8016 (tt0) cc_final: 0.7523 (mt-10) REVERT: B 1221 PHE cc_start: 0.8514 (m-80) cc_final: 0.8250 (m-80) REVERT: B 1282 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: B 1284 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: D 161 LYS cc_start: 0.8210 (tttt) cc_final: 0.8003 (tttm) REVERT: D 228 PHE cc_start: 0.6325 (p90) cc_final: 0.5718 (p90) REVERT: D 233 PHE cc_start: 0.8706 (m-80) cc_final: 0.7944 (m-80) REVERT: D 309 MET cc_start: 0.8403 (ttt) cc_final: 0.8172 (ttt) REVERT: D 396 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8696 (tp) REVERT: D 483 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7263 (mtm110) REVERT: E 32 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8044 (mtp180) REVERT: E 84 MET cc_start: 0.8475 (mtt) cc_final: 0.8162 (mtt) REVERT: E 165 SER cc_start: 0.8598 (t) cc_final: 0.8201 (p) REVERT: E 209 SER cc_start: 0.8313 (m) cc_final: 0.7523 (p) REVERT: E 227 ASN cc_start: 0.6427 (p0) cc_final: 0.6092 (p0) REVERT: E 293 LYS cc_start: 0.8458 (tppt) cc_final: 0.7985 (tttm) REVERT: E 309 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7742 (ttm) REVERT: E 338 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8254 (mm-30) outliers start: 62 outliers final: 41 residues processed: 269 average time/residue: 0.1165 time to fit residues: 46.3673 Evaluate side-chains 261 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU 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 183 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 1071 HIS Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain B residue 61 THR 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 1121 LEU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1172 ASN 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 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 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 386 VAL 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 367 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 100 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 158 optimal weight: 0.0000 chunk 181 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN D 322 ASN D 330 GLN E 317 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.157029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122525 restraints weight = 22390.376| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.84 r_work: 0.3277 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17171 Z= 0.151 Angle : 0.549 9.782 23317 Z= 0.288 Chirality : 0.041 0.144 2580 Planarity : 0.003 0.045 2837 Dihedral : 17.571 172.105 2726 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.51 % Allowed : 22.26 % 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: 0.34 (0.19), residues: 1916 helix: 2.00 (0.18), residues: 811 sheet: -0.84 (0.27), residues: 366 loop : -1.21 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 349 TYR 0.015 0.001 TYR B 212 PHE 0.022 0.001 PHE B1088 TRP 0.011 0.001 TRP D 243 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00350 (17171) covalent geometry : angle 0.54857 (23317) hydrogen bonds : bond 0.03630 ( 791) hydrogen bonds : angle 4.35131 ( 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 295 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 216 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8110 (pt) cc_final: 0.7907 (mt) REVERT: A 21 ASP cc_start: 0.7928 (m-30) cc_final: 0.7080 (t0) REVERT: A 126 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7101 (tptp) REVERT: A 140 MET cc_start: 0.8671 (mmm) cc_final: 0.7895 (mmm) REVERT: A 211 LYS cc_start: 0.8742 (tttt) cc_final: 0.8460 (ttmt) REVERT: A 1083 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: A 1103 LYS cc_start: 0.8227 (mmmm) cc_final: 0.7554 (mtmt) REVERT: A 1161 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: A 1275 GLU cc_start: 0.7940 (pt0) cc_final: 0.7730 (pt0) REVERT: B 224 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7193 (ttm110) REVERT: B 1111 MET cc_start: 0.7748 (tmm) cc_final: 0.7353 (tmm) REVERT: B 1219 GLU cc_start: 0.8017 (tt0) cc_final: 0.7522 (mt-10) REVERT: B 1221 PHE cc_start: 0.8585 (m-80) cc_final: 0.8351 (m-80) REVERT: B 1282 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.6091 (m-80) REVERT: D 23 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7836 (mp) REVERT: D 161 LYS cc_start: 0.8235 (tttt) cc_final: 0.8031 (tttm) REVERT: D 233 PHE cc_start: 0.8705 (m-80) cc_final: 0.8005 (m-80) REVERT: D 396 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8697 (tp) REVERT: D 483 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7290 (mtm110) REVERT: E 32 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8158 (mtp180) REVERT: E 84 MET cc_start: 0.8493 (mtt) cc_final: 0.8178 (mtt) REVERT: E 165 SER cc_start: 0.8608 (t) cc_final: 0.8206 (p) REVERT: E 189 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7849 (tm) REVERT: E 209 SER cc_start: 0.8315 (m) cc_final: 0.7523 (p) REVERT: E 227 ASN cc_start: 0.6494 (p0) cc_final: 0.6157 (p0) REVERT: E 293 LYS cc_start: 0.8472 (tppt) cc_final: 0.8012 (tttm) REVERT: E 309 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7669 (ttm) REVERT: E 338 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8263 (mm-30) REVERT: E 502 ARG cc_start: 0.7452 (ttp-110) cc_final: 0.6846 (ptt90) outliers start: 79 outliers final: 51 residues processed: 278 average time/residue: 0.1200 time to fit residues: 49.4096 Evaluate side-chains 268 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 209 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 234 LEU Chi-restraints excluded: chain A residue 1071 HIS 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 1300 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 61 THR 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 1121 LEU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1172 ASN 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 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 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 100 ASN 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 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: 0.0980 chunk 162 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 174 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 GLN E 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.154441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120071 restraints weight = 22255.369| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.85 r_work: 0.3297 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1852 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= 0.137 Angle : 0.541 9.424 23317 Z= 0.284 Chirality : 0.041 0.143 2580 Planarity : 0.003 0.047 2837 Dihedral : 17.456 172.800 2726 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.28 % Allowed : 22.66 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1916 helix: 2.05 (0.18), residues: 811 sheet: -0.80 (0.27), residues: 366 loop : -1.18 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 349 TYR 0.014 0.001 TYR D 111 PHE 0.015 0.001 PHE E 233 TRP 0.011 0.001 TRP D 243 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00316 (17171) covalent geometry : angle 0.54068 (23317) hydrogen bonds : bond 0.03524 ( 791) hydrogen bonds : angle 4.29420 ( 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 298 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 223 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.8649 (mmm) cc_final: 0.7854 (mmm) REVERT: A 211 LYS cc_start: 0.8727 (tttt) cc_final: 0.8467 (ttmt) REVERT: A 1083 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: A 1103 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7516 (mtmt) REVERT: A 1161 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: A 1275 GLU cc_start: 0.7914 (pt0) cc_final: 0.7701 (pt0) REVERT: B 224 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7150 (ttm110) REVERT: B 1111 MET cc_start: 0.7711 (tmm) cc_final: 0.7361 (tmm) REVERT: B 1186 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8555 (t) REVERT: B 1219 GLU cc_start: 0.7979 (tt0) cc_final: 0.7493 (mt-10) REVERT: B 1221 PHE cc_start: 0.8581 (m-80) cc_final: 0.8373 (m-80) REVERT: B 1282 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: B 1284 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: D 23 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7851 (mp) REVERT: D 161 LYS cc_start: 0.8218 (tttt) cc_final: 0.8011 (tttm) REVERT: D 233 PHE cc_start: 0.8714 (m-80) cc_final: 0.7998 (m-80) REVERT: D 396 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8684 (tp) REVERT: D 483 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7282 (mtm110) REVERT: E 32 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8159 (mtp180) REVERT: E 84 MET cc_start: 0.8481 (mtt) cc_final: 0.8144 (mtt) REVERT: E 165 SER cc_start: 0.8596 (t) cc_final: 0.8176 (p) REVERT: E 189 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7872 (tm) REVERT: E 209 SER cc_start: 0.8277 (m) cc_final: 0.7489 (p) REVERT: E 227 ASN cc_start: 0.6391 (p0) cc_final: 0.6084 (p0) REVERT: E 293 LYS cc_start: 0.8461 (tppt) cc_final: 0.7990 (tttm) REVERT: E 309 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7653 (ttm) REVERT: E 502 ARG cc_start: 0.7443 (ttp-110) cc_final: 0.6853 (ptt90) outliers start: 75 outliers final: 53 residues processed: 281 average time/residue: 0.1341 time to fit residues: 55.0434 Evaluate side-chains 275 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 212 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 234 LEU Chi-restraints excluded: chain A residue 1071 HIS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain B residue 25 ILE 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 147 SER 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 1172 ASN 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 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 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 100 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 137 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 158 optimal weight: 0.0770 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 GLN B 207 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120888 restraints weight = 22364.188| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.67 r_work: 0.3306 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1964 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= 0.138 Angle : 0.561 10.355 23317 Z= 0.290 Chirality : 0.042 0.219 2580 Planarity : 0.003 0.046 2837 Dihedral : 17.364 173.234 2725 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.94 % Allowed : 22.95 % 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: 0.43 (0.19), residues: 1916 helix: 2.06 (0.18), residues: 811 sheet: -0.78 (0.27), residues: 366 loop : -1.17 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 349 TYR 0.011 0.001 TYR B1287 PHE 0.016 0.001 PHE E 237 TRP 0.011 0.001 TRP D 243 HIS 0.002 0.001 HIS B1312 Details of bonding type rmsd covalent geometry : bond 0.00319 (17171) covalent geometry : angle 0.56070 (23317) hydrogen bonds : bond 0.03510 ( 791) hydrogen bonds : angle 4.27529 ( 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 284 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 215 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7841 (m-30) cc_final: 0.7150 (t0) REVERT: A 140 MET cc_start: 0.8642 (mmm) cc_final: 0.7843 (mmm) REVERT: A 211 LYS cc_start: 0.8662 (tttt) cc_final: 0.8420 (ttmt) REVERT: A 1083 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: A 1103 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7559 (mtmt) REVERT: A 1161 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: A 1275 GLU cc_start: 0.7894 (pt0) cc_final: 0.7679 (pt0) REVERT: B 224 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7100 (ttm110) REVERT: B 1111 MET cc_start: 0.7744 (tmm) cc_final: 0.7388 (tmm) REVERT: B 1219 GLU cc_start: 0.7954 (tt0) cc_final: 0.7487 (mt-10) REVERT: B 1282 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6037 (m-80) REVERT: D 23 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7949 (mp) REVERT: D 233 PHE cc_start: 0.8674 (m-80) cc_final: 0.7964 (m-80) REVERT: D 396 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8584 (tp) REVERT: D 483 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7268 (mtm110) REVERT: E 32 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8184 (mtp180) REVERT: E 84 MET cc_start: 0.8529 (mtt) cc_final: 0.8198 (mtt) REVERT: E 165 SER cc_start: 0.8571 (t) cc_final: 0.8147 (p) REVERT: E 189 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7851 (tm) REVERT: E 209 SER cc_start: 0.8217 (m) cc_final: 0.7475 (p) REVERT: E 227 ASN cc_start: 0.6386 (p0) cc_final: 0.6070 (p0) REVERT: E 293 LYS cc_start: 0.8484 (tppt) cc_final: 0.7973 (tttm) REVERT: E 309 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7600 (ttm) outliers start: 69 outliers final: 53 residues processed: 267 average time/residue: 0.1395 time to fit residues: 55.0177 Evaluate side-chains 268 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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 234 LEU Chi-restraints excluded: chain A residue 1071 HIS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain B residue 25 ILE 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 147 SER 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 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 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 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 D residue 503 ARG 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 93 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 100 ASN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 172 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 GLN B 194 GLN B 215 GLN D 330 GLN D 509 GLN E 317 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.153363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118371 restraints weight = 22253.179| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.88 r_work: 0.3272 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17171 Z= 0.175 Angle : 0.585 10.842 23317 Z= 0.303 Chirality : 0.043 0.227 2580 Planarity : 0.004 0.056 2837 Dihedral : 17.383 173.360 2723 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.94 % Allowed : 23.06 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1916 helix: 1.98 (0.18), residues: 810 sheet: -0.77 (0.27), residues: 365 loop : -1.21 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 349 TYR 0.015 0.002 TYR D 111 PHE 0.016 0.001 PHE A1097 TRP 0.009 0.001 TRP D 243 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00414 (17171) covalent geometry : angle 0.58511 (23317) hydrogen bonds : bond 0.03698 ( 791) hydrogen bonds : angle 4.31758 ( 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: 69 poor density : 212 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: A 120 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.6755 (ttm-80) REVERT: A 140 MET cc_start: 0.8644 (mmm) cc_final: 0.7809 (mmm) REVERT: A 211 LYS cc_start: 0.8690 (tttt) cc_final: 0.8440 (ttmt) REVERT: A 1083 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: A 1103 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7502 (mtmt) REVERT: A 1161 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: B 224 ARG cc_start: 0.7509 (mtm110) cc_final: 0.7121 (ttm110) REVERT: B 1090 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7368 (pptt) REVERT: B 1111 MET cc_start: 0.7679 (tmm) cc_final: 0.7298 (tmm) REVERT: B 1219 GLU cc_start: 0.7925 (tt0) cc_final: 0.7450 (mt-10) REVERT: B 1282 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.5966 (m-80) REVERT: B 1284 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: D 23 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8128 (mp) REVERT: D 233 PHE cc_start: 0.8727 (m-80) cc_final: 0.8028 (m-80) REVERT: D 255 LYS cc_start: 0.7871 (tppt) cc_final: 0.7068 (mmmt) REVERT: D 396 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8604 (tp) REVERT: D 483 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7291 (mtm110) REVERT: E 32 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8283 (mtp180) REVERT: E 84 MET cc_start: 0.8546 (mtt) cc_final: 0.8216 (mtt) REVERT: E 165 SER cc_start: 0.8614 (t) cc_final: 0.8189 (p) REVERT: E 189 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7896 (tm) REVERT: E 209 SER cc_start: 0.8233 (m) cc_final: 0.7467 (p) REVERT: E 227 ASN cc_start: 0.6546 (p0) cc_final: 0.6161 (p0) REVERT: E 293 LYS cc_start: 0.8474 (tppt) cc_final: 0.7902 (tttm) REVERT: E 309 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7653 (ttm) REVERT: E 502 ARG cc_start: 0.7661 (ttp-110) cc_final: 0.7078 (ptt90) outliers start: 69 outliers final: 48 residues processed: 264 average time/residue: 0.1488 time to fit residues: 57.4229 Evaluate side-chains 267 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 85 GLN 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 136 ILE 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 1071 HIS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain B residue 25 ILE 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 147 SER Chi-restraints excluded: chain B residue 1090 LYS 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 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 198 VAL 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 503 ARG 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 100 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 185 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 GLN D 330 GLN E 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.153849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119071 restraints weight = 22269.792| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.86 r_work: 0.3304 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17171 Z= 0.148 Angle : 0.574 10.643 23317 Z= 0.298 Chirality : 0.042 0.222 2580 Planarity : 0.003 0.058 2837 Dihedral : 17.290 173.844 2723 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.60 % Allowed : 23.63 % Favored : 72.77 % 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: 0.38 (0.19), residues: 1916 helix: 2.01 (0.18), residues: 810 sheet: -0.77 (0.27), residues: 365 loop : -1.20 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 349 TYR 0.011 0.001 TYR B1104 PHE 0.023 0.001 PHE A1097 TRP 0.010 0.001 TRP D 243 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00344 (17171) covalent geometry : angle 0.57426 (23317) hydrogen bonds : bond 0.03556 ( 791) hydrogen bonds : angle 4.29700 ( 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 278 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: A 140 MET cc_start: 0.8604 (mmm) cc_final: 0.7923 (mmm) REVERT: A 211 LYS cc_start: 0.8693 (tttt) cc_final: 0.8448 (ttmt) REVERT: A 1083 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: A 1103 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7558 (mtmt) REVERT: A 1107 MET cc_start: 0.8129 (tpp) cc_final: 0.7875 (tpp) REVERT: A 1108 MET cc_start: 0.8321 (tpt) cc_final: 0.8058 (tpp) REVERT: A 1161 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: B 224 ARG cc_start: 0.7459 (mtm110) cc_final: 0.7195 (ttm110) REVERT: B 1090 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7351 (pptt) REVERT: B 1111 MET cc_start: 0.7727 (tmm) cc_final: 0.7378 (tmm) REVERT: B 1219 GLU cc_start: 0.7996 (tt0) cc_final: 0.7524 (mt-10) REVERT: B 1282 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6080 (m-80) REVERT: D 23 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7915 (mp) REVERT: D 161 LYS cc_start: 0.8130 (tttm) cc_final: 0.7896 (tptp) REVERT: D 233 PHE cc_start: 0.8680 (m-80) cc_final: 0.8043 (m-80) REVERT: D 255 LYS cc_start: 0.7687 (tppt) cc_final: 0.7071 (mmmt) REVERT: D 396 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8599 (tp) REVERT: D 483 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.7293 (mtm110) REVERT: E 32 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8265 (mtp180) REVERT: E 84 MET cc_start: 0.8574 (mtt) cc_final: 0.8243 (mtt) REVERT: E 165 SER cc_start: 0.8600 (t) cc_final: 0.8171 (p) REVERT: E 189 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7921 (tm) REVERT: E 209 SER cc_start: 0.8234 (m) cc_final: 0.7478 (p) REVERT: E 227 ASN cc_start: 0.6736 (p0) cc_final: 0.6377 (p0) REVERT: E 293 LYS cc_start: 0.8483 (tppt) cc_final: 0.7933 (tttm) REVERT: E 309 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7639 (ttm) REVERT: E 338 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8051 (mm-30) REVERT: E 502 ARG cc_start: 0.7647 (ttp-110) cc_final: 0.7093 (ptt90) outliers start: 63 outliers final: 49 residues processed: 264 average time/residue: 0.1463 time to fit residues: 56.7336 Evaluate side-chains 267 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 85 GLN 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 234 LEU Chi-restraints excluded: chain A residue 1071 HIS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1244 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain B residue 25 ILE 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 147 SER Chi-restraints excluded: chain B residue 1090 LYS 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 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 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 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 503 ARG 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 100 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 159 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 154 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 36 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 overall best weight: 0.8154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 GLN D 330 GLN E 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.153251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.119246 restraints weight = 22167.136| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.72 r_work: 0.3286 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17171 Z= 0.159 Angle : 0.580 11.030 23317 Z= 0.300 Chirality : 0.042 0.224 2580 Planarity : 0.004 0.058 2837 Dihedral : 17.233 174.037 2719 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.65 % Allowed : 23.40 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1916 helix: 2.01 (0.18), residues: 810 sheet: -0.73 (0.27), residues: 365 loop : -1.22 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 349 TYR 0.013 0.002 TYR D 111 PHE 0.019 0.001 PHE A1097 TRP 0.009 0.001 TRP D 243 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00372 (17171) covalent geometry : angle 0.57964 (23317) hydrogen bonds : bond 0.03606 ( 791) hydrogen bonds : angle 4.29548 ( 2234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4261.16 seconds wall clock time: 73 minutes 45.22 seconds (4425.22 seconds total)