Starting phenix.real_space_refine on Sat Sep 12 19:49:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7las_23250/09_2026/7las_23250_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7las_23250/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7las_23250/09_2026/7las_23250_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7las_23250/09_2026/7las_23250_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7las_23250/09_2026/7las_23250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7las_23250/09_2026/7las_23250.map" } 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-2.2.1-6174/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: 3.84, per 1000 atoms: 0.21 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: 1.88 Conformation dependent library (CDL) restraints added in 826.7 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 13 sheets defined 36.2% alpha, 13.3% beta 1 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.540A pdb=" N SER A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.609A pdb=" N PHE A 143 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.671A pdb=" N ALA A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.697A pdb=" N TRP A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.575A pdb=" N THR A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.651A pdb=" N TRP A 262 " --> pdb=" O PRO A 259 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 removed outlier: 4.332A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 128 removed outlier: 3.582A pdb=" N GLU B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.934A pdb=" N LEU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 186 removed outlier: 4.074A pdb=" N TRP B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.724A pdb=" N CYS B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.978A pdb=" N TYR B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 130 removed outlier: 3.625A pdb=" N GLU C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.731A pdb=" N VAL C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 removed outlier: 3.609A pdb=" N ARG C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.629A pdb=" N GLY C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 186 Processing helix chain 'C' and resid 222 through 230 removed outlier: 4.145A pdb=" N CYS C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.549A pdb=" N TRP C 262 " --> pdb=" O PRO C 259 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 263 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 removed outlier: 4.027A pdb=" N TYR C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.867A pdb=" N VAL D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 143 Processing helix chain 'D' and resid 146 through 158 removed outlier: 3.604A pdb=" N GLY D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 186 removed outlier: 3.593A pdb=" N TRP D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 184 " --> pdb=" O LYS D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 271 through 276 removed outlier: 3.620A pdb=" N TYR D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 removed outlier: 3.784A pdb=" N GLU E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 139 Processing helix chain 'E' and resid 140 through 145 removed outlier: 3.752A pdb=" N ARG E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 158 removed outlier: 3.514A pdb=" N ALA E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY E 158 " --> pdb=" O LEU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 187 removed outlier: 3.508A pdb=" N TRP E 183 " --> pdb=" O GLY E 179 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE E 187 " --> pdb=" O TRP E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 3.748A pdb=" N CYS E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 127 Processing helix chain 'F' and resid 131 through 139 removed outlier: 3.884A pdb=" N VAL F 135 " --> pdb=" O SER F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 removed outlier: 4.118A pdb=" N ARG F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 158 Processing helix chain 'F' and resid 179 through 186 removed outlier: 3.531A pdb=" N TRP F 183 " --> pdb=" O GLY F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 188 No H-bonds generated for 'chain 'F' and resid 187 through 188' Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'F' and resid 222 through 230 removed outlier: 3.612A pdb=" N CYS F 230 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 removed outlier: 3.506A pdb=" N TRP F 262 " --> pdb=" O PRO F 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 196 removed outlier: 6.986A pdb=" N TYR A 194 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU A 210 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 250 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 214 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN A 168 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 253 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS A 170 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 169 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 282 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 171 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TRP A 284 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 291 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 239 Processing sheet with id=AA3, first strand: chain 'B' and resid 194 through 195 removed outlier: 6.670A pdb=" N GLU B 210 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN B 168 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE B 253 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N HIS B 170 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER B 255 " --> pdb=" O HIS B 170 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE B 172 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 169 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL B 282 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL B 171 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 236 through 239 removed outlier: 3.554A pdb=" N GLY B 242 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 195 removed outlier: 7.220A pdb=" N ASN C 168 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE C 253 " --> pdb=" O ASN C 168 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N HIS C 170 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 169 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU C 281 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 171 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE C 283 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 173 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS C 285 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 285 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AA7, first strand: chain 'D' and resid 193 through 194 removed outlier: 6.590A pdb=" N VAL D 212 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR D 254 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 214 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASN D 168 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE D 253 " --> pdb=" O ASN D 168 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS D 170 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL D 169 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL D 282 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 171 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 236 through 239 Processing sheet with id=AA9, first strand: chain 'E' and resid 170 through 172 removed outlier: 6.719A pdb=" N VAL E 171 " --> pdb=" O VAL E 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.871A pdb=" N TYR E 194 " --> pdb=" O VAL E 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 236 through 239 Processing sheet with id=AB3, first strand: chain 'F' and resid 210 through 212 removed outlier: 6.973A pdb=" N GLU F 210 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER F 250 " --> pdb=" O GLU F 210 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASN F 168 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL F 169 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL F 282 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL F 171 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N TRP F 284 " --> pdb=" O VAL F 171 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 235 through 239 removed outlier: 4.636A pdb=" N LEU F 235 " --> pdb=" O PHE F 246 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY F 242 " --> pdb=" O THR F 239 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 2.56 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 1.20e-02 6.94e+03 1.81e+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: 1 33.87 - 42.34: 2 Bond angle restraints: 32963 Sorted by residual: angle pdb=" C3' DT G 4 " pdb=" O3' DT G 4 " pdb=" P DT G 5 " ideal model delta sigma weight residual 119.70 86.10 33.60 1.20e+00 6.94e-01 7.84e+02 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 1.90e+00 2.77e-01 3.40e+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: 1.930 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: 0.120 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.340 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- 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= 0.476 Angle : 1.369 42.339 13393 Z= 0.791 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 / 0.47 ( 9711) covalent geometry : angle 1.36915 / 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 : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2607 time to fit residues: 162.3360 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 : 0.468 ------------------------------------------------------------------------------- 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: 9.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 HIS B 168 ASN D 138 GLN D 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109741 restraints weight = 46724.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114637 restraints weight = 23793.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117965 restraints weight = 14999.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120058 restraints weight = 10840.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121598 restraints weight = 8657.601| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9712 Z= 0.214 Angle : 0.867 16.288 13393 Z= 0.442 Chirality : 0.050 0.275 1480 Planarity : 0.006 0.104 1576 Dihedral : 18.037 178.770 1480 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.25 % Rotamer: Outliers : 0.10 % Allowed : 2.41 % Favored : 97.48 % 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: -2.52 (0.24), residues: 1086 helix: -0.92 (0.27), residues: 308 sheet: -1.64 (0.40), residues: 166 loop : -2.13 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 163 TYR 0.027 0.002 TYR E 275 PHE 0.021 0.002 PHE C 283 TRP 0.030 0.002 TRP F 202 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 ( 9711) covalent geometry : angle 0.86652 / 0.44 (13393) hydrogen bonds : bond 0.05693 / 3.86 ( 218) hydrogen bonds : angle 6.34861 / 4.50 ( 598) Misc. bond : bond 0.00129 / 0.07 ( 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 334 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.9027 (p90) cc_final: 0.8480 (p90) REVERT: A 201 LYS cc_start: 0.7789 (pttp) cc_final: 0.7431 (pttp) REVERT: A 207 HIS cc_start: 0.7436 (m90) cc_final: 0.6978 (m90) REVERT: A 218 TYR cc_start: 0.7478 (p90) cc_final: 0.7095 (p90) REVERT: B 148 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7728 (tpp-160) REVERT: B 161 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7644 (mt0) REVERT: B 168 ASN cc_start: 0.8764 (m-40) cc_final: 0.8553 (m110) REVERT: B 195 TRP cc_start: 0.9176 (m100) cc_final: 0.8681 (m100) REVERT: B 225 ASP cc_start: 0.8930 (t0) cc_final: 0.8689 (t0) REVERT: B 256 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7736 (m-40) REVERT: B 281 LEU cc_start: 0.8754 (tt) cc_final: 0.8509 (tt) REVERT: B 299 VAL cc_start: 0.5603 (m) cc_final: 0.5154 (m) REVERT: D 148 ARG cc_start: 0.8391 (tpt90) cc_final: 0.8097 (mtm-85) REVERT: D 161 GLN cc_start: 0.8675 (mt0) cc_final: 0.8048 (tp-100) REVERT: D 178 CYS cc_start: 0.8896 (p) cc_final: 0.8513 (p) REVERT: D 238 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7203 (mt-10) REVERT: D 276 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7513 (tpp-160) REVERT: D 278 ILE cc_start: 0.9140 (mm) cc_final: 0.8748 (mm) REVERT: D 285 LYS cc_start: 0.6439 (ptpt) cc_final: 0.6236 (ptpt) REVERT: E 166 LYS cc_start: 0.8079 (tptp) cc_final: 0.7418 (ptpp) REVERT: E 207 HIS cc_start: 0.6601 (t70) cc_final: 0.6153 (t70) REVERT: E 228 ARG cc_start: 0.8836 (ttm-80) cc_final: 0.8513 (mtm-85) REVERT: E 247 LEU cc_start: 0.8986 (pt) cc_final: 0.8511 (pp) REVERT: E 261 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7523 (tm-30) REVERT: F 137 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8312 (tm-30) REVERT: F 140 PRO cc_start: 0.9325 (Cg_endo) cc_final: 0.8883 (Cg_exo) REVERT: F 196 LYS cc_start: 0.8690 (tttp) cc_final: 0.8411 (tttp) REVERT: F 216 ASP cc_start: 0.7796 (t0) cc_final: 0.7115 (p0) REVERT: F 217 PHE cc_start: 0.7938 (t80) cc_final: 0.7671 (t80) REVERT: F 224 ASP cc_start: 0.8729 (p0) cc_final: 0.8449 (p0) REVERT: F 232 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.7027 (mtm180) REVERT: F 276 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7133 (mmm160) REVERT: F 278 ILE cc_start: 0.8726 (mt) cc_final: 0.8505 (mt) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.2507 time to fit residues: 111.6566 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 : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108713 restraints weight = 47137.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113390 restraints weight = 23831.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116515 restraints weight = 15114.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118710 restraints weight = 11033.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120057 restraints weight = 8802.894| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5133 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= 0.155 Angle : 0.753 13.296 13393 Z= 0.374 Chirality : 0.046 0.263 1480 Planarity : 0.005 0.050 1576 Dihedral : 17.527 172.708 1480 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: -2.15 (0.25), residues: 1086 helix: -0.36 (0.28), residues: 309 sheet: -1.64 (0.39), residues: 162 loop : -1.98 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 163 TYR 0.026 0.002 TYR F 194 PHE 0.010 0.001 PHE D 283 TRP 0.022 0.001 TRP F 202 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9711) covalent geometry : angle 0.75327 / 0.37 (13393) hydrogen bonds : bond 0.04464 / 3.08 ( 218) hydrogen bonds : angle 5.85446 / 4.15 ( 598) Misc. bond : bond 0.00196 / 0.10 ( 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 309 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.515 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 134 THR cc_start: 0.8382 (m) cc_final: 0.8167 (p) REVERT: A 147 PHE cc_start: 0.9074 (p90) cc_final: 0.8539 (p90) REVERT: A 201 LYS cc_start: 0.7693 (pttp) cc_final: 0.7344 (pttp) REVERT: A 207 HIS cc_start: 0.7345 (m90) cc_final: 0.7033 (m90) REVERT: A 238 GLU cc_start: 0.8654 (pm20) cc_final: 0.8436 (pm20) REVERT: B 161 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7457 (mt0) REVERT: B 225 ASP cc_start: 0.8869 (t0) cc_final: 0.8619 (t0) REVERT: B 281 LEU cc_start: 0.8746 (tt) cc_final: 0.8493 (tt) REVERT: C 187 PHE cc_start: 0.8599 (t80) cc_final: 0.8328 (t80) REVERT: D 148 ARG cc_start: 0.8431 (tpt90) cc_final: 0.8201 (mtm-85) REVERT: D 161 GLN cc_start: 0.8720 (mt0) cc_final: 0.8066 (tp-100) REVERT: D 178 CYS cc_start: 0.8873 (p) cc_final: 0.8424 (p) REVERT: D 238 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6977 (mp0) REVERT: D 276 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7486 (tpp-160) REVERT: D 278 ILE cc_start: 0.9162 (mm) cc_final: 0.8755 (mm) REVERT: E 166 LYS cc_start: 0.8142 (tptp) cc_final: 0.7382 (ptpp) REVERT: E 207 HIS cc_start: 0.6623 (t70) cc_final: 0.6100 (t70) REVERT: E 228 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8525 (mtm-85) REVERT: F 137 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8291 (tm-30) REVERT: F 140 PRO cc_start: 0.9219 (Cg_endo) cc_final: 0.8873 (Cg_exo) REVERT: F 232 ARG cc_start: 0.7274 (mtm-85) cc_final: 0.6961 (mtm180) REVERT: F 276 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.6918 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2499 time to fit residues: 103.8554 Evaluate side-chains 267 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 109 optimal weight: 50.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.135454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.105900 restraints weight = 47359.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110377 restraints weight = 24276.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113407 restraints weight = 15544.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115463 restraints weight = 11414.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116798 restraints weight = 9195.663| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9712 Z= 0.179 Angle : 0.735 15.841 13393 Z= 0.371 Chirality : 0.045 0.217 1480 Planarity : 0.006 0.091 1576 Dihedral : 17.425 164.154 1480 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -2.04 (0.25), residues: 1086 helix: -0.24 (0.29), residues: 309 sheet: -1.57 (0.40), residues: 155 loop : -1.93 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 199 TYR 0.026 0.002 TYR F 206 PHE 0.008 0.001 PHE E 147 TRP 0.032 0.001 TRP D 202 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 9711) covalent geometry : angle 0.73517 / 0.37 (13393) hydrogen bonds : bond 0.03961 / 2.65 ( 218) hydrogen bonds : angle 5.76632 / 4.10 ( 598) Misc. bond : bond 0.00165 / 0.09 ( 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 312 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.372 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: A 134 THR cc_start: 0.8376 (m) cc_final: 0.8147 (t) REVERT: A 147 PHE cc_start: 0.9081 (p90) cc_final: 0.8539 (p90) REVERT: A 201 LYS cc_start: 0.7706 (pttp) cc_final: 0.7364 (pttp) REVERT: A 207 HIS cc_start: 0.7351 (m90) cc_final: 0.6995 (m90) REVERT: A 238 GLU cc_start: 0.8674 (pm20) cc_final: 0.8448 (pm20) REVERT: B 161 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7508 (mt0) REVERT: B 225 ASP cc_start: 0.8923 (t70) cc_final: 0.8715 (t0) REVERT: C 138 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8553 (mm-40) REVERT: C 187 PHE cc_start: 0.8554 (t80) cc_final: 0.8284 (t80) REVERT: D 148 ARG cc_start: 0.8476 (tpt90) cc_final: 0.8258 (mtm-85) REVERT: D 161 GLN cc_start: 0.8702 (mt0) cc_final: 0.8131 (tp-100) REVERT: D 178 CYS cc_start: 0.8848 (p) cc_final: 0.8450 (p) REVERT: D 202 TRP cc_start: 0.7941 (m-90) cc_final: 0.7723 (m-10) REVERT: D 227 LEU cc_start: 0.8690 (mt) cc_final: 0.8489 (tp) REVERT: D 238 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6994 (mp0) REVERT: D 276 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7511 (tpp-160) REVERT: E 166 LYS cc_start: 0.8198 (tptp) cc_final: 0.7395 (ptpp) REVERT: E 207 HIS cc_start: 0.6626 (t70) cc_final: 0.6099 (t70) REVERT: F 137 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8291 (tm-30) REVERT: F 140 PRO cc_start: 0.9222 (Cg_endo) cc_final: 0.8887 (Cg_exo) REVERT: F 142 THR cc_start: 0.8356 (p) cc_final: 0.8095 (p) REVERT: F 224 ASP cc_start: 0.8611 (p0) cc_final: 0.8372 (p0) REVERT: F 232 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.7147 (mtm180) REVERT: F 276 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.7004 (mmm160) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2249 time to fit residues: 95.3096 Evaluate side-chains 263 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 109 optimal weight: 50.0000 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104990 restraints weight = 47300.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109368 restraints weight = 24137.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112387 restraints weight = 15499.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.114340 restraints weight = 11441.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115763 restraints weight = 9294.052| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9712 Z= 0.184 Angle : 0.719 12.822 13393 Z= 0.358 Chirality : 0.045 0.217 1480 Planarity : 0.005 0.054 1576 Dihedral : 17.208 162.305 1480 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: -1.98 (0.25), residues: 1086 helix: -0.09 (0.29), residues: 309 sheet: -1.73 (0.39), residues: 162 loop : -1.89 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 199 TYR 0.022 0.002 TYR F 194 PHE 0.042 0.002 PHE B 283 TRP 0.014 0.001 TRP F 203 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 9711) covalent geometry : angle 0.71915 / 0.36 (13393) hydrogen bonds : bond 0.03615 / 2.44 ( 218) hydrogen bonds : angle 5.55028 / 3.96 ( 598) Misc. bond : bond 0.01785 / 0.94 ( 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 295 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.483 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: 0.9089 (p90) cc_final: 0.8539 (p90) REVERT: A 201 LYS cc_start: 0.7661 (pttp) cc_final: 0.7418 (pttp) REVERT: A 207 HIS cc_start: 0.7342 (m90) cc_final: 0.7111 (m-70) REVERT: A 238 GLU cc_start: 0.8678 (pm20) cc_final: 0.8474 (pm20) REVERT: B 161 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7605 (mt0) REVERT: C 138 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8640 (mm-40) REVERT: C 187 PHE cc_start: 0.8532 (t80) cc_final: 0.8268 (t80) REVERT: D 129 SER cc_start: 0.7613 (p) cc_final: 0.7337 (p) REVERT: D 137 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7996 (tm-30) REVERT: D 161 GLN cc_start: 0.8682 (mt0) cc_final: 0.8080 (tp-100) REVERT: D 164 ASP cc_start: 0.8565 (p0) cc_final: 0.8360 (p0) REVERT: D 178 CYS cc_start: 0.8876 (p) cc_final: 0.8492 (p) REVERT: D 202 TRP cc_start: 0.8231 (m-90) cc_final: 0.7764 (m-10) REVERT: D 217 PHE cc_start: 0.9406 (t80) cc_final: 0.8650 (t80) REVERT: D 227 LEU cc_start: 0.8733 (mt) cc_final: 0.8506 (tp) REVERT: D 238 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7120 (mp0) REVERT: D 276 ARG cc_start: 0.7946 (ttm110) cc_final: 0.7449 (tpp-160) REVERT: E 166 LYS cc_start: 0.8234 (tptp) cc_final: 0.7423 (ptpp) REVERT: E 202 TRP cc_start: 0.8633 (m-90) cc_final: 0.8419 (m-90) REVERT: E 207 HIS cc_start: 0.6609 (t70) cc_final: 0.6077 (t70) REVERT: F 137 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8288 (tm-30) REVERT: F 140 PRO cc_start: 0.9208 (Cg_endo) cc_final: 0.8881 (Cg_exo) REVERT: F 142 THR cc_start: 0.8314 (p) cc_final: 0.8044 (p) REVERT: F 200 ASN cc_start: 0.6567 (p0) cc_final: 0.6356 (m-40) REVERT: F 224 ASP cc_start: 0.8464 (p0) cc_final: 0.8235 (p0) REVERT: F 232 ARG cc_start: 0.7305 (mtm-85) cc_final: 0.6759 (mtm180) REVERT: F 276 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.7011 (mmm160) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2245 time to fit residues: 90.9411 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 : 0.502 ------------------------------------------------------------------------------- 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: 7.9990 chunk 75 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 107 optimal weight: 30.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN B 139 HIS B 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103614 restraints weight = 47063.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107950 restraints weight = 24414.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.110863 restraints weight = 15739.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112826 restraints weight = 11694.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114163 restraints weight = 9484.897| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9712 Z= 0.189 Angle : 0.714 15.539 13393 Z= 0.360 Chirality : 0.045 0.190 1480 Planarity : 0.005 0.053 1576 Dihedral : 17.137 152.584 1480 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.25), residues: 1086 helix: -0.14 (0.29), residues: 309 sheet: -1.73 (0.39), residues: 162 loop : -1.91 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 163 TYR 0.026 0.002 TYR F 206 PHE 0.014 0.001 PHE B 283 TRP 0.020 0.001 TRP F 203 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 ( 9711) covalent geometry : angle 0.71394 / 0.36 (13393) hydrogen bonds : bond 0.03425 / 2.32 ( 218) hydrogen bonds : angle 5.59991 / 4.01 ( 598) Misc. bond : bond 0.01133 / 0.60 ( 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 295 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.514 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: 0.9079 (p90) cc_final: 0.8545 (p90) REVERT: A 200 ASN cc_start: 0.7701 (t0) cc_final: 0.7431 (t0) REVERT: A 201 LYS cc_start: 0.7638 (pttp) cc_final: 0.7161 (pttp) REVERT: A 206 TYR cc_start: 0.8530 (t80) cc_final: 0.8323 (t80) REVERT: A 207 HIS cc_start: 0.7273 (m90) cc_final: 0.7013 (m90) REVERT: B 161 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7604 (mt0) REVERT: B 183 TRP cc_start: 0.8451 (t60) cc_final: 0.7616 (t-100) REVERT: C 138 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8710 (mm-40) REVERT: C 187 PHE cc_start: 0.8514 (t80) cc_final: 0.8280 (t80) REVERT: D 129 SER cc_start: 0.7754 (p) cc_final: 0.7164 (p) REVERT: D 137 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8060 (tm-30) REVERT: D 161 GLN cc_start: 0.8686 (mt0) cc_final: 0.8054 (tp-100) REVERT: D 164 ASP cc_start: 0.8555 (p0) cc_final: 0.8345 (p0) REVERT: D 178 CYS cc_start: 0.8926 (p) cc_final: 0.8549 (p) REVERT: D 202 TRP cc_start: 0.8417 (m-90) cc_final: 0.7847 (m-10) REVERT: D 217 PHE cc_start: 0.9417 (t80) cc_final: 0.8647 (t80) REVERT: D 227 LEU cc_start: 0.8734 (mt) cc_final: 0.8527 (tp) REVERT: D 238 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7225 (mp0) REVERT: D 276 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7455 (tpp-160) REVERT: E 166 LYS cc_start: 0.8310 (tptp) cc_final: 0.7451 (ptpp) REVERT: E 207 HIS cc_start: 0.6611 (t70) cc_final: 0.6074 (t70) REVERT: E 247 LEU cc_start: 0.8993 (pt) cc_final: 0.8585 (pp) REVERT: F 137 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8265 (tm-30) REVERT: F 140 PRO cc_start: 0.9217 (Cg_endo) cc_final: 0.8876 (Cg_exo) REVERT: F 142 THR cc_start: 0.8299 (p) cc_final: 0.8032 (p) REVERT: F 232 ARG cc_start: 0.7253 (mtm-85) cc_final: 0.6857 (mtm180) REVERT: F 276 ARG cc_start: 0.7485 (ttm-80) cc_final: 0.7017 (mmm160) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2321 time to fit residues: 93.8148 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 : 0.398 ------------------------------------------------------------------------------- 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: 5.9990 chunk 96 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 109 optimal weight: 50.0000 chunk 17 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.132600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101673 restraints weight = 48148.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106066 restraints weight = 25840.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109088 restraints weight = 16858.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111029 restraints weight = 12545.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.112472 restraints weight = 10250.928| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.6160 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= 0.222 Angle : 0.720 13.413 13393 Z= 0.364 Chirality : 0.045 0.212 1480 Planarity : 0.005 0.070 1576 Dihedral : 17.010 140.296 1480 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.10 (0.25), residues: 1086 helix: -0.25 (0.29), residues: 309 sheet: -1.78 (0.37), residues: 176 loop : -1.93 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 228 TYR 0.017 0.002 TYR A 206 PHE 0.034 0.002 PHE E 147 TRP 0.018 0.001 TRP F 203 HIS 0.004 0.001 HIS E 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 ( 9711) covalent geometry : angle 0.71969 / 0.36 (13393) hydrogen bonds : bond 0.03465 / 2.33 ( 218) hydrogen bonds : angle 5.69144 / 4.08 ( 598) Misc. bond : bond 0.00861 / 0.45 ( 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 282 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.9064 (p90) cc_final: 0.8519 (p90) REVERT: A 200 ASN cc_start: 0.7685 (t0) cc_final: 0.7389 (t0) REVERT: A 201 LYS cc_start: 0.7650 (pttp) cc_final: 0.7216 (pttp) REVERT: B 161 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7508 (mt0) REVERT: B 183 TRP cc_start: 0.8379 (t60) cc_final: 0.7673 (t-100) REVERT: C 138 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8798 (mm-40) REVERT: C 187 PHE cc_start: 0.8532 (t80) cc_final: 0.8291 (t80) REVERT: C 189 ASP cc_start: 0.8291 (p0) cc_final: 0.7982 (p0) REVERT: C 276 ARG cc_start: 0.5364 (tpm170) cc_final: 0.4837 (tpm170) REVERT: D 129 SER cc_start: 0.7766 (p) cc_final: 0.7417 (p) REVERT: D 161 GLN cc_start: 0.8643 (mt0) cc_final: 0.8020 (tp-100) REVERT: D 164 ASP cc_start: 0.8532 (p0) cc_final: 0.8306 (p0) REVERT: D 178 CYS cc_start: 0.8971 (p) cc_final: 0.8564 (p) REVERT: D 202 TRP cc_start: 0.8571 (m-90) cc_final: 0.7879 (m-10) REVERT: D 227 LEU cc_start: 0.8755 (mt) cc_final: 0.8523 (tp) REVERT: D 238 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7267 (mp0) REVERT: D 276 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7436 (tpp-160) REVERT: D 278 ILE cc_start: 0.9219 (mm) cc_final: 0.8989 (mm) REVERT: E 166 LYS cc_start: 0.8330 (tptp) cc_final: 0.7479 (ptpp) REVERT: E 247 LEU cc_start: 0.8934 (pt) cc_final: 0.8511 (pp) REVERT: F 137 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8273 (tm-30) REVERT: F 140 PRO cc_start: 0.9258 (Cg_endo) cc_final: 0.8906 (Cg_exo) REVERT: F 142 THR cc_start: 0.8310 (p) cc_final: 0.8016 (p) REVERT: F 224 ASP cc_start: 0.8688 (p0) cc_final: 0.8409 (p0) REVERT: F 232 ARG cc_start: 0.7308 (mtm-85) cc_final: 0.6829 (mtm180) REVERT: F 276 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7024 (mmm160) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2351 time to fit residues: 90.3509 Evaluate side-chains 251 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 1.9990 chunk 88 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.133782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103795 restraints weight = 46915.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108283 restraints weight = 24066.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111281 restraints weight = 15334.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113312 restraints weight = 11307.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114636 restraints weight = 9123.738| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9712 Z= 0.126 Angle : 0.676 13.016 13393 Z= 0.336 Chirality : 0.044 0.175 1480 Planarity : 0.005 0.068 1576 Dihedral : 16.861 136.218 1480 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -1.88 (0.25), residues: 1086 helix: 0.05 (0.29), residues: 309 sheet: -1.64 (0.42), residues: 152 loop : -1.88 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 228 TYR 0.014 0.002 TYR A 206 PHE 0.033 0.001 PHE B 283 TRP 0.020 0.001 TRP F 203 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9711) covalent geometry : angle 0.67601 / 0.34 (13393) hydrogen bonds : bond 0.03148 / 2.12 ( 218) hydrogen bonds : angle 5.37892 / 3.86 ( 598) Misc. bond : bond 0.00043 / 0.02 ( 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 300 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 THR cc_start: 0.8417 (p) cc_final: 0.8120 (t) REVERT: A 147 PHE cc_start: 0.9049 (p90) cc_final: 0.8495 (p90) REVERT: A 200 ASN cc_start: 0.7702 (t0) cc_final: 0.7420 (t0) REVERT: A 201 LYS cc_start: 0.7622 (pttp) cc_final: 0.7189 (ptmm) REVERT: B 161 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7648 (mt0) REVERT: B 183 TRP cc_start: 0.8279 (t60) cc_final: 0.7596 (t-100) REVERT: C 187 PHE cc_start: 0.8415 (t80) cc_final: 0.8181 (t80) REVERT: C 189 ASP cc_start: 0.8235 (p0) cc_final: 0.7823 (p0) REVERT: C 276 ARG cc_start: 0.5287 (tpm170) cc_final: 0.4756 (tpm170) REVERT: D 161 GLN cc_start: 0.8574 (mt0) cc_final: 0.7934 (tp-100) REVERT: D 164 ASP cc_start: 0.8505 (p0) cc_final: 0.8302 (p0) REVERT: D 178 CYS cc_start: 0.8940 (p) cc_final: 0.8527 (p) REVERT: D 202 TRP cc_start: 0.8522 (m-90) cc_final: 0.7794 (m-10) REVERT: D 217 PHE cc_start: 0.9404 (t80) cc_final: 0.8578 (t80) REVERT: D 227 LEU cc_start: 0.8694 (mt) cc_final: 0.8481 (tp) REVERT: D 238 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7302 (mp0) REVERT: D 276 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7645 (tpt90) REVERT: E 166 LYS cc_start: 0.8326 (tptp) cc_final: 0.7481 (ptpp) REVERT: E 247 LEU cc_start: 0.8866 (pt) cc_final: 0.8446 (pp) REVERT: F 137 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8299 (tm-30) REVERT: F 140 PRO cc_start: 0.9264 (Cg_endo) cc_final: 0.8910 (Cg_exo) REVERT: F 142 THR cc_start: 0.8297 (p) cc_final: 0.7991 (p) REVERT: F 224 ASP cc_start: 0.8649 (p0) cc_final: 0.8328 (p0) REVERT: F 232 ARG cc_start: 0.7238 (mtm-85) cc_final: 0.6817 (mtm180) REVERT: F 276 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.6999 (mmm160) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2421 time to fit residues: 98.3605 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 : 0.473 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 0.3980 chunk 72 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.131907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101524 restraints weight = 48141.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.105874 restraints weight = 25467.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108824 restraints weight = 16593.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110814 restraints weight = 12375.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112184 restraints weight = 10067.966| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9712 Z= 0.182 Angle : 0.695 12.262 13393 Z= 0.348 Chirality : 0.044 0.169 1480 Planarity : 0.005 0.072 1576 Dihedral : 16.702 115.803 1480 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % 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 : 0.29 % 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: -1.90 (0.25), residues: 1086 helix: -0.02 (0.29), residues: 310 sheet: -1.56 (0.42), residues: 152 loop : -1.89 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 228 TYR 0.024 0.002 TYR E 194 PHE 0.020 0.001 PHE B 283 TRP 0.013 0.001 TRP F 202 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 9711) covalent geometry : angle 0.69526 / 0.35 (13393) hydrogen bonds : bond 0.03246 / 2.17 ( 218) hydrogen bonds : angle 5.40526 / 3.87 ( 598) Misc. bond : bond 0.00926 / 0.49 ( 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 282 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.499 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 134 THR cc_start: 0.8419 (p) cc_final: 0.8167 (t) REVERT: A 147 PHE cc_start: 0.9066 (p90) cc_final: 0.8566 (p90) REVERT: A 200 ASN cc_start: 0.7659 (t0) cc_final: 0.7380 (t0) REVERT: A 201 LYS cc_start: 0.7648 (pttp) cc_final: 0.7136 (pttp) REVERT: B 161 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7512 (mt0) REVERT: C 189 ASP cc_start: 0.8287 (p0) cc_final: 0.7999 (p0) REVERT: C 276 ARG cc_start: 0.5336 (tpm170) cc_final: 0.4788 (tpm170) REVERT: D 129 SER cc_start: 0.7608 (p) cc_final: 0.7205 (p) REVERT: D 161 GLN cc_start: 0.8622 (mt0) cc_final: 0.7975 (tp-100) REVERT: D 164 ASP cc_start: 0.8501 (p0) cc_final: 0.8301 (p0) REVERT: D 178 CYS cc_start: 0.8971 (p) cc_final: 0.8585 (p) REVERT: D 202 TRP cc_start: 0.8609 (m-90) cc_final: 0.7782 (m-10) REVERT: D 227 LEU cc_start: 0.8739 (mt) cc_final: 0.8498 (tp) REVERT: D 238 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7322 (mp0) REVERT: D 276 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7665 (tpt90) REVERT: E 166 LYS cc_start: 0.8332 (tptp) cc_final: 0.7506 (ptpp) REVERT: E 247 LEU cc_start: 0.8916 (pt) cc_final: 0.8515 (pp) REVERT: F 137 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8309 (tm-30) REVERT: F 140 PRO cc_start: 0.9262 (Cg_endo) cc_final: 0.8901 (Cg_exo) REVERT: F 142 THR cc_start: 0.8366 (p) cc_final: 0.8065 (p) REVERT: F 224 ASP cc_start: 0.8616 (p0) cc_final: 0.8305 (p0) REVERT: F 232 ARG cc_start: 0.7228 (mtm-85) cc_final: 0.6803 (mtm180) REVERT: F 276 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7040 (mmm160) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2329 time to fit residues: 90.0339 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 : 0.486 ------------------------------------------------------------------------------- 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: 5.9990 chunk 39 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 54 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.133336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102763 restraints weight = 47579.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.107154 restraints weight = 25511.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110183 restraints weight = 16687.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112173 restraints weight = 12434.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113548 restraints weight = 10150.863| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.6485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9712 Z= 0.130 Angle : 0.685 15.523 13393 Z= 0.342 Chirality : 0.043 0.153 1480 Planarity : 0.005 0.075 1576 Dihedral : 16.525 114.743 1480 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % 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: -1.72 (0.25), residues: 1086 helix: 0.22 (0.30), residues: 310 sheet: -1.49 (0.41), residues: 152 loop : -1.82 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 228 TYR 0.032 0.002 TYR F 206 PHE 0.038 0.001 PHE E 147 TRP 0.017 0.001 TRP F 203 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9711) covalent geometry : angle 0.68547 / 0.34 (13393) hydrogen bonds : bond 0.03024 / 2.02 ( 218) hydrogen bonds : angle 5.24250 / 3.77 ( 598) Misc. bond : bond 0.00102 / 0.05 ( 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 290 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.621 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: A 134 THR cc_start: 0.8423 (p) cc_final: 0.8141 (t) REVERT: A 147 PHE cc_start: 0.9047 (p90) cc_final: 0.8525 (p90) REVERT: A 200 ASN cc_start: 0.7619 (t0) cc_final: 0.7327 (m-40) REVERT: B 161 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7587 (mt0) REVERT: C 189 ASP cc_start: 0.8252 (p0) cc_final: 0.7843 (p0) REVERT: C 276 ARG cc_start: 0.5230 (tpm170) cc_final: 0.4702 (tpm170) REVERT: D 128 GLU cc_start: 0.8431 (pp20) cc_final: 0.8218 (pp20) REVERT: D 161 GLN cc_start: 0.8557 (mt0) cc_final: 0.7944 (tp-100) REVERT: D 164 ASP cc_start: 0.8402 (p0) cc_final: 0.8201 (p0) REVERT: D 178 CYS cc_start: 0.8934 (p) cc_final: 0.8547 (p) REVERT: D 202 TRP cc_start: 0.8604 (m-90) cc_final: 0.8386 (m-90) REVERT: D 217 PHE cc_start: 0.9402 (t80) cc_final: 0.8573 (t80) REVERT: D 227 LEU cc_start: 0.8729 (mt) cc_final: 0.8513 (tp) REVERT: D 238 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7309 (mp0) REVERT: D 247 LEU cc_start: 0.9244 (mt) cc_final: 0.9038 (mt) REVERT: D 276 ARG cc_start: 0.8097 (ttm110) cc_final: 0.7620 (tpt90) REVERT: D 278 ILE cc_start: 0.9194 (mm) cc_final: 0.8990 (mm) REVERT: E 166 LYS cc_start: 0.8332 (tptp) cc_final: 0.7489 (ptpp) REVERT: E 247 LEU cc_start: 0.8884 (pt) cc_final: 0.8495 (pp) REVERT: F 137 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8311 (tm-30) REVERT: F 140 PRO cc_start: 0.9257 (Cg_endo) cc_final: 0.8907 (Cg_exo) REVERT: F 142 THR cc_start: 0.8329 (p) cc_final: 0.7993 (p) REVERT: F 165 TRP cc_start: 0.8525 (p90) cc_final: 0.8158 (p90) REVERT: F 224 ASP cc_start: 0.8533 (p0) cc_final: 0.8223 (p0) REVERT: F 232 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6760 (mtm180) REVERT: F 276 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7055 (mmm160) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2437 time to fit residues: 95.5369 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 : 0.487 ------------------------------------------------------------------------------- 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: 7.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.133184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.103207 restraints weight = 47676.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107618 restraints weight = 24705.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.110573 restraints weight = 15916.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.112610 restraints weight = 11817.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113929 restraints weight = 9576.262| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9712 Z= 0.134 Angle : 0.680 14.589 13393 Z= 0.338 Chirality : 0.043 0.144 1480 Planarity : 0.005 0.093 1576 Dihedral : 16.402 110.537 1480 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.25), residues: 1086 helix: 0.30 (0.30), residues: 310 sheet: -1.30 (0.42), residues: 141 loop : -1.82 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 249 TYR 0.016 0.002 TYR D 275 PHE 0.019 0.001 PHE F 246 TRP 0.034 0.001 TRP A 202 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9711) covalent geometry : angle 0.67962 / 0.34 (13393) hydrogen bonds : bond 0.03048 / 2.04 ( 218) hydrogen bonds : angle 5.17263 / 3.73 ( 598) Misc. bond : bond 0.00083 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3447.30 seconds wall clock time: 59 minutes 31.98 seconds (3571.98 seconds total)