Starting phenix.real_space_refine on Thu Mar 5 01:23:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7las_23250/03_2026/7las_23250_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7las_23250/03_2026/7las_23250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7las_23250/03_2026/7las_23250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7las_23250/03_2026/7las_23250.map" model { file = "/net/cci-nas-00/data/ceres_data/7las_23250/03_2026/7las_23250_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7las_23250/03_2026/7las_23250_trim.cif" } resolution = 4.4 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= 0.008 sd= 0.157 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: 7 Type Number sf(0) Gaussians P 32 5.49 5 Mg 4 5.21 5 S 18 5.16 5 C 5951 2.51 5 N 1579 2.21 5 O 1803 1.98 5 H 8624 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18011 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2901 Classifications: {'peptide': 183} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 170} Chain: "B" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2902 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain: "C" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2901 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain: "D" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2902 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain: "E" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2901 Classifications: {'peptide': 183} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 169} Chain: "F" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2901 Classifications: {'peptide': 183} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 169} Chain: "G" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 284 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "H" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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: 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: "C" 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: "D" 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} Time building chain proxies: 3.38, per 1000 atoms: 0.19 Number of scatterers: 18011 At special positions: 0 Unit cell: (104, 98.176, 109.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 18 16.00 P 32 15.00 Mg 4 11.99 O 1803 8.00 N 1579 7.00 C 5951 6.00 H 8624 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 363.5 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 13 sheets defined 36.2% alpha, 13.3% beta 1 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.540A pdb=" N SER A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.609A pdb=" N PHE A 143 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.671A pdb=" N ALA A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.697A pdb=" N TRP A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.575A pdb=" N THR A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.651A pdb=" N TRP A 262 " --> pdb=" O PRO A 259 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 removed outlier: 4.332A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 128 removed outlier: 3.582A pdb=" N GLU B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.934A pdb=" N LEU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 186 removed outlier: 4.074A pdb=" N TRP B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.724A pdb=" N CYS B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.978A pdb=" N TYR B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 130 removed outlier: 3.625A pdb=" N GLU C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.731A pdb=" N VAL C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 removed outlier: 3.609A pdb=" N ARG C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.629A pdb=" N GLY C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 186 Processing helix chain 'C' and resid 222 through 230 removed outlier: 4.145A pdb=" N CYS C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.549A pdb=" N TRP C 262 " --> pdb=" O PRO C 259 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 263 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 removed outlier: 4.027A pdb=" N TYR C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.867A pdb=" N VAL D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 143 Processing helix chain 'D' and resid 146 through 158 removed outlier: 3.604A pdb=" N GLY D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 186 removed outlier: 3.593A pdb=" N TRP D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 184 " --> pdb=" O LYS D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 271 through 276 removed outlier: 3.620A pdb=" N TYR D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 removed outlier: 3.784A pdb=" N GLU E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 139 Processing helix chain 'E' and resid 140 through 145 removed outlier: 3.752A pdb=" N ARG E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 158 removed outlier: 3.514A pdb=" N ALA E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY E 158 " --> pdb=" O LEU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 187 removed outlier: 3.508A pdb=" N TRP E 183 " --> pdb=" O GLY E 179 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE E 187 " --> pdb=" O TRP E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 3.748A pdb=" N CYS E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 127 Processing helix chain 'F' and resid 131 through 139 removed outlier: 3.884A pdb=" N VAL F 135 " --> pdb=" O SER F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 removed outlier: 4.118A pdb=" N ARG F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 158 Processing helix chain 'F' and resid 179 through 186 removed outlier: 3.531A pdb=" N TRP F 183 " --> pdb=" O GLY F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 188 No H-bonds generated for 'chain 'F' and resid 187 through 188' Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'F' and resid 222 through 230 removed outlier: 3.612A pdb=" N CYS F 230 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 removed outlier: 3.506A pdb=" N TRP F 262 " --> pdb=" O PRO F 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 196 removed outlier: 6.986A pdb=" N TYR A 194 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU A 210 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 250 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 214 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN A 168 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 253 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS A 170 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 169 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 282 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 171 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TRP A 284 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 291 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 239 Processing sheet with id=AA3, first strand: chain 'B' and resid 194 through 195 removed outlier: 6.670A pdb=" N GLU B 210 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN B 168 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE B 253 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N HIS B 170 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER B 255 " --> pdb=" O HIS B 170 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE B 172 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 169 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL B 282 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL B 171 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 236 through 239 removed outlier: 3.554A pdb=" N GLY B 242 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 195 removed outlier: 7.220A pdb=" N ASN C 168 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE C 253 " --> pdb=" O ASN C 168 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N HIS C 170 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 169 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU C 281 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 171 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE C 283 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 173 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS C 285 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 285 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AA7, first strand: chain 'D' and resid 193 through 194 removed outlier: 6.590A pdb=" N VAL D 212 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR D 254 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 214 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASN D 168 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE D 253 " --> pdb=" O ASN D 168 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS D 170 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL D 169 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL D 282 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 171 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 236 through 239 Processing sheet with id=AA9, first strand: chain 'E' and resid 170 through 172 removed outlier: 6.719A pdb=" N VAL E 171 " --> pdb=" O VAL E 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.871A pdb=" N TYR E 194 " --> pdb=" O VAL E 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 236 through 239 Processing sheet with id=AB3, first strand: chain 'F' and resid 210 through 212 removed outlier: 6.973A pdb=" N GLU F 210 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER F 250 " --> pdb=" O GLU F 210 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASN F 168 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL F 169 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL F 282 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL F 171 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N TRP F 284 " --> pdb=" O VAL F 171 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 235 through 239 removed outlier: 4.636A pdb=" N LEU F 235 " --> pdb=" O PHE F 246 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY F 242 " --> pdb=" O THR F 239 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8612 1.03 - 1.23: 70 1.23 - 1.42: 4120 1.42 - 1.61: 5509 1.61 - 1.81: 24 Bond restraints: 18335 Sorted by residual: bond pdb=" O3' DT G 4 " pdb=" P DT G 5 " ideal model delta sigma weight residual 1.607 1.446 0.161 1.50e-02 4.44e+03 1.16e+02 bond pdb=" CG ASP F 215 " pdb=" OD2 ASP F 215 " ideal model delta sigma weight residual 1.249 1.327 -0.078 1.90e-02 2.77e+03 1.69e+01 bond pdb=" CG ASP C 215 " pdb=" OD1 ASP C 215 " ideal model delta sigma weight residual 1.249 1.326 -0.077 1.90e-02 2.77e+03 1.63e+01 bond pdb=" CG ASP D 215 " pdb=" OD2 ASP D 215 " ideal model delta sigma weight residual 1.249 1.325 -0.076 1.90e-02 2.77e+03 1.60e+01 bond pdb=" CG ASP B 215 " pdb=" OD2 ASP B 215 " ideal model delta sigma weight residual 1.249 1.325 -0.076 1.90e-02 2.77e+03 1.59e+01 ... (remaining 18330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.47: 32942 8.47 - 16.94: 15 16.94 - 25.40: 3 25.40 - 33.87: 0 33.87 - 42.34: 3 Bond angle restraints: 32963 Sorted by residual: angle pdb=" O3' DT G 4 " pdb=" P DT G 5 " pdb=" O5' DT G 5 " ideal model delta sigma weight residual 104.00 68.99 35.01 1.50e+00 4.44e-01 5.45e+02 angle pdb=" C3' DT G 4 " pdb=" O3' DT G 4 " pdb=" P DT G 5 " ideal model delta sigma weight residual 120.20 86.10 34.10 1.50e+00 4.44e-01 5.17e+02 angle pdb=" O3' DT G 4 " pdb=" P DT G 5 " pdb=" OP2 DT G 5 " ideal model delta sigma weight residual 108.00 150.34 -42.34 3.00e+00 1.11e-01 1.99e+02 angle pdb=" C PHE E 217 " pdb=" N TYR E 218 " pdb=" CA TYR E 218 " ideal model delta sigma weight residual 121.98 138.38 -16.40 1.53e+00 4.27e-01 1.15e+02 angle pdb=" C GLU B 209 " pdb=" N GLU B 210 " pdb=" CA GLU B 210 " ideal model delta sigma weight residual 121.54 141.04 -19.50 1.91e+00 2.74e-01 1.04e+02 ... (remaining 32958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 8070 29.56 - 59.12: 530 59.12 - 88.69: 29 88.69 - 118.25: 2 118.25 - 147.81: 4 Dihedral angle restraints: 8635 sinusoidal: 4735 harmonic: 3900 Sorted by residual: dihedral pdb=" CA GLY B 208 " pdb=" C GLY B 208 " pdb=" N GLU B 209 " pdb=" CA GLU B 209 " ideal model delta harmonic sigma weight residual 180.00 78.09 101.91 0 5.00e+00 4.00e-02 4.15e+02 dihedral pdb=" CA GLU B 209 " pdb=" C GLU B 209 " pdb=" N GLU B 210 " pdb=" CA GLU B 210 " ideal model delta harmonic sigma weight residual 180.00 99.48 80.52 0 5.00e+00 4.00e-02 2.59e+02 dihedral pdb=" CA GLY C 208 " pdb=" C GLY C 208 " pdb=" N GLU C 209 " pdb=" CA GLU C 209 " ideal model delta harmonic sigma weight residual 180.00 102.89 77.11 0 5.00e+00 4.00e-02 2.38e+02 ... (remaining 8632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1262 0.086 - 0.172: 213 0.172 - 0.258: 3 0.258 - 0.344: 1 0.344 - 0.429: 1 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CA GLU B 210 " pdb=" N GLU B 210 " pdb=" C GLU B 210 " pdb=" CB GLU B 210 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA GLU A 210 " pdb=" N GLU A 210 " pdb=" C GLU A 210 " pdb=" CB GLU A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CG LEU A 154 " pdb=" CB LEU A 154 " pdb=" CD1 LEU A 154 " pdb=" CD2 LEU A 154 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 1477 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 277 " 0.515 9.50e-02 1.11e+02 1.72e-01 3.13e+01 pdb=" NE ARG D 277 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 277 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 277 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 277 " 0.005 2.00e-02 2.50e+03 pdb="HH11 ARG D 277 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG D 277 " 0.005 2.00e-02 2.50e+03 pdb="HH21 ARG D 277 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 277 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 276 " -0.467 9.50e-02 1.11e+02 1.56e-01 2.57e+01 pdb=" NE ARG C 276 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 276 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 276 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 276 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG C 276 " 0.008 2.00e-02 2.50e+03 pdb="HH12 ARG C 276 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG C 276 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 276 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 151 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ALA C 151 " 0.057 2.00e-02 2.50e+03 pdb=" O ALA C 151 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU C 152 " -0.019 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 160 2.03 - 2.67: 25180 2.67 - 3.31: 49719 3.31 - 3.96: 64553 3.96 - 4.60: 100745 Nonbonded interactions: 240357 Sorted by model distance: nonbonded pdb=" CZ2 TRP F 202 " pdb=" OP1 DG G 7 " model vdw 1.386 3.150 nonbonded pdb=" HZ1 LYS E 240 " pdb=" OP1 DC G 6 " model vdw 1.397 2.450 nonbonded pdb=" HZ2 TRP F 202 " pdb=" OP2 DG G 7 " model vdw 1.546 2.450 nonbonded pdb=" HZ1 LYS A 180 " pdb=" O1A ADP A 400 " model vdw 1.591 2.450 nonbonded pdb=" HH TYR D 194 " pdb=" O ASP D 204 " model vdw 1.602 2.450 ... (remaining 240352 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 119 through 180 or (resid 181 and (name N or name CA or na \ me C or name O or name CB or name OG or name H or name HA or name HB2 or name HB \ 3)) or resid 182 through 217 or (resid 218 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or n \ ame CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD2 or \ name HE1 or name HE2 or name HH )) or resid 219 through 240 or (resid 241 and (n \ ame N or name CA or name C or name O or name HA2 or name HA3)) or resid 242 thro \ ugh 301)) selection = (chain 'B' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2 or name HH )) or resid 219 through 240 or (r \ esid 241 and (name N or name CA or name C or name O or name HA2 or name HA3)) or \ resid 242 through 301)) selection = (chain 'C' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or resid 181 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HH \ )) or resid 219 through 240 or (resid 241 and (name N or name CA or name C or n \ ame O or name HA2 or name HA3)) or resid 242 through 301)) selection = (chain 'D' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2 or name HH )) or resid 219 through 240 or (r \ esid 241 and (name N or name CA or name C or name O or name HA2 or name HA3)) or \ resid 242 through 301)) selection = (chain 'E' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 240 or (resid 241 and (name N or name CA \ or name C or name O or name HA2 or name HA3)) or resid 242 through 301)) selection = (chain 'F' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2 or name HH )) or resid 219 through 301)) } 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 group one per residue 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: 1.160 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: 0.100 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.110 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.009 0.161 9712 Z= 0.424 Angle : 1.366 42.339 13393 Z= 0.740 Chirality : 0.060 0.429 1480 Planarity : 0.010 0.223 1576 Dihedral : 19.048 147.811 3496 Min Nonbonded Distance : 1.386 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 7.55 % Allowed : 10.38 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.97 % 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: -2.56 (0.25), residues: 1086 helix: -0.96 (0.28), residues: 291 sheet: -1.56 (0.44), residues: 141 loop : -2.17 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 228 TYR 0.029 0.003 TYR B 206 PHE 0.026 0.003 PHE B 217 TRP 0.017 0.003 TRP B 202 HIS 0.005 0.002 HIS D 170 Details of bonding type rmsd covalent geometry : bond 0.00940 ( 9711) covalent geometry : angle 1.36643 (13393) hydrogen bonds : bond 0.22504 ( 218) hydrogen bonds : angle 8.96742 ( 598) Misc. bond : bond 0.06290 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 507 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 435 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.9056 (p90) cc_final: 0.8646 (p90) REVERT: A 249 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7791 (mtm-85) REVERT: B 137 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 142 THR cc_start: 0.9280 (m) cc_final: 0.8909 (t) REVERT: B 146 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8227 (p0) REVERT: B 161 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: B 204 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8417 (t70) REVERT: B 225 ASP cc_start: 0.8940 (t0) cc_final: 0.8683 (t0) REVERT: B 275 TYR cc_start: 0.8591 (m-10) cc_final: 0.8335 (m-80) REVERT: C 128 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: C 132 LEU cc_start: 0.8789 (mp) cc_final: 0.8507 (tp) REVERT: C 271 VAL cc_start: 0.9162 (m) cc_final: 0.8958 (p) REVERT: C 283 PHE cc_start: 0.7303 (t80) cc_final: 0.6619 (t80) REVERT: D 161 GLN cc_start: 0.8214 (tt0) cc_final: 0.7900 (tp40) REVERT: D 178 CYS cc_start: 0.9033 (p) cc_final: 0.8538 (p) REVERT: D 180 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8020 (mtmt) REVERT: D 209 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6997 (mm-30) REVERT: D 276 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7668 (mmm160) REVERT: D 278 ILE cc_start: 0.9071 (mm) cc_final: 0.8553 (mm) REVERT: D 285 LYS cc_start: 0.6609 (ptpt) cc_final: 0.6272 (ptpt) REVERT: E 166 LYS cc_start: 0.8101 (tptp) cc_final: 0.7359 (ptpp) REVERT: E 207 HIS cc_start: 0.6774 (t70) cc_final: 0.6127 (t70) REVERT: E 220 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.8544 (p90) REVERT: E 236 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9031 (p) REVERT: E 243 THR cc_start: 0.7730 (p) cc_final: 0.7452 (p) REVERT: E 247 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.8841 (pp) REVERT: E 271 VAL cc_start: 0.7521 (m) cc_final: 0.7047 (t) REVERT: E 275 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: F 137 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8333 (tm-30) REVERT: F 140 PRO cc_start: 0.9326 (Cg_endo) cc_final: 0.9020 (Cg_exo) REVERT: F 201 LYS cc_start: 0.8157 (mppt) cc_final: 0.7599 (tptt) REVERT: F 228 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8217 (ttm110) REVERT: F 232 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6913 (mtm180) REVERT: F 247 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8373 (pt) REVERT: F 258 THR cc_start: 0.8419 (p) cc_final: 0.7822 (t) REVERT: F 276 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7174 (mmm160) outliers start: 72 outliers final: 21 residues processed: 472 average time/residue: 0.2622 time to fit residues: 160.4025 Evaluate side-chains 317 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS D 138 GLN D 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109379 restraints weight = 47015.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.114149 restraints weight = 24308.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117266 restraints weight = 15535.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119490 restraints weight = 11379.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120863 restraints weight = 9066.829| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9712 Z= 0.211 Angle : 0.806 15.877 13393 Z= 0.412 Chirality : 0.047 0.276 1480 Planarity : 0.006 0.085 1576 Dihedral : 17.631 171.059 1480 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.21 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.88 % 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: -2.45 (0.25), residues: 1086 helix: -0.81 (0.27), residues: 309 sheet: -1.62 (0.40), residues: 166 loop : -2.11 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 232 TYR 0.019 0.002 TYR E 275 PHE 0.013 0.002 PHE D 283 TRP 0.029 0.002 TRP F 202 HIS 0.007 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 9711) covalent geometry : angle 0.80615 (13393) hydrogen bonds : bond 0.05246 ( 218) hydrogen bonds : angle 6.20226 ( 598) Misc. bond : bond 0.00350 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.9027 (p90) cc_final: 0.8489 (p90) REVERT: A 201 LYS cc_start: 0.7789 (pttp) cc_final: 0.7374 (pttp) REVERT: A 207 HIS cc_start: 0.7420 (m90) cc_final: 0.6958 (m90) REVERT: B 148 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7714 (tpp-160) REVERT: B 161 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7449 (mt0) REVERT: B 225 ASP cc_start: 0.8919 (t0) cc_final: 0.8598 (t0) REVERT: B 256 ASN cc_start: 0.7952 (m-40) cc_final: 0.7682 (m-40) REVERT: B 281 LEU cc_start: 0.8820 (tt) cc_final: 0.8609 (tt) REVERT: B 299 VAL cc_start: 0.5652 (m) cc_final: 0.5139 (m) REVERT: D 148 ARG cc_start: 0.8422 (tpt90) cc_final: 0.8161 (mtm-85) REVERT: D 161 GLN cc_start: 0.8675 (mt0) cc_final: 0.8069 (tp-100) REVERT: D 178 CYS cc_start: 0.8899 (p) cc_final: 0.8509 (p) REVERT: D 238 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7324 (mt-10) REVERT: D 243 THR cc_start: 0.7424 (p) cc_final: 0.7208 (p) REVERT: D 276 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7515 (tpp-160) REVERT: D 278 ILE cc_start: 0.9192 (mm) cc_final: 0.8816 (mm) REVERT: D 285 LYS cc_start: 0.6509 (ptpt) cc_final: 0.6299 (ptpt) REVERT: E 166 LYS cc_start: 0.8112 (tptp) cc_final: 0.7440 (ptpp) REVERT: E 207 HIS cc_start: 0.6569 (t70) cc_final: 0.6141 (t70) REVERT: E 228 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8502 (mtm-85) REVERT: E 247 LEU cc_start: 0.8999 (pt) cc_final: 0.8531 (pp) REVERT: E 261 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7543 (tm-30) REVERT: F 137 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8285 (tm-30) REVERT: F 140 PRO cc_start: 0.9332 (Cg_endo) cc_final: 0.8972 (Cg_exo) REVERT: F 216 ASP cc_start: 0.7793 (t0) cc_final: 0.7139 (p0) REVERT: F 217 PHE cc_start: 0.7992 (t80) cc_final: 0.7709 (t80) REVERT: F 232 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.7089 (mtm180) REVERT: F 276 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.6935 (mmm-85) REVERT: F 278 ILE cc_start: 0.8709 (mt) cc_final: 0.8495 (mt) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2620 time to fit residues: 112.9719 Evaluate side-chains 272 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105025 restraints weight = 47279.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109577 restraints weight = 24496.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112690 restraints weight = 15722.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.114747 restraints weight = 11548.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116008 restraints weight = 9295.666| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 9712 Z= 0.199 Angle : 0.726 12.182 13393 Z= 0.367 Chirality : 0.045 0.211 1480 Planarity : 0.006 0.094 1576 Dihedral : 17.274 177.672 1480 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: -2.03 (0.25), residues: 1086 helix: -0.20 (0.29), residues: 295 sheet: -1.58 (0.40), residues: 155 loop : -1.91 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 163 TYR 0.026 0.002 TYR F 194 PHE 0.011 0.001 PHE B 217 TRP 0.019 0.001 TRP F 202 HIS 0.006 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9711) covalent geometry : angle 0.72579 (13393) hydrogen bonds : bond 0.04254 ( 218) hydrogen bonds : angle 5.73787 ( 598) Misc. bond : bond 0.00182 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 THR cc_start: 0.8479 (m) cc_final: 0.8278 (p) REVERT: A 147 PHE cc_start: 0.9059 (p90) cc_final: 0.8492 (p90) REVERT: A 201 LYS cc_start: 0.7701 (pttp) cc_final: 0.7228 (pttp) REVERT: A 206 TYR cc_start: 0.8475 (t80) cc_final: 0.8212 (t80) REVERT: A 207 HIS cc_start: 0.7318 (m90) cc_final: 0.7002 (m90) REVERT: A 238 GLU cc_start: 0.8728 (pm20) cc_final: 0.8481 (pm20) REVERT: B 161 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7617 (mt0) REVERT: B 225 ASP cc_start: 0.8990 (t0) cc_final: 0.8744 (t0) REVERT: C 138 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8553 (mm-40) REVERT: C 187 PHE cc_start: 0.8622 (t80) cc_final: 0.8373 (t80) REVERT: D 137 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7817 (tm-30) REVERT: D 148 ARG cc_start: 0.8514 (tpt90) cc_final: 0.8305 (mtm-85) REVERT: D 161 GLN cc_start: 0.8721 (mt0) cc_final: 0.8103 (tp-100) REVERT: D 178 CYS cc_start: 0.8913 (p) cc_final: 0.8516 (p) REVERT: D 217 PHE cc_start: 0.9387 (t80) cc_final: 0.8574 (t80) REVERT: D 227 LEU cc_start: 0.8697 (mt) cc_final: 0.8483 (tp) REVERT: D 238 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7087 (mp0) REVERT: D 276 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7514 (tpp-160) REVERT: E 166 LYS cc_start: 0.8218 (tptp) cc_final: 0.7416 (ptpp) REVERT: E 182 LYS cc_start: 0.8578 (tttm) cc_final: 0.8256 (tppt) REVERT: E 207 HIS cc_start: 0.6614 (t70) cc_final: 0.6138 (t70) REVERT: E 228 ARG cc_start: 0.8747 (ttm-80) cc_final: 0.8337 (mtm-85) REVERT: E 247 LEU cc_start: 0.9032 (pt) cc_final: 0.8536 (pp) REVERT: F 137 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8285 (tm-30) REVERT: F 140 PRO cc_start: 0.9287 (Cg_endo) cc_final: 0.8941 (Cg_exo) REVERT: F 196 LYS cc_start: 0.8561 (tttp) cc_final: 0.8352 (tttp) REVERT: F 232 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.7140 (mtm180) REVERT: F 276 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.7070 (mmm160) outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.2449 time to fit residues: 100.4315 Evaluate side-chains 270 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.102449 restraints weight = 47665.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.106882 restraints weight = 24603.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109858 restraints weight = 15803.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111881 restraints weight = 11650.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113210 restraints weight = 9438.334| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9712 Z= 0.226 Angle : 0.737 14.483 13393 Z= 0.375 Chirality : 0.045 0.208 1480 Planarity : 0.005 0.066 1576 Dihedral : 17.273 163.992 1480 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: -2.13 (0.25), residues: 1086 helix: -0.25 (0.29), residues: 296 sheet: -1.88 (0.38), residues: 162 loop : -1.90 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 199 TYR 0.016 0.002 TYR F 206 PHE 0.028 0.002 PHE B 283 TRP 0.022 0.001 TRP F 202 HIS 0.005 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 9711) covalent geometry : angle 0.73685 (13393) hydrogen bonds : bond 0.03786 ( 218) hydrogen bonds : angle 5.67787 ( 598) Misc. bond : bond 0.00324 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 THR cc_start: 0.8389 (m) cc_final: 0.8182 (t) REVERT: A 147 PHE cc_start: 0.9073 (p90) cc_final: 0.8520 (p90) REVERT: A 201 LYS cc_start: 0.7553 (pttp) cc_final: 0.7147 (pttp) REVERT: A 206 TYR cc_start: 0.8680 (t80) cc_final: 0.8452 (t80) REVERT: A 207 HIS cc_start: 0.7312 (m90) cc_final: 0.7084 (m-70) REVERT: A 238 GLU cc_start: 0.8748 (pm20) cc_final: 0.8486 (pm20) REVERT: B 161 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7557 (mt0) REVERT: B 183 TRP cc_start: 0.8508 (t60) cc_final: 0.7585 (t-100) REVERT: C 138 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8710 (mm-40) REVERT: C 187 PHE cc_start: 0.8600 (t80) cc_final: 0.8343 (t80) REVERT: D 137 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 148 ARG cc_start: 0.8507 (tpt90) cc_final: 0.8290 (mtm-85) REVERT: D 161 GLN cc_start: 0.8705 (mt0) cc_final: 0.8097 (tp-100) REVERT: D 178 CYS cc_start: 0.8950 (p) cc_final: 0.8605 (p) REVERT: D 227 LEU cc_start: 0.8744 (mt) cc_final: 0.8498 (tp) REVERT: D 238 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7128 (mp0) REVERT: D 276 ARG cc_start: 0.8039 (ttm110) cc_final: 0.7478 (tpp-160) REVERT: E 166 LYS cc_start: 0.8289 (tptp) cc_final: 0.7457 (ptpp) REVERT: E 247 LEU cc_start: 0.8991 (pt) cc_final: 0.8560 (pp) REVERT: F 137 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8243 (tm-30) REVERT: F 142 THR cc_start: 0.8342 (p) cc_final: 0.8079 (p) REVERT: F 232 ARG cc_start: 0.7219 (mtm-85) cc_final: 0.6874 (mtm180) REVERT: F 276 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7027 (mmm160) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2345 time to fit residues: 96.1741 Evaluate side-chains 258 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104790 restraints weight = 47193.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109342 restraints weight = 23911.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.112449 restraints weight = 15172.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114554 restraints weight = 11066.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115935 restraints weight = 8851.689| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9712 Z= 0.128 Angle : 0.663 12.579 13393 Z= 0.329 Chirality : 0.043 0.180 1480 Planarity : 0.005 0.077 1576 Dihedral : 17.072 163.522 1480 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.87 (0.25), residues: 1086 helix: 0.09 (0.30), residues: 297 sheet: -1.48 (0.43), residues: 141 loop : -1.90 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 163 TYR 0.011 0.001 TYR E 206 PHE 0.026 0.001 PHE B 283 TRP 0.012 0.001 TRP F 203 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9711) covalent geometry : angle 0.66286 (13393) hydrogen bonds : bond 0.03240 ( 218) hydrogen bonds : angle 5.30241 ( 598) Misc. bond : bond 0.00132 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 303 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.9081 (p90) cc_final: 0.8511 (p90) REVERT: A 200 ASN cc_start: 0.7764 (t0) cc_final: 0.7445 (m-40) REVERT: A 201 LYS cc_start: 0.7628 (pttp) cc_final: 0.7370 (ptmm) REVERT: A 206 TYR cc_start: 0.8589 (t80) cc_final: 0.8366 (t80) REVERT: B 161 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7674 (mt0) REVERT: B 183 TRP cc_start: 0.8270 (t60) cc_final: 0.7589 (t-100) REVERT: C 138 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8708 (mm-40) REVERT: C 187 PHE cc_start: 0.8503 (t80) cc_final: 0.8189 (t80) REVERT: C 189 ASP cc_start: 0.8163 (p0) cc_final: 0.7863 (p0) REVERT: C 276 ARG cc_start: 0.5367 (tpm170) cc_final: 0.4789 (tpm170) REVERT: D 148 ARG cc_start: 0.8483 (tpt90) cc_final: 0.8277 (mtm-85) REVERT: D 161 GLN cc_start: 0.8636 (mt0) cc_final: 0.7978 (tp-100) REVERT: D 178 CYS cc_start: 0.8937 (p) cc_final: 0.8547 (p) REVERT: D 217 PHE cc_start: 0.9444 (t80) cc_final: 0.8605 (t80) REVERT: D 227 LEU cc_start: 0.8696 (mt) cc_final: 0.8490 (tp) REVERT: D 238 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7114 (mp0) REVERT: D 276 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7482 (tpp-160) REVERT: D 278 ILE cc_start: 0.9202 (mm) cc_final: 0.8964 (mm) REVERT: E 166 LYS cc_start: 0.8296 (tptp) cc_final: 0.7440 (ptpp) REVERT: E 202 TRP cc_start: 0.8437 (m-90) cc_final: 0.8146 (m-90) REVERT: F 137 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8235 (tm-30) REVERT: F 142 THR cc_start: 0.8347 (p) cc_final: 0.8085 (p) REVERT: F 224 ASP cc_start: 0.8709 (p0) cc_final: 0.8477 (p0) REVERT: F 232 ARG cc_start: 0.7191 (mtm-85) cc_final: 0.6795 (mtm180) REVERT: F 276 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.7026 (mmm160) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2438 time to fit residues: 97.2619 Evaluate side-chains 261 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 207 HIS A 256 ASN B 139 HIS D 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.130044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.099686 restraints weight = 48049.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.103953 restraints weight = 25336.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106840 restraints weight = 16530.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.108820 restraints weight = 12418.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110113 restraints weight = 10120.356| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9712 Z= 0.246 Angle : 0.732 13.412 13393 Z= 0.370 Chirality : 0.045 0.214 1480 Planarity : 0.005 0.069 1576 Dihedral : 16.811 155.122 1480 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: -2.16 (0.24), residues: 1086 helix: -0.23 (0.28), residues: 313 sheet: -1.64 (0.39), residues: 161 loop : -2.08 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 199 TYR 0.034 0.002 TYR F 194 PHE 0.023 0.002 PHE E 147 TRP 0.024 0.002 TRP A 202 HIS 0.004 0.001 HIS E 170 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 9711) covalent geometry : angle 0.73244 (13393) hydrogen bonds : bond 0.03479 ( 218) hydrogen bonds : angle 5.48914 ( 598) Misc. bond : bond 0.00904 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.9042 (p90) cc_final: 0.8514 (p90) REVERT: A 201 LYS cc_start: 0.7966 (pttp) cc_final: 0.7563 (ptmm) REVERT: A 206 TYR cc_start: 0.8840 (t80) cc_final: 0.8388 (t80) REVERT: A 216 ASP cc_start: 0.8148 (t0) cc_final: 0.7812 (m-30) REVERT: B 161 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7576 (mt0) REVERT: B 183 TRP cc_start: 0.8453 (t60) cc_final: 0.7653 (t-100) REVERT: C 138 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8852 (mm-40) REVERT: C 189 ASP cc_start: 0.8272 (p0) cc_final: 0.8038 (p0) REVERT: C 276 ARG cc_start: 0.5270 (tpm170) cc_final: 0.4770 (tpm170) REVERT: D 137 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7974 (tm-30) REVERT: D 148 ARG cc_start: 0.8542 (tpt90) cc_final: 0.8308 (mtm-85) REVERT: D 161 GLN cc_start: 0.8604 (mt0) cc_final: 0.8042 (tp-100) REVERT: D 164 ASP cc_start: 0.8546 (p0) cc_final: 0.8323 (p0) REVERT: D 178 CYS cc_start: 0.9026 (p) cc_final: 0.8680 (p) REVERT: D 227 LEU cc_start: 0.8714 (mt) cc_final: 0.8487 (tp) REVERT: D 238 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7184 (mp0) REVERT: D 276 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7432 (tpp-160) REVERT: E 166 LYS cc_start: 0.8335 (tptp) cc_final: 0.7508 (ptpp) REVERT: E 247 LEU cc_start: 0.8909 (pt) cc_final: 0.8607 (pp) REVERT: F 137 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8262 (tm-30) REVERT: F 142 THR cc_start: 0.8350 (p) cc_final: 0.8046 (p) REVERT: F 201 LYS cc_start: 0.6771 (tptt) cc_final: 0.6037 (tptt) REVERT: F 224 ASP cc_start: 0.8720 (p0) cc_final: 0.8404 (p0) REVERT: F 232 ARG cc_start: 0.7115 (mtm-85) cc_final: 0.6737 (mtm180) REVERT: F 276 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7076 (mmm160) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2406 time to fit residues: 92.2447 Evaluate side-chains 253 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.101060 restraints weight = 48653.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105412 restraints weight = 26474.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108405 restraints weight = 17412.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110424 restraints weight = 12975.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111506 restraints weight = 10556.725| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9712 Z= 0.196 Angle : 0.696 12.220 13393 Z= 0.351 Chirality : 0.044 0.178 1480 Planarity : 0.005 0.078 1576 Dihedral : 16.581 141.931 1480 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -2.11 (0.25), residues: 1086 helix: -0.20 (0.29), residues: 310 sheet: -1.60 (0.39), residues: 161 loop : -2.04 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 228 TYR 0.014 0.002 TYR C 275 PHE 0.024 0.002 PHE B 283 TRP 0.015 0.001 TRP F 202 HIS 0.006 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9711) covalent geometry : angle 0.69618 (13393) hydrogen bonds : bond 0.03354 ( 218) hydrogen bonds : angle 5.49812 ( 598) Misc. bond : bond 0.00336 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.9047 (p90) cc_final: 0.8515 (p90) REVERT: A 200 ASN cc_start: 0.7579 (t0) cc_final: 0.7200 (m-40) REVERT: A 201 LYS cc_start: 0.7940 (pttp) cc_final: 0.7592 (pttp) REVERT: A 206 TYR cc_start: 0.8810 (t80) cc_final: 0.8317 (t80) REVERT: A 216 ASP cc_start: 0.8079 (t0) cc_final: 0.7871 (m-30) REVERT: A 256 ASN cc_start: 0.8476 (m110) cc_final: 0.8236 (m-40) REVERT: A 257 GLN cc_start: 0.7772 (mp10) cc_final: 0.6776 (tt0) REVERT: B 161 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7477 (tt0) REVERT: C 189 ASP cc_start: 0.8219 (p0) cc_final: 0.7973 (p0) REVERT: C 276 ARG cc_start: 0.5133 (tpm170) cc_final: 0.4652 (tpm170) REVERT: D 137 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8093 (tm-30) REVERT: D 148 ARG cc_start: 0.8505 (tpt90) cc_final: 0.8179 (ttp-110) REVERT: D 161 GLN cc_start: 0.8531 (mt0) cc_final: 0.7988 (tp-100) REVERT: D 164 ASP cc_start: 0.8444 (p0) cc_final: 0.8223 (p0) REVERT: D 178 CYS cc_start: 0.8995 (p) cc_final: 0.8676 (p) REVERT: D 238 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7178 (mp0) REVERT: D 276 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7358 (tpp-160) REVERT: E 166 LYS cc_start: 0.8369 (tptp) cc_final: 0.7558 (ptpp) REVERT: E 182 LYS cc_start: 0.8492 (tttm) cc_final: 0.8064 (tppt) REVERT: E 247 LEU cc_start: 0.8972 (pt) cc_final: 0.8604 (pp) REVERT: F 137 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8262 (tm-30) REVERT: F 142 THR cc_start: 0.8358 (p) cc_final: 0.8043 (p) REVERT: F 165 TRP cc_start: 0.8393 (p90) cc_final: 0.7890 (p90) REVERT: F 224 ASP cc_start: 0.8621 (p0) cc_final: 0.8294 (p0) REVERT: F 276 ARG cc_start: 0.7596 (ttm-80) cc_final: 0.7061 (mmm160) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2471 time to fit residues: 94.1662 Evaluate side-chains 251 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103430 restraints weight = 47428.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107717 restraints weight = 24576.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110637 restraints weight = 15879.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112570 restraints weight = 11770.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113915 restraints weight = 9549.722| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9712 Z= 0.120 Angle : 0.672 14.227 13393 Z= 0.333 Chirality : 0.043 0.168 1480 Planarity : 0.005 0.080 1576 Dihedral : 16.249 136.282 1480 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.76 (0.25), residues: 1086 helix: 0.23 (0.30), residues: 310 sheet: -1.43 (0.43), residues: 141 loop : -1.90 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 199 TYR 0.019 0.002 TYR F 206 PHE 0.027 0.001 PHE E 147 TRP 0.025 0.001 TRP D 220 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9711) covalent geometry : angle 0.67203 (13393) hydrogen bonds : bond 0.03025 ( 218) hydrogen bonds : angle 5.17321 ( 598) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.9060 (p90) cc_final: 0.8494 (p90) REVERT: A 200 ASN cc_start: 0.7456 (t0) cc_final: 0.7044 (m-40) REVERT: A 201 LYS cc_start: 0.7851 (pttp) cc_final: 0.7455 (pttp) REVERT: A 206 TYR cc_start: 0.8664 (t80) cc_final: 0.8136 (t80) REVERT: A 215 ASP cc_start: 0.8580 (t0) cc_final: 0.8287 (t0) REVERT: A 216 ASP cc_start: 0.8046 (t0) cc_final: 0.7751 (m-30) REVERT: A 256 ASN cc_start: 0.8518 (m110) cc_final: 0.8199 (m-40) REVERT: A 257 GLN cc_start: 0.7742 (mp10) cc_final: 0.6773 (tt0) REVERT: B 161 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7502 (tt0) REVERT: B 240 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7700 (mtpp) REVERT: C 189 ASP cc_start: 0.8084 (p0) cc_final: 0.7793 (p0) REVERT: C 276 ARG cc_start: 0.5168 (tpm170) cc_final: 0.4646 (tpm170) REVERT: D 137 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8118 (tm-30) REVERT: D 148 ARG cc_start: 0.8435 (tpt90) cc_final: 0.8117 (ttp-110) REVERT: D 161 GLN cc_start: 0.8472 (mt0) cc_final: 0.7940 (tp-100) REVERT: D 178 CYS cc_start: 0.8968 (p) cc_final: 0.8630 (p) REVERT: D 217 PHE cc_start: 0.9469 (t80) cc_final: 0.8634 (t80) REVERT: D 238 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7222 (mp0) REVERT: D 276 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7475 (mmm160) REVERT: E 166 LYS cc_start: 0.8354 (tptp) cc_final: 0.7507 (ptpp) REVERT: E 182 LYS cc_start: 0.8465 (tttm) cc_final: 0.8076 (tppt) REVERT: E 202 TRP cc_start: 0.8454 (m-90) cc_final: 0.8207 (m-90) REVERT: E 247 LEU cc_start: 0.8943 (pt) cc_final: 0.8580 (pp) REVERT: F 137 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8265 (tm-30) REVERT: F 142 THR cc_start: 0.8337 (p) cc_final: 0.8042 (p) REVERT: F 165 TRP cc_start: 0.8392 (p90) cc_final: 0.7891 (p90) REVERT: F 196 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8058 (ttmm) REVERT: F 224 ASP cc_start: 0.8506 (p0) cc_final: 0.8176 (p0) REVERT: F 238 GLU cc_start: 0.8313 (pm20) cc_final: 0.8029 (pm20) REVERT: F 276 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.6949 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2392 time to fit residues: 91.0152 Evaluate side-chains 259 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 256 ASN B 139 HIS C 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103824 restraints weight = 47841.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108224 restraints weight = 25119.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111196 restraints weight = 16272.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113203 restraints weight = 12092.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114495 restraints weight = 9803.725| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9712 Z= 0.129 Angle : 0.665 14.565 13393 Z= 0.329 Chirality : 0.043 0.157 1480 Planarity : 0.005 0.077 1576 Dihedral : 16.055 127.374 1480 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.66 (0.25), residues: 1086 helix: 0.24 (0.30), residues: 317 sheet: -1.36 (0.43), residues: 143 loop : -1.82 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 277 TYR 0.019 0.002 TYR B 206 PHE 0.023 0.001 PHE E 147 TRP 0.021 0.001 TRP D 220 HIS 0.007 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9711) covalent geometry : angle 0.66467 (13393) hydrogen bonds : bond 0.02909 ( 218) hydrogen bonds : angle 5.06153 ( 598) Misc. bond : bond 0.00106 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.9087 (p90) cc_final: 0.8524 (p90) REVERT: A 200 ASN cc_start: 0.7389 (t0) cc_final: 0.6976 (m-40) REVERT: A 201 LYS cc_start: 0.7799 (pttp) cc_final: 0.7536 (pttp) REVERT: A 206 TYR cc_start: 0.8675 (t80) cc_final: 0.8097 (t80) REVERT: A 215 ASP cc_start: 0.8578 (t0) cc_final: 0.8259 (t0) REVERT: A 216 ASP cc_start: 0.8023 (t0) cc_final: 0.7705 (m-30) REVERT: A 256 ASN cc_start: 0.8550 (m-40) cc_final: 0.8233 (m-40) REVERT: A 257 GLN cc_start: 0.7731 (mp10) cc_final: 0.6792 (tt0) REVERT: B 161 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7557 (tt0) REVERT: B 183 TRP cc_start: 0.8367 (t60) cc_final: 0.8086 (t60) REVERT: C 189 ASP cc_start: 0.8051 (p0) cc_final: 0.7762 (p0) REVERT: C 276 ARG cc_start: 0.5246 (tpm170) cc_final: 0.4721 (tpm170) REVERT: D 161 GLN cc_start: 0.8518 (mt0) cc_final: 0.7935 (tp-100) REVERT: D 178 CYS cc_start: 0.8963 (p) cc_final: 0.8614 (p) REVERT: D 217 PHE cc_start: 0.9446 (t80) cc_final: 0.8759 (t80) REVERT: D 238 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7080 (mp0) REVERT: D 271 VAL cc_start: 0.9146 (m) cc_final: 0.8847 (m) REVERT: D 276 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7569 (tpt90) REVERT: E 166 LYS cc_start: 0.8360 (tptp) cc_final: 0.7501 (ptpp) REVERT: E 182 LYS cc_start: 0.8466 (tttm) cc_final: 0.8071 (tppt) REVERT: E 247 LEU cc_start: 0.8959 (pt) cc_final: 0.8600 (pp) REVERT: F 137 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8297 (tm-30) REVERT: F 142 THR cc_start: 0.8322 (p) cc_final: 0.8014 (p) REVERT: F 165 TRP cc_start: 0.8358 (p90) cc_final: 0.7836 (p90) REVERT: F 224 ASP cc_start: 0.8424 (p0) cc_final: 0.8101 (p0) REVERT: F 276 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.7060 (mmm160) REVERT: F 294 GLU cc_start: 0.7874 (mm-30) cc_final: 0.6882 (tm-30) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2488 time to fit residues: 95.8172 Evaluate side-chains 261 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.103073 restraints weight = 47814.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107380 restraints weight = 25061.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110345 restraints weight = 16273.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.112330 restraints weight = 12059.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113490 restraints weight = 9781.506| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.7015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9712 Z= 0.140 Angle : 0.658 12.698 13393 Z= 0.326 Chirality : 0.043 0.179 1480 Planarity : 0.005 0.077 1576 Dihedral : 15.924 117.404 1480 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: -1.56 (0.25), residues: 1086 helix: 0.33 (0.30), residues: 317 sheet: -1.24 (0.43), residues: 143 loop : -1.77 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 199 TYR 0.018 0.002 TYR F 275 PHE 0.021 0.001 PHE B 283 TRP 0.021 0.001 TRP F 220 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9711) covalent geometry : angle 0.65815 (13393) hydrogen bonds : bond 0.02891 ( 218) hydrogen bonds : angle 4.97039 ( 598) Misc. bond : bond 0.00102 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.9052 (p90) cc_final: 0.8518 (p90) REVERT: A 200 ASN cc_start: 0.7490 (t0) cc_final: 0.7058 (m-40) REVERT: A 201 LYS cc_start: 0.7807 (pttp) cc_final: 0.7531 (pttp) REVERT: A 206 TYR cc_start: 0.8747 (t80) cc_final: 0.8120 (t80) REVERT: A 215 ASP cc_start: 0.8534 (t0) cc_final: 0.8147 (t0) REVERT: A 216 ASP cc_start: 0.7854 (t0) cc_final: 0.7511 (m-30) REVERT: A 256 ASN cc_start: 0.8568 (m-40) cc_final: 0.8208 (m-40) REVERT: A 257 GLN cc_start: 0.7740 (mp10) cc_final: 0.6805 (tt0) REVERT: B 161 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7557 (tt0) REVERT: B 183 TRP cc_start: 0.8374 (t60) cc_final: 0.8071 (t60) REVERT: C 180 LYS cc_start: 0.8873 (mtmm) cc_final: 0.8620 (mtmm) REVERT: C 189 ASP cc_start: 0.8025 (p0) cc_final: 0.7742 (p0) REVERT: C 276 ARG cc_start: 0.5201 (tpm170) cc_final: 0.4699 (tpm170) REVERT: D 125 THR cc_start: 0.8527 (t) cc_final: 0.8315 (t) REVERT: D 161 GLN cc_start: 0.8494 (mt0) cc_final: 0.7941 (tp-100) REVERT: D 178 CYS cc_start: 0.9007 (p) cc_final: 0.8639 (p) REVERT: D 217 PHE cc_start: 0.9411 (t80) cc_final: 0.8734 (t80) REVERT: D 238 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7092 (mp0) REVERT: D 276 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7460 (mmm160) REVERT: E 166 LYS cc_start: 0.8402 (tptp) cc_final: 0.7526 (ptpp) REVERT: E 182 LYS cc_start: 0.8469 (tttm) cc_final: 0.8066 (tppt) REVERT: E 247 LEU cc_start: 0.8949 (pt) cc_final: 0.8551 (pp) REVERT: F 137 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8337 (tm-30) REVERT: F 142 THR cc_start: 0.8345 (p) cc_final: 0.8026 (p) REVERT: F 165 TRP cc_start: 0.8371 (p90) cc_final: 0.7813 (p90) REVERT: F 207 HIS cc_start: 0.6436 (m170) cc_final: 0.6206 (m170) REVERT: F 224 ASP cc_start: 0.8388 (p0) cc_final: 0.8063 (p0) REVERT: F 276 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7105 (mmm160) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2477 time to fit residues: 93.2397 Evaluate side-chains 259 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102754 restraints weight = 47544.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107081 restraints weight = 24965.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110061 restraints weight = 16251.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112053 restraints weight = 12081.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113279 restraints weight = 9837.757| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9712 Z= 0.122 Angle : 0.646 12.453 13393 Z= 0.318 Chirality : 0.043 0.176 1480 Planarity : 0.005 0.078 1576 Dihedral : 15.775 110.002 1480 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: -1.41 (0.26), residues: 1086 helix: 0.55 (0.31), residues: 312 sheet: -1.12 (0.43), residues: 143 loop : -1.73 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 199 TYR 0.019 0.002 TYR B 206 PHE 0.014 0.001 PHE F 143 TRP 0.017 0.001 TRP B 203 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9711) covalent geometry : angle 0.64595 (13393) hydrogen bonds : bond 0.02847 ( 218) hydrogen bonds : angle 4.87982 ( 598) Misc. bond : bond 0.00499 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3265.42 seconds wall clock time: 56 minutes 18.58 seconds (3378.58 seconds total)