Starting phenix.real_space_refine on Sat Jul 4 03:22:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7las_23250/07_2026/7las_23250_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7las_23250/07_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_23250/07_2026/7las_23250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7las_23250/07_2026/7las_23250.map" model { file = "/net/cci-nas-00/data/ceres_data/7las_23250/07_2026/7las_23250_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7las_23250/07_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-6108/lib/python3.11/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: 2.95, per 1000 atoms: 0.16 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: 1.44 Conformation dependent library (CDL) restraints added in 526.8 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: 2.68 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: 2.88 Time building geometry restraints manager: 2.04 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: 1254 0.086 - 0.172: 220 0.172 - 0.258: 4 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=" C3' DT G 4 " pdb=" C4' DT G 4 " pdb=" O3' DT G 4 " pdb=" C2' DT G 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.61e-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: 0.970 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: 0.110 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.160 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.010 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.010 0.161 9712 Z= 0.469 Angle : 1.371 42.339 13393 Z= 0.789 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/Z covalent geometry : bond 0.00949 / 0.46 ( 9711) covalent geometry : angle 1.37050 / 0.79 (13393) hydrogen bonds : bond 0.22504 / 15.42 ( 218) hydrogen bonds : angle 8.96742 / 6.91 ( 598) Misc. bond : bond 0.06290 / 3.31 ( 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 : 0.315 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: 0.2225 time to fit residues: 137.9603 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 : 0.467 ------------------------------------------------------------------------------- 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: 10.0000 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... 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 = 0.3627 r_free = 0.3627 target = 0.139615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109394 restraints weight = 47014.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114351 restraints weight = 24050.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117614 restraints weight = 15162.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119842 restraints weight = 11003.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121138 restraints weight = 8729.151| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 9712 Z= 0.221 Angle : 0.874 16.345 13393 Z= 0.445 Chirality : 0.050 0.293 1480 Planarity : 0.006 0.103 1576 Dihedral : 18.053 174.413 1480 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.66 % Favored : 91.16 % Rotamer: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.27 % 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: -2.55 (0.24), residues: 1086 helix: -0.95 (0.27), residues: 308 sheet: -1.65 (0.40), residues: 166 loop : -2.14 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 163 TYR 0.030 0.002 TYR E 275 PHE 0.021 0.002 PHE C 283 TRP 0.030 0.002 TRP F 202 HIS 0.008 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 ( 9711) covalent geometry : angle 0.87438 / 0.44 (13393) hydrogen bonds : bond 0.05669 / 3.83 ( 218) hydrogen bonds : angle 6.34423 / 4.50 ( 598) Misc. bond : bond 0.00090 / 0.05 ( 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 330 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 0.508 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: 0.9029 (p90) cc_final: 0.8476 (p90) REVERT: A 201 LYS cc_start: 0.7781 (pttp) cc_final: 0.7422 (pttp) REVERT: A 207 HIS cc_start: 0.7448 (m90) cc_final: 0.6999 (m90) REVERT: B 148 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7730 (tpp-160) REVERT: B 161 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7582 (mt0) REVERT: B 225 ASP cc_start: 0.8925 (t0) cc_final: 0.8674 (t0) REVERT: B 256 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7711 (m-40) REVERT: B 281 LEU cc_start: 0.8754 (tt) cc_final: 0.8510 (tt) REVERT: B 299 VAL cc_start: 0.5613 (m) cc_final: 0.5152 (m) REVERT: D 148 ARG cc_start: 0.8399 (tpt90) cc_final: 0.8096 (mtm-85) REVERT: D 161 GLN cc_start: 0.8677 (mt0) cc_final: 0.8054 (tp-100) REVERT: D 178 CYS cc_start: 0.8896 (p) cc_final: 0.8517 (p) REVERT: D 238 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7207 (mt-10) REVERT: D 276 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7516 (tpp-160) REVERT: D 278 ILE cc_start: 0.9168 (mm) cc_final: 0.8787 (mm) REVERT: D 285 LYS cc_start: 0.6478 (ptpt) cc_final: 0.6272 (ptpt) REVERT: E 166 LYS cc_start: 0.8087 (tptp) cc_final: 0.7421 (ptpp) REVERT: E 207 HIS cc_start: 0.6596 (t70) cc_final: 0.6144 (t70) REVERT: E 228 ARG cc_start: 0.8862 (ttm-80) cc_final: 0.8531 (mtm-85) REVERT: E 247 LEU cc_start: 0.8982 (pt) cc_final: 0.8508 (pp) REVERT: E 261 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7549 (tm-30) REVERT: F 137 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8317 (tm-30) REVERT: F 140 PRO cc_start: 0.9319 (Cg_endo) cc_final: 0.8950 (Cg_exo) REVERT: F 196 LYS cc_start: 0.8701 (tttp) cc_final: 0.8439 (tttp) REVERT: F 216 ASP cc_start: 0.7814 (t0) cc_final: 0.7120 (p0) REVERT: F 217 PHE cc_start: 0.7965 (t80) cc_final: 0.7688 (t80) REVERT: F 224 ASP cc_start: 0.8714 (p0) cc_final: 0.8449 (p0) REVERT: F 232 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.7012 (mtm180) REVERT: F 276 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.7158 (mmm160) REVERT: F 278 ILE cc_start: 0.8743 (mt) cc_final: 0.8518 (mt) outliers start: 1 outliers final: 0 residues processed: 329 average time/residue: 0.2086 time to fit residues: 91.3574 Evaluate side-chains 277 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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: 6.9990 chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 ASN C 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.106589 restraints weight = 47328.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.111198 restraints weight = 24306.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114341 restraints weight = 15501.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116449 restraints weight = 11304.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117868 restraints weight = 9053.241| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9712 Z= 0.189 Angle : 0.761 13.166 13393 Z= 0.381 Chirality : 0.047 0.266 1480 Planarity : 0.005 0.053 1576 Dihedral : 17.604 173.947 1480 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -0.37 (0.28), residues: 297 sheet: -1.72 (0.40), residues: 162 loop : -1.89 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 163 TYR 0.021 0.002 TYR F 194 PHE 0.010 0.001 PHE D 283 TRP 0.021 0.001 TRP F 202 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 9711) covalent geometry : angle 0.76087 / 0.38 (13393) hydrogen bonds : bond 0.04628 / 3.19 ( 218) hydrogen bonds : angle 5.95150 / 4.22 ( 598) Misc. bond : bond 0.01146 / 0.60 ( 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 310 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.420 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: A 147 PHE cc_start: 0.9077 (p90) cc_final: 0.8556 (p90) REVERT: A 201 LYS cc_start: 0.7744 (pttp) cc_final: 0.7379 (pttp) REVERT: A 206 TYR cc_start: 0.8416 (t80) cc_final: 0.8165 (t80) REVERT: A 207 HIS cc_start: 0.7366 (m90) cc_final: 0.7047 (m90) REVERT: A 238 GLU cc_start: 0.8649 (pm20) cc_final: 0.8426 (pm20) REVERT: B 161 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7511 (mt0) REVERT: B 225 ASP cc_start: 0.8930 (t0) cc_final: 0.8679 (t0) REVERT: C 187 PHE cc_start: 0.8636 (t80) cc_final: 0.8373 (t80) REVERT: D 148 ARG cc_start: 0.8463 (tpt90) cc_final: 0.8206 (mtm-85) REVERT: D 161 GLN cc_start: 0.8723 (mt0) cc_final: 0.8101 (tp-100) REVERT: D 178 CYS cc_start: 0.8919 (p) cc_final: 0.8494 (p) REVERT: D 227 LEU cc_start: 0.8687 (mt) cc_final: 0.8464 (tp) REVERT: D 238 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7030 (mp0) REVERT: D 276 ARG cc_start: 0.7865 (ttm110) cc_final: 0.7532 (tpp-160) REVERT: D 278 ILE cc_start: 0.9182 (mm) cc_final: 0.8775 (mm) REVERT: E 166 LYS cc_start: 0.8187 (tptp) cc_final: 0.7407 (ptpp) REVERT: E 207 HIS cc_start: 0.6647 (t70) cc_final: 0.6154 (t70) REVERT: E 228 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.8306 (mtm-85) REVERT: E 247 LEU cc_start: 0.9022 (pt) cc_final: 0.8527 (pp) REVERT: F 137 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8288 (tm-30) REVERT: F 140 PRO cc_start: 0.9292 (Cg_endo) cc_final: 0.8949 (Cg_exo) REVERT: F 238 GLU cc_start: 0.7095 (pp20) cc_final: 0.6863 (pp20) REVERT: F 276 ARG cc_start: 0.7646 (ttm-80) cc_final: 0.6987 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2110 time to fit residues: 88.3677 Evaluate side-chains 268 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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: 7.9990 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 50.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN B 168 ASN C 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.105765 restraints weight = 47379.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110380 restraints weight = 24165.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113472 restraints weight = 15306.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115588 restraints weight = 11150.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117013 restraints weight = 8881.969| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9712 Z= 0.162 Angle : 0.726 15.534 13393 Z= 0.366 Chirality : 0.044 0.193 1480 Planarity : 0.006 0.083 1576 Dihedral : 17.498 165.597 1480 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % 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 : 0.58 % 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: -2.06 (0.25), residues: 1086 helix: -0.21 (0.29), residues: 309 sheet: -1.64 (0.40), residues: 155 loop : -1.96 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 249 TYR 0.028 0.002 TYR F 206 PHE 0.009 0.001 PHE E 147 TRP 0.035 0.001 TRP D 202 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9711) covalent geometry : angle 0.72609 / 0.37 (13393) hydrogen bonds : bond 0.03871 / 2.65 ( 218) hydrogen bonds : angle 5.73496 / 4.07 ( 598) Misc. bond : bond 0.00570 / 0.30 ( 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 310 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.406 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: A 147 PHE cc_start: 0.9070 (p90) cc_final: 0.8537 (p90) REVERT: A 165 TRP cc_start: 0.7851 (p90) cc_final: 0.7626 (p90) REVERT: A 201 LYS cc_start: 0.7681 (pttp) cc_final: 0.7363 (pttp) REVERT: A 207 HIS cc_start: 0.7324 (m90) cc_final: 0.7000 (m90) REVERT: A 238 GLU cc_start: 0.8679 (pm20) cc_final: 0.8454 (pm20) REVERT: B 161 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7542 (mt0) REVERT: C 138 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8559 (mm-40) REVERT: C 187 PHE cc_start: 0.8581 (t80) cc_final: 0.8291 (t80) REVERT: D 137 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7860 (tm-30) REVERT: D 148 ARG cc_start: 0.8474 (tpt90) cc_final: 0.8237 (mtm-85) REVERT: D 161 GLN cc_start: 0.8692 (mt0) cc_final: 0.8102 (tp-100) REVERT: D 178 CYS cc_start: 0.8861 (p) cc_final: 0.8475 (p) REVERT: D 202 TRP cc_start: 0.7963 (m-90) cc_final: 0.7759 (m-10) REVERT: D 217 PHE cc_start: 0.9338 (t80) cc_final: 0.8579 (t80) REVERT: D 227 LEU cc_start: 0.8691 (mt) cc_final: 0.8449 (tp) REVERT: D 238 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7032 (mp0) REVERT: D 276 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7496 (tpp-160) REVERT: E 166 LYS cc_start: 0.8214 (tptp) cc_final: 0.7410 (ptpp) REVERT: E 207 HIS cc_start: 0.6654 (t70) cc_final: 0.6102 (t70) REVERT: F 137 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8293 (tm-30) REVERT: F 140 PRO cc_start: 0.9308 (Cg_endo) cc_final: 0.8985 (Cg_exo) REVERT: F 142 THR cc_start: 0.8394 (p) cc_final: 0.8108 (p) REVERT: F 224 ASP cc_start: 0.8586 (p0) cc_final: 0.8335 (p0) REVERT: F 276 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.7010 (mmm160) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1934 time to fit residues: 81.8040 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 : 0.470 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 109 optimal weight: 50.0000 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107096 restraints weight = 47094.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.111749 restraints weight = 23890.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114908 restraints weight = 15054.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116989 restraints weight = 10937.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118373 restraints weight = 8759.705| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5651 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 : 0.694 13.597 13393 Z= 0.345 Chirality : 0.044 0.227 1480 Planarity : 0.005 0.047 1576 Dihedral : 17.280 169.341 1480 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -1.89 (0.25), residues: 1086 helix: 0.06 (0.29), residues: 309 sheet: -1.61 (0.40), residues: 155 loop : -1.91 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 228 TYR 0.024 0.002 TYR F 194 PHE 0.035 0.002 PHE B 283 TRP 0.016 0.001 TRP F 203 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9711) covalent geometry : angle 0.69406 / 0.34 (13393) hydrogen bonds : bond 0.03529 / 2.40 ( 218) hydrogen bonds : angle 5.46831 / 3.91 ( 598) Misc. bond : bond 0.00001 / 0.00 ( 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 298 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.315 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 147 PHE cc_start: 0.9074 (p90) cc_final: 0.8524 (p90) REVERT: A 201 LYS cc_start: 0.7654 (pttp) cc_final: 0.7292 (pttp) REVERT: A 207 HIS cc_start: 0.7312 (m90) cc_final: 0.7050 (m90) REVERT: A 238 GLU cc_start: 0.8659 (pm20) cc_final: 0.8443 (pm20) REVERT: B 161 GLN cc_start: 0.7969 (tp-100) cc_final: 0.7600 (mt0) REVERT: C 138 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8590 (mm-40) REVERT: C 187 PHE cc_start: 0.8487 (t80) cc_final: 0.8218 (t80) REVERT: D 129 SER cc_start: 0.7534 (p) cc_final: 0.7250 (p) REVERT: D 148 ARG cc_start: 0.8430 (tpt90) cc_final: 0.8230 (mtm-85) REVERT: D 161 GLN cc_start: 0.8669 (mt0) cc_final: 0.8076 (tp-100) REVERT: D 178 CYS cc_start: 0.8839 (p) cc_final: 0.8450 (p) REVERT: D 202 TRP cc_start: 0.8131 (m-90) cc_final: 0.7655 (m-10) REVERT: D 217 PHE cc_start: 0.9343 (t80) cc_final: 0.8551 (t80) REVERT: D 227 LEU cc_start: 0.8693 (mt) cc_final: 0.8460 (tp) REVERT: D 238 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7084 (mp0) REVERT: D 276 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7475 (tpp-160) REVERT: D 278 ILE cc_start: 0.9168 (mm) cc_final: 0.8928 (mm) REVERT: E 166 LYS cc_start: 0.8211 (tptp) cc_final: 0.7399 (ptpp) REVERT: E 207 HIS cc_start: 0.6651 (t70) cc_final: 0.6113 (t70) REVERT: F 137 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8292 (tm-30) REVERT: F 140 PRO cc_start: 0.9305 (Cg_endo) cc_final: 0.8949 (Cg_exo) REVERT: F 142 THR cc_start: 0.8336 (p) cc_final: 0.8045 (p) REVERT: F 196 LYS cc_start: 0.8709 (tttt) cc_final: 0.8444 (tttp) REVERT: F 276 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.6965 (mmm160) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1948 time to fit residues: 78.8025 Evaluate side-chains 256 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 3.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 HIS C 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105344 restraints weight = 46826.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109908 restraints weight = 24082.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.113010 restraints weight = 15393.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114947 restraints weight = 11272.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116443 restraints weight = 9140.783| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9712 Z= 0.156 Angle : 0.694 15.803 13393 Z= 0.347 Chirality : 0.044 0.190 1480 Planarity : 0.005 0.057 1576 Dihedral : 17.126 160.401 1480 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % 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 : 0.39 % 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: -1.88 (0.25), residues: 1086 helix: 0.01 (0.29), residues: 309 sheet: -1.43 (0.46), residues: 131 loop : -1.91 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.025 0.002 TYR F 206 PHE 0.020 0.001 PHE B 283 TRP 0.021 0.001 TRP F 203 HIS 0.003 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 9711) covalent geometry : angle 0.69362 / 0.35 (13393) hydrogen bonds : bond 0.03402 / 2.31 ( 218) hydrogen bonds : angle 5.52396 / 3.96 ( 598) Misc. bond : bond 0.00161 / 0.08 ( 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 299 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.301 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 147 PHE cc_start: 0.9099 (p90) cc_final: 0.8536 (p90) REVERT: A 201 LYS cc_start: 0.7651 (pttp) cc_final: 0.7395 (pttp) REVERT: A 207 HIS cc_start: 0.7272 (m90) cc_final: 0.7042 (m90) REVERT: A 238 GLU cc_start: 0.8675 (pm20) cc_final: 0.8470 (pm20) REVERT: B 161 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7607 (mt0) REVERT: C 138 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8683 (mm-40) REVERT: C 187 PHE cc_start: 0.8489 (t80) cc_final: 0.8256 (t80) REVERT: D 129 SER cc_start: 0.7638 (p) cc_final: 0.7055 (p) REVERT: D 161 GLN cc_start: 0.8637 (mt0) cc_final: 0.8044 (tp-100) REVERT: D 178 CYS cc_start: 0.8877 (p) cc_final: 0.8476 (p) REVERT: D 202 TRP cc_start: 0.8281 (m-90) cc_final: 0.7704 (m-10) REVERT: D 217 PHE cc_start: 0.9389 (t80) cc_final: 0.8564 (t80) REVERT: D 238 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7172 (mp0) REVERT: D 276 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7434 (tpp-160) REVERT: E 166 LYS cc_start: 0.8249 (tptp) cc_final: 0.7419 (ptpp) REVERT: E 199 ARG cc_start: 0.7384 (mtm110) cc_final: 0.6683 (mtm110) REVERT: E 202 TRP cc_start: 0.8566 (m-90) cc_final: 0.8350 (m-90) REVERT: E 207 HIS cc_start: 0.6618 (t70) cc_final: 0.6055 (t70) REVERT: E 247 LEU cc_start: 0.8945 (pt) cc_final: 0.8546 (pp) REVERT: F 137 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8244 (tm-30) REVERT: F 142 THR cc_start: 0.8291 (p) cc_final: 0.8026 (p) REVERT: F 199 ARG cc_start: 0.5610 (mmt180) cc_final: 0.4745 (mmt180) REVERT: F 201 LYS cc_start: 0.6737 (tptt) cc_final: 0.5434 (tptt) REVERT: F 224 ASP cc_start: 0.8658 (p0) cc_final: 0.8446 (p0) REVERT: F 276 ARG cc_start: 0.7444 (ttm-80) cc_final: 0.7027 (mmm160) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1930 time to fit residues: 78.0825 Evaluate side-chains 254 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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: 7.9990 chunk 96 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 109 optimal weight: 50.0000 chunk 17 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.103079 restraints weight = 48034.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107417 restraints weight = 24842.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.110405 restraints weight = 16043.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112324 restraints weight = 11837.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113708 restraints weight = 9643.520| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9712 Z= 0.220 Angle : 0.721 14.347 13393 Z= 0.365 Chirality : 0.045 0.244 1480 Planarity : 0.005 0.056 1576 Dihedral : 17.049 147.239 1480 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -1.99 (0.25), residues: 1086 helix: -0.14 (0.29), residues: 309 sheet: -1.54 (0.40), residues: 161 loop : -1.94 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 228 TYR 0.028 0.002 TYR F 194 PHE 0.024 0.002 PHE B 283 TRP 0.014 0.001 TRP B 203 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 ( 9711) covalent geometry : angle 0.72096 / 0.37 (13393) hydrogen bonds : bond 0.03401 / 2.30 ( 218) hydrogen bonds : angle 5.63443 / 4.04 ( 598) Misc. bond : bond 0.00015 / 0.01 ( 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 290 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.457 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 147 PHE cc_start: 0.9081 (p90) cc_final: 0.8543 (p90) REVERT: A 200 ASN cc_start: 0.7773 (t0) cc_final: 0.7467 (t0) REVERT: A 201 LYS cc_start: 0.7627 (pttp) cc_final: 0.7141 (ptmm) REVERT: A 238 GLU cc_start: 0.8694 (pm20) cc_final: 0.8474 (pm20) REVERT: B 161 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7537 (mt0) REVERT: B 240 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7660 (mtpp) REVERT: C 138 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8776 (mm-40) REVERT: C 189 ASP cc_start: 0.8256 (p0) cc_final: 0.7975 (p0) REVERT: D 129 SER cc_start: 0.7702 (p) cc_final: 0.7335 (p) REVERT: D 161 GLN cc_start: 0.8680 (mt0) cc_final: 0.8058 (tp-100) REVERT: D 178 CYS cc_start: 0.8982 (p) cc_final: 0.8597 (p) REVERT: D 202 TRP cc_start: 0.8493 (m-90) cc_final: 0.7818 (m-10) REVERT: D 238 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7234 (mp0) REVERT: D 276 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7427 (tpp-160) REVERT: E 166 LYS cc_start: 0.8314 (tptp) cc_final: 0.7454 (ptpp) REVERT: E 199 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7377 (mtm110) REVERT: E 247 LEU cc_start: 0.8932 (pt) cc_final: 0.8520 (pp) REVERT: F 137 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8241 (tm-30) REVERT: F 142 THR cc_start: 0.8318 (p) cc_final: 0.8029 (p) REVERT: F 201 LYS cc_start: 0.6659 (tptt) cc_final: 0.6129 (tptt) REVERT: F 224 ASP cc_start: 0.8647 (p0) cc_final: 0.8445 (p0) REVERT: F 238 GLU cc_start: 0.8568 (pm20) cc_final: 0.8277 (pm20) REVERT: F 276 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.7028 (mmm160) REVERT: F 278 ILE cc_start: 0.8721 (mt) cc_final: 0.8503 (mt) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1916 time to fit residues: 76.3265 Evaluate side-chains 246 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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: 0.6980 chunk 88 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3561 r_free = 0.3561 target = 0.134646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104785 restraints weight = 47018.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.109397 restraints weight = 24252.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112483 restraints weight = 15477.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114371 restraints weight = 11361.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115966 restraints weight = 9256.486| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9712 Z= 0.125 Angle : 0.672 13.385 13393 Z= 0.335 Chirality : 0.044 0.193 1480 Planarity : 0.005 0.058 1576 Dihedral : 16.886 142.074 1480 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.82 (0.25), residues: 1086 helix: 0.07 (0.30), residues: 309 sheet: -1.41 (0.44), residues: 141 loop : -1.88 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 277 TYR 0.032 0.002 TYR F 194 PHE 0.035 0.002 PHE E 147 TRP 0.021 0.001 TRP F 203 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9711) covalent geometry : angle 0.67201 / 0.33 (13393) hydrogen bonds : bond 0.03095 / 2.09 ( 218) hydrogen bonds : angle 5.42811 / 3.91 ( 598) Misc. bond : bond 0.00059 / 0.03 ( 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 292 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.300 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: 0.9057 (p90) cc_final: 0.8515 (p90) REVERT: A 201 LYS cc_start: 0.7599 (pttp) cc_final: 0.7287 (ptmm) REVERT: A 238 GLU cc_start: 0.8724 (pm20) cc_final: 0.8497 (pm20) REVERT: B 161 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7664 (mt0) REVERT: B 183 TRP cc_start: 0.8443 (t60) cc_final: 0.7599 (t-100) REVERT: B 240 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7627 (mtpp) REVERT: B 293 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7404 (tm-30) REVERT: C 189 ASP cc_start: 0.8238 (p0) cc_final: 0.7936 (p0) REVERT: D 137 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8086 (tm-30) REVERT: D 161 GLN cc_start: 0.8605 (mt0) cc_final: 0.7966 (tp-100) REVERT: D 178 CYS cc_start: 0.8917 (p) cc_final: 0.8483 (p) REVERT: D 202 TRP cc_start: 0.8476 (m-90) cc_final: 0.7684 (m-10) REVERT: D 217 PHE cc_start: 0.9403 (t80) cc_final: 0.8563 (t80) REVERT: D 238 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7296 (mp0) REVERT: D 276 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7618 (tpt90) REVERT: D 278 ILE cc_start: 0.9167 (mm) cc_final: 0.8890 (mm) REVERT: E 166 LYS cc_start: 0.8299 (tptp) cc_final: 0.7410 (ptpp) REVERT: E 199 ARG cc_start: 0.7549 (mtm110) cc_final: 0.7135 (mtm110) REVERT: E 200 ASN cc_start: 0.8736 (t0) cc_final: 0.8383 (m-40) REVERT: E 207 HIS cc_start: 0.6631 (t70) cc_final: 0.6087 (t70) REVERT: E 215 ASP cc_start: 0.8765 (t0) cc_final: 0.8562 (t0) REVERT: E 247 LEU cc_start: 0.8900 (pt) cc_final: 0.8526 (pp) REVERT: F 137 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8259 (tm-30) REVERT: F 142 THR cc_start: 0.8282 (p) cc_final: 0.7976 (p) REVERT: F 201 LYS cc_start: 0.6506 (tptt) cc_final: 0.6114 (tptt) REVERT: F 276 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.6970 (mmm160) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1971 time to fit residues: 78.5767 Evaluate side-chains 248 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 0.8980 chunk 72 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3528 r_free = 0.3528 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102428 restraints weight = 47569.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106742 restraints weight = 24937.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109704 restraints weight = 16163.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111700 restraints weight = 11978.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.113041 restraints weight = 9721.338| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9712 Z= 0.208 Angle : 0.723 13.558 13393 Z= 0.362 Chirality : 0.044 0.166 1480 Planarity : 0.005 0.046 1576 Dihedral : 16.869 130.951 1480 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.89 (0.25), residues: 1086 helix: -0.13 (0.29), residues: 310 sheet: -1.37 (0.44), residues: 141 loop : -1.86 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 277 TYR 0.053 0.002 TYR F 194 PHE 0.020 0.002 PHE E 147 TRP 0.016 0.001 TRP F 203 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 ( 9711) covalent geometry : angle 0.72251 / 0.36 (13393) hydrogen bonds : bond 0.03324 / 2.22 ( 218) hydrogen bonds : angle 5.49635 / 3.96 ( 598) Misc. bond : bond 0.01407 / 0.74 ( 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 281 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.489 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: 0.9069 (p90) cc_final: 0.8535 (p90) REVERT: A 200 ASN cc_start: 0.7821 (t0) cc_final: 0.7443 (m-40) REVERT: A 201 LYS cc_start: 0.7651 (pttp) cc_final: 0.7174 (ptmm) REVERT: A 216 ASP cc_start: 0.8102 (t0) cc_final: 0.7787 (m-30) REVERT: B 161 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7542 (mt0) REVERT: B 183 TRP cc_start: 0.8371 (t60) cc_final: 0.7651 (t-100) REVERT: C 189 ASP cc_start: 0.8268 (p0) cc_final: 0.7971 (p0) REVERT: C 276 ARG cc_start: 0.5382 (tpm170) cc_final: 0.4825 (tpm170) REVERT: D 161 GLN cc_start: 0.8602 (mt0) cc_final: 0.7984 (tp-100) REVERT: D 178 CYS cc_start: 0.8983 (p) cc_final: 0.8593 (p) REVERT: D 202 TRP cc_start: 0.8614 (m-90) cc_final: 0.8377 (m-90) REVERT: D 238 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7238 (mp0) REVERT: D 276 ARG cc_start: 0.8057 (ttm110) cc_final: 0.7618 (tpt90) REVERT: E 166 LYS cc_start: 0.8337 (tptp) cc_final: 0.7467 (ptpp) REVERT: E 215 ASP cc_start: 0.8883 (t0) cc_final: 0.8680 (t0) REVERT: E 247 LEU cc_start: 0.8950 (pt) cc_final: 0.8533 (pp) REVERT: F 137 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8245 (tm-30) REVERT: F 142 THR cc_start: 0.8320 (p) cc_final: 0.8024 (p) REVERT: F 276 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7017 (mmm160) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.1944 time to fit residues: 74.8139 Evaluate side-chains 247 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 0.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3554 r_free = 0.3554 target = 0.133973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104273 restraints weight = 46913.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108740 restraints weight = 24397.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111767 restraints weight = 15726.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113756 restraints weight = 11566.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115015 restraints weight = 9363.018| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9712 Z= 0.127 Angle : 0.687 16.447 13393 Z= 0.342 Chirality : 0.043 0.147 1480 Planarity : 0.005 0.078 1576 Dihedral : 16.610 122.936 1480 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.27 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 : 0.19 % 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: -1.65 (0.25), residues: 1086 helix: 0.21 (0.30), residues: 310 sheet: -1.28 (0.43), residues: 141 loop : -1.78 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 199 TYR 0.041 0.002 TYR F 194 PHE 0.031 0.001 PHE E 147 TRP 0.031 0.001 TRP F 203 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 9711) covalent geometry : angle 0.68663 / 0.34 (13393) hydrogen bonds : bond 0.03013 / 2.01 ( 218) hydrogen bonds : angle 5.21133 / 3.75 ( 598) Misc. bond : bond 0.00409 / 0.22 ( 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 286 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.520 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: A 147 PHE cc_start: 0.9050 (p90) cc_final: 0.8514 (p90) REVERT: A 215 ASP cc_start: 0.8482 (t0) cc_final: 0.8202 (t0) REVERT: A 216 ASP cc_start: 0.8003 (t0) cc_final: 0.7669 (m-30) REVERT: B 161 GLN cc_start: 0.8011 (tp-100) cc_final: 0.7633 (mt0) REVERT: C 189 ASP cc_start: 0.8193 (p0) cc_final: 0.7796 (p0) REVERT: C 276 ARG cc_start: 0.5291 (tpm170) cc_final: 0.4731 (tpm170) REVERT: D 128 GLU cc_start: 0.8447 (pp20) cc_final: 0.8101 (pp20) REVERT: D 129 SER cc_start: 0.7607 (p) cc_final: 0.6978 (p) REVERT: D 161 GLN cc_start: 0.8552 (mt0) cc_final: 0.7927 (tp-100) REVERT: D 178 CYS cc_start: 0.8908 (p) cc_final: 0.8500 (p) REVERT: D 202 TRP cc_start: 0.8597 (m-90) cc_final: 0.8303 (m-90) REVERT: D 217 PHE cc_start: 0.9392 (t80) cc_final: 0.8555 (t80) REVERT: D 238 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7270 (mp0) REVERT: D 247 LEU cc_start: 0.9189 (mt) cc_final: 0.8977 (mt) REVERT: D 276 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7568 (tpt90) REVERT: E 166 LYS cc_start: 0.8315 (tptp) cc_final: 0.7471 (ptpp) REVERT: E 200 ASN cc_start: 0.8791 (t0) cc_final: 0.8431 (m-40) REVERT: E 207 HIS cc_start: 0.6560 (t70) cc_final: 0.6040 (t70) REVERT: E 247 LEU cc_start: 0.8921 (pt) cc_final: 0.8539 (pp) REVERT: F 137 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8274 (tm-30) REVERT: F 142 THR cc_start: 0.8317 (p) cc_final: 0.8009 (p) REVERT: F 165 TRP cc_start: 0.8545 (p90) cc_final: 0.8167 (p90) REVERT: F 224 ASP cc_start: 0.8698 (p0) cc_final: 0.8402 (p0) REVERT: F 276 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7027 (mmm160) REVERT: F 278 ILE cc_start: 0.8678 (mt) cc_final: 0.8434 (mt) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2339 time to fit residues: 91.3770 Evaluate side-chains 252 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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: 8.9990 chunk 2 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3561 r_free = 0.3561 target = 0.134408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.104773 restraints weight = 47328.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109191 restraints weight = 24400.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.112245 restraints weight = 15661.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114258 restraints weight = 11506.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115578 restraints weight = 9303.601| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9712 Z= 0.120 Angle : 0.672 16.266 13393 Z= 0.334 Chirality : 0.043 0.161 1480 Planarity : 0.005 0.078 1576 Dihedral : 16.450 116.877 1480 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % 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 : 0.29 % 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: 0.34 (0.30), residues: 310 sheet: -1.27 (0.42), residues: 141 loop : -1.75 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 199 TYR 0.039 0.002 TYR F 194 PHE 0.013 0.001 PHE B 283 TRP 0.027 0.001 TRP A 202 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9711) covalent geometry : angle 0.67237 / 0.33 (13393) hydrogen bonds : bond 0.02905 / 1.94 ( 218) hydrogen bonds : angle 5.13568 / 3.71 ( 598) Misc. bond : bond 0.00235 / 0.12 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.45 seconds wall clock time: 51 minutes 34.11 seconds (3094.11 seconds total)