Starting phenix.real_space_refine on Sat Jul 4 02:22:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lar_23249/07_2026/7lar_23249_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lar_23249/07_2026/7lar_23249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lar_23249/07_2026/7lar_23249_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lar_23249/07_2026/7lar_23249_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lar_23249/07_2026/7lar_23249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lar_23249/07_2026/7lar_23249.map" } resolution = 3.8 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= 0.007 sd= 0.177 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 14 5.49 5 Mg 4 5.21 5 S 18 5.16 5 C 5776 2.51 5 N 1508 2.21 5 O 1697 1.98 5 H 8697 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17714 Number of models: 1 Model: "" Number of chains: 11 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: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 194 Classifications: {'DNA': 6} Modifications used: {'3*END': 1, 'p5*END': 1} Link IDs: {'rna3p': 5} 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: 4.38, per 1000 atoms: 0.25 Number of scatterers: 17714 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 14 15.00 Mg 4 11.99 O 1697 8.00 N 1508 7.00 C 5776 6.00 H 8697 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 573.7 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 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 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: 3.608A pdb=" N PHE A 143 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 3.759A 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: 3.859A 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: 3.567A 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: 3.581A 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: 3.933A pdb=" N LEU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.571A 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: 3.732A 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: 3.628A 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: 4.146A 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: 3.778A 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: 3.511A pdb=" N PHE E 187 " --> pdb=" O TRP E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 3.747A 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: 4.117A 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: 3.613A pdb=" N CYS F 230 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 removed outlier: 3.505A 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: 6.985A pdb=" N TYR A 194 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.973A 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: 7.932A pdb=" N VAL A 282 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.380A 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: 3.770A 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: 6.019A 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: 6.044A 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: 7.221A 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: 6.326A pdb=" N HIS C 170 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.747A 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: 6.746A 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: 6.599A pdb=" N LYS C 285 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS C 285 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 3.952A 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: 6.589A pdb=" N VAL D 212 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.180A 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: 7.284A 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: 6.974A 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: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 2.23 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: 8685 1.03 - 1.23: 78 1.23 - 1.42: 3928 1.42 - 1.62: 5278 1.62 - 1.81: 24 Bond restraints: 17993 Sorted by residual: 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 1.67e+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 1.65e+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 1.61e+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 E 215 " pdb=" OD1 ASP E 215 " ideal model delta sigma weight residual 1.249 1.322 -0.073 1.90e-02 2.77e+03 1.49e+01 ... (remaining 17988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 32271 3.89 - 7.79: 205 7.79 - 11.68: 16 11.68 - 15.58: 3 15.58 - 19.47: 5 Bond angle restraints: 32500 Sorted by residual: angle pdb=" C PHE E 217 " pdb=" N TYR E 218 " pdb=" CA TYR E 218 " ideal model delta sigma weight residual 121.98 138.41 -16.43 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 121.54 141.01 -19.47 1.91e+00 2.74e-01 1.04e+02 angle pdb=" C GLU A 209 " pdb=" N GLU A 210 " pdb=" CA GLU A 210 " ideal model delta sigma weight residual 121.54 140.75 -19.21 1.91e+00 2.74e-01 1.01e+02 angle pdb=" C GLY F 205 " pdb=" N TYR F 206 " pdb=" CA TYR F 206 " ideal model delta sigma weight residual 121.70 138.34 -16.64 1.80e+00 3.09e-01 8.54e+01 angle pdb=" C LYS F 240 " pdb=" N GLY F 241 " pdb=" CA GLY F 241 " ideal model delta sigma weight residual 121.51 134.99 -13.48 1.52e+00 4.33e-01 7.86e+01 ... (remaining 32495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 8001 29.56 - 59.12: 409 59.12 - 88.67: 29 88.67 - 118.23: 2 118.23 - 147.79: 4 Dihedral angle restraints: 8445 sinusoidal: 4545 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 99.46 80.54 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 180.00 102.92 77.08 0 5.00e+00 4.00e-02 2.38e+02 ... (remaining 8442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1213 0.086 - 0.172: 189 0.172 - 0.258: 4 0.258 - 0.345: 1 0.345 - 0.431: 1 Chirality restraints: 1408 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 4.64e+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 2.57e+00 chirality pdb=" CG LEU A 154 " pdb=" CB LEU A 154 " pdb=" CD1 LEU A 154 " pdb=" CD2 LEU A 154 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 1405 not shown) Planarity restraints: 2582 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 " -0.004 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 3.32e-02 1.10e+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 " -0.020 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1202 2.20 - 2.80: 35537 2.80 - 3.40: 45977 3.40 - 4.00: 62526 4.00 - 4.60: 94987 Nonbonded interactions: 240229 Sorted by model distance: nonbonded pdb=" HH TYR D 194 " pdb=" O ASP D 204 " model vdw 1.602 2.450 nonbonded pdb=" HH TYR C 194 " pdb=" O ASP C 204 " model vdw 1.612 2.450 nonbonded pdb=" HZ1 LYS E 240 " pdb=" OP1 DT G 6 " model vdw 1.617 2.450 nonbonded pdb=" OD1 ASP A 231 " pdb=" HE ARG A 277 " model vdw 1.630 2.450 nonbonded pdb=" O SER E 131 " pdb=" HG1 THR E 134 " model vdw 1.663 2.450 ... (remaining 240224 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.300 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 9297 Z= 0.423 Angle : 1.206 19.475 12755 Z= 0.660 Chirality : 0.059 0.431 1408 Planarity : 0.010 0.223 1558 Dihedral : 17.513 147.790 3299 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 7.44 % Allowed : 10.59 % Favored : 81.97 % 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 0.010 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 0.00935 / 0.42 ( 9296) covalent geometry : angle 1.20630 / 0.66 (12755) hydrogen bonds : bond 0.22558 / 15.47 ( 216) hydrogen bonds : angle 8.07563 / 5.84 ( 594) Misc. bond : bond 0.00122 / 0.06 ( 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 334 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 263 time to evaluate : 0.426 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: A 247 LEU cc_start: 0.8689 (mt) cc_final: 0.8350 (mp) REVERT: A 291 SER cc_start: 0.7463 (p) cc_final: 0.7108 (m) REVERT: B 216 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7355 (t0) REVERT: B 283 PHE cc_start: 0.8032 (t80) cc_final: 0.7803 (t80) REVERT: C 139 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7023 (p90) REVERT: C 152 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7367 (tm-30) REVERT: C 200 ASN cc_start: 0.8629 (p0) cc_final: 0.8136 (p0) REVERT: C 202 TRP cc_start: 0.8827 (OUTLIER) cc_final: 0.7984 (m-90) REVERT: C 215 ASP cc_start: 0.8563 (t70) cc_final: 0.8032 (p0) REVERT: C 216 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7339 (t0) REVERT: C 276 ARG cc_start: 0.8613 (mtm110) cc_final: 0.7725 (tpm170) REVERT: D 155 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7970 (mtpp) REVERT: D 204 ASP cc_start: 0.7933 (t0) cc_final: 0.7674 (t70) REVERT: D 209 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6180 (mm-30) REVERT: D 244 VAL cc_start: 0.9651 (t) cc_final: 0.9400 (m) REVERT: D 250 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8788 (m) REVERT: E 139 HIS cc_start: 0.8554 (m90) cc_final: 0.8294 (m-70) REVERT: E 167 THR cc_start: 0.9233 (m) cc_final: 0.8981 (p) REVERT: E 261 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6775 (tm-30) REVERT: E 275 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.5847 (m-80) REVERT: E 276 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.6613 (tpp-160) REVERT: E 288 THR cc_start: 0.4601 (OUTLIER) cc_final: 0.4089 (m) REVERT: E 293 GLU cc_start: 0.7267 (tp30) cc_final: 0.7035 (tp30) REVERT: F 159 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6313 (mmmt) outliers start: 71 outliers final: 34 residues processed: 310 average time/residue: 0.2179 time to fit residues: 91.7559 Evaluate side-chains 228 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 218 TYR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 220 TRP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 138 GLN D 200 ASN D 257 GLN F 146 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.106822 restraints weight = 39969.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111257 restraints weight = 20868.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114157 restraints weight = 13402.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.116305 restraints weight = 9808.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.117622 restraints weight = 7772.105| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9297 Z= 0.127 Angle : 0.720 10.123 12755 Z= 0.354 Chirality : 0.044 0.236 1408 Planarity : 0.005 0.064 1558 Dihedral : 15.251 155.931 1374 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.20 % Favored : 91.71 % Rotamer: Outliers : 5.24 % Allowed : 17.09 % Favored : 77.67 % 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: -2.23 (0.25), residues: 1086 helix: -0.55 (0.28), residues: 303 sheet: -1.60 (0.39), residues: 168 loop : -1.97 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 163 TYR 0.020 0.002 TYR F 218 PHE 0.014 0.001 PHE A 147 TRP 0.010 0.001 TRP B 203 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9296) covalent geometry : angle 0.71989 / 0.35 (12755) hydrogen bonds : bond 0.04229 / 2.87 ( 216) hydrogen bonds : angle 6.08852 / 4.32 ( 594) Misc. bond : bond 0.00100 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 0.471 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: A 293 GLU cc_start: 0.7232 (tp30) cc_final: 0.6966 (tp30) REVERT: C 152 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: C 200 ASN cc_start: 0.8716 (p0) cc_final: 0.8446 (p0) REVERT: C 215 ASP cc_start: 0.8370 (t70) cc_final: 0.8005 (p0) REVERT: C 216 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7462 (t0) REVERT: C 240 LYS cc_start: 0.8447 (mmtp) cc_final: 0.8102 (mttp) REVERT: C 276 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7762 (tpm170) REVERT: D 155 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7837 (mtpp) REVERT: D 244 VAL cc_start: 0.9565 (t) cc_final: 0.9284 (m) REVERT: D 250 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8768 (m) REVERT: E 167 THR cc_start: 0.9352 (m) cc_final: 0.9096 (p) REVERT: E 186 ASN cc_start: 0.8654 (t0) cc_final: 0.8390 (t0) REVERT: E 275 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.5834 (m-80) REVERT: E 276 ARG cc_start: 0.7636 (ttm-80) cc_final: 0.6626 (tpp-160) REVERT: E 288 THR cc_start: 0.4611 (OUTLIER) cc_final: 0.4058 (m) REVERT: F 159 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6354 (mmmt) REVERT: F 256 ASN cc_start: 0.8097 (p0) cc_final: 0.6819 (t0) outliers start: 50 outliers final: 34 residues processed: 236 average time/residue: 0.1861 time to fit residues: 62.0592 Evaluate side-chains 226 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 218 TYR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 220 TRP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 256 ASN C 207 HIS D 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.129511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.105271 restraints weight = 40382.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.109572 restraints weight = 21033.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112575 restraints weight = 13521.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114453 restraints weight = 9811.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115946 restraints weight = 7841.184| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9297 Z= 0.172 Angle : 0.685 9.405 12755 Z= 0.337 Chirality : 0.044 0.207 1408 Planarity : 0.004 0.045 1558 Dihedral : 14.211 144.928 1347 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.77 % Allowed : 17.82 % Favored : 76.42 % 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: -2.12 (0.25), residues: 1086 helix: -0.23 (0.29), residues: 302 sheet: -1.84 (0.38), residues: 161 loop : -1.94 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.021 0.002 TYR F 218 PHE 0.014 0.001 PHE A 147 TRP 0.010 0.001 TRP E 223 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 9296) covalent geometry : angle 0.68489 / 0.34 (12755) hydrogen bonds : bond 0.03825 / 2.60 ( 216) hydrogen bonds : angle 5.70925 / 4.05 ( 594) Misc. bond : bond 0.00058 / 0.03 ( 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 249 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 194 time to evaluate : 0.429 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: A 201 LYS cc_start: 0.8529 (pttp) cc_final: 0.8284 (pttm) REVERT: B 250 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8216 (p) REVERT: C 139 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.6848 (p90) REVERT: C 152 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: C 200 ASN cc_start: 0.8742 (p0) cc_final: 0.8474 (p0) REVERT: C 215 ASP cc_start: 0.8426 (t70) cc_final: 0.7990 (p0) REVERT: C 216 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: C 240 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8234 (mttp) REVERT: C 276 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7769 (tpm170) REVERT: D 155 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7782 (mtpp) REVERT: D 244 VAL cc_start: 0.9549 (t) cc_final: 0.9264 (m) REVERT: D 250 SER cc_start: 0.9136 (OUTLIER) cc_final: 0.8786 (m) REVERT: E 186 ASN cc_start: 0.8632 (t0) cc_final: 0.8343 (t0) REVERT: E 261 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6854 (tm-30) REVERT: E 275 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.5791 (m-80) REVERT: E 276 ARG cc_start: 0.7638 (ttm-80) cc_final: 0.6659 (tpp-160) REVERT: E 288 THR cc_start: 0.4811 (OUTLIER) cc_final: 0.4269 (m) REVERT: F 159 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6345 (mmmt) outliers start: 55 outliers final: 36 residues processed: 226 average time/residue: 0.1884 time to fit residues: 60.2018 Evaluate side-chains 227 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 218 TYR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 220 TRP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 283 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 0.0570 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.107261 restraints weight = 39936.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111732 restraints weight = 20905.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114709 restraints weight = 13348.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116729 restraints weight = 9692.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117977 restraints weight = 7654.076| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9297 Z= 0.148 Angle : 0.653 9.152 12755 Z= 0.318 Chirality : 0.043 0.188 1408 Planarity : 0.004 0.045 1558 Dihedral : 13.616 136.478 1343 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.77 % Allowed : 17.51 % Favored : 76.73 % 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: -1.97 (0.26), residues: 1086 helix: 0.06 (0.30), residues: 302 sheet: -1.88 (0.39), residues: 161 loop : -1.90 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 277 TYR 0.020 0.002 TYR F 218 PHE 0.015 0.001 PHE A 147 TRP 0.009 0.001 TRP E 223 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 9296) covalent geometry : angle 0.65316 / 0.32 (12755) hydrogen bonds : bond 0.03108 / 2.09 ( 216) hydrogen bonds : angle 5.44735 / 3.88 ( 594) Misc. bond : bond 0.00067 / 0.04 ( 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 244 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.8609 (pttp) cc_final: 0.8301 (pttm) REVERT: B 250 SER cc_start: 0.8782 (m) cc_final: 0.8208 (p) REVERT: C 139 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.6690 (p90) REVERT: C 152 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: C 200 ASN cc_start: 0.8769 (p0) cc_final: 0.8444 (p0) REVERT: C 215 ASP cc_start: 0.8316 (t70) cc_final: 0.7990 (p0) REVERT: C 276 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7757 (tpm170) REVERT: D 155 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7761 (mtpp) REVERT: D 209 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6116 (mm-30) REVERT: D 250 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8801 (m) REVERT: D 276 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7572 (tpt170) REVERT: E 186 ASN cc_start: 0.8647 (t0) cc_final: 0.8366 (t0) REVERT: E 275 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.5832 (m-80) REVERT: E 276 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.6694 (tpp-160) REVERT: E 288 THR cc_start: 0.4704 (OUTLIER) cc_final: 0.4142 (m) REVERT: F 159 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6335 (mmmt) REVERT: F 194 TYR cc_start: 0.7877 (t80) cc_final: 0.7635 (t80) REVERT: F 256 ASN cc_start: 0.7971 (p0) cc_final: 0.6748 (t0) outliers start: 55 outliers final: 38 residues processed: 220 average time/residue: 0.1999 time to fit residues: 61.6630 Evaluate side-chains 229 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 220 TRP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 283 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 7.9990 chunk 95 optimal weight: 0.0870 chunk 76 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 0.0270 chunk 43 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.104180 restraints weight = 40261.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.108479 restraints weight = 21520.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.111375 restraints weight = 13915.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.113214 restraints weight = 10212.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114626 restraints weight = 8209.823| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9297 Z= 0.176 Angle : 0.656 8.909 12755 Z= 0.320 Chirality : 0.044 0.183 1408 Planarity : 0.004 0.056 1558 Dihedral : 13.147 139.705 1331 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 5.35 % Allowed : 18.66 % Favored : 76.00 % 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: -1.99 (0.26), residues: 1086 helix: 0.10 (0.30), residues: 302 sheet: -1.95 (0.38), residues: 161 loop : -1.93 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 199 TYR 0.021 0.002 TYR F 218 PHE 0.016 0.001 PHE A 147 TRP 0.009 0.001 TRP E 223 HIS 0.009 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 9296) covalent geometry : angle 0.65577 / 0.32 (12755) hydrogen bonds : bond 0.03047 / 2.05 ( 216) hydrogen bonds : angle 5.37933 / 3.84 ( 594) Misc. bond : bond 0.00088 / 0.05 ( 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 230 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.8609 (pttp) cc_final: 0.8322 (pttm) REVERT: B 250 SER cc_start: 0.8773 (m) cc_final: 0.8198 (p) REVERT: C 139 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.6570 (p90) REVERT: C 152 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7277 (tm-30) REVERT: C 200 ASN cc_start: 0.8749 (p0) cc_final: 0.8022 (p0) REVERT: C 202 TRP cc_start: 0.8873 (OUTLIER) cc_final: 0.7500 (m-90) REVERT: C 215 ASP cc_start: 0.8317 (t70) cc_final: 0.8015 (p0) REVERT: C 276 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7745 (tpm170) REVERT: D 155 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7763 (mtpp) REVERT: D 209 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6154 (mm-30) REVERT: D 250 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8804 (m) REVERT: D 276 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7576 (tpt170) REVERT: E 261 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6904 (tm-30) REVERT: E 275 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.5717 (m-80) REVERT: E 276 ARG cc_start: 0.7638 (ttm-80) cc_final: 0.6696 (tpp-160) REVERT: E 288 THR cc_start: 0.4845 (OUTLIER) cc_final: 0.4274 (m) REVERT: F 159 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6300 (mmmt) REVERT: F 194 TYR cc_start: 0.7900 (t80) cc_final: 0.7665 (t80) outliers start: 51 outliers final: 35 residues processed: 209 average time/residue: 0.1968 time to fit residues: 57.9915 Evaluate side-chains 220 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 220 TRP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 283 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.104559 restraints weight = 40069.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108718 restraints weight = 21097.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111591 restraints weight = 13670.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113341 restraints weight = 10000.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.114814 restraints weight = 8084.363| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9297 Z= 0.154 Angle : 0.639 8.815 12755 Z= 0.310 Chirality : 0.043 0.168 1408 Planarity : 0.004 0.040 1558 Dihedral : 12.841 142.231 1331 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.45 % Allowed : 18.24 % Favored : 76.31 % 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: -1.96 (0.26), residues: 1086 helix: 0.22 (0.30), residues: 302 sheet: -2.15 (0.39), residues: 151 loop : -1.91 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.020 0.002 TYR F 218 PHE 0.016 0.001 PHE A 147 TRP 0.009 0.001 TRP E 223 HIS 0.013 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9296) covalent geometry : angle 0.63889 / 0.31 (12755) hydrogen bonds : bond 0.02814 / 1.89 ( 216) hydrogen bonds : angle 5.24101 / 3.74 ( 594) Misc. bond : bond 0.00074 / 0.04 ( 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 231 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 VAL cc_start: 0.9253 (t) cc_final: 0.8916 (m) REVERT: A 201 LYS cc_start: 0.8621 (pttp) cc_final: 0.8301 (pttm) REVERT: B 250 SER cc_start: 0.8753 (m) cc_final: 0.8176 (p) REVERT: C 139 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.6534 (p90) REVERT: C 152 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: C 200 ASN cc_start: 0.8721 (p0) cc_final: 0.7985 (p0) REVERT: C 202 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.7485 (m-90) REVERT: C 215 ASP cc_start: 0.8269 (t70) cc_final: 0.8049 (p0) REVERT: C 276 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7747 (tpm170) REVERT: D 209 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: D 250 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8805 (m) REVERT: D 276 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7575 (tpt170) REVERT: E 275 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.5773 (m-80) REVERT: E 276 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.6707 (tpp-160) REVERT: E 288 THR cc_start: 0.4751 (OUTLIER) cc_final: 0.4173 (m) REVERT: F 159 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6329 (mmmt) REVERT: F 194 TYR cc_start: 0.7896 (t80) cc_final: 0.7669 (t80) outliers start: 52 outliers final: 38 residues processed: 211 average time/residue: 0.2079 time to fit residues: 61.6661 Evaluate side-chains 221 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 220 TRP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 283 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105689 restraints weight = 39922.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.110055 restraints weight = 20778.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113001 restraints weight = 13277.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115064 restraints weight = 9608.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.116311 restraints weight = 7565.631| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9297 Z= 0.124 Angle : 0.624 8.547 12755 Z= 0.300 Chirality : 0.043 0.147 1408 Planarity : 0.004 0.042 1558 Dihedral : 12.493 142.027 1331 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.72 % Allowed : 19.60 % Favored : 75.68 % 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: -1.80 (0.26), residues: 1086 helix: 0.39 (0.30), residues: 308 sheet: -2.04 (0.39), residues: 150 loop : -1.86 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 228 TYR 0.022 0.002 TYR F 218 PHE 0.018 0.001 PHE A 147 TRP 0.009 0.001 TRP E 223 HIS 0.008 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 9296) covalent geometry : angle 0.62413 / 0.30 (12755) hydrogen bonds : bond 0.02606 / 1.73 ( 216) hydrogen bonds : angle 5.06632 / 3.63 ( 594) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 VAL cc_start: 0.9256 (t) cc_final: 0.8921 (m) REVERT: A 201 LYS cc_start: 0.8584 (pttp) cc_final: 0.8256 (pttm) REVERT: C 152 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: C 202 TRP cc_start: 0.8824 (OUTLIER) cc_final: 0.7576 (m-90) REVERT: C 276 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7806 (tpm170) REVERT: D 244 VAL cc_start: 0.9491 (t) cc_final: 0.9235 (m) REVERT: D 250 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8831 (m) REVERT: D 276 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7589 (tpt170) REVERT: E 186 ASN cc_start: 0.8697 (t0) cc_final: 0.8420 (t0) REVERT: E 261 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6898 (tm-30) REVERT: E 276 ARG cc_start: 0.7645 (ttm-80) cc_final: 0.6724 (tpp-160) REVERT: F 159 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6349 (mmmt) REVERT: F 194 TYR cc_start: 0.7870 (t80) cc_final: 0.7624 (t80) outliers start: 45 outliers final: 36 residues processed: 212 average time/residue: 0.2085 time to fit residues: 61.7897 Evaluate side-chains 225 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 220 TRP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 283 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.108756 restraints weight = 39828.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113269 restraints weight = 20737.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116279 restraints weight = 13112.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.118309 restraints weight = 9484.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119550 restraints weight = 7473.241| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9297 Z= 0.142 Angle : 0.621 8.414 12755 Z= 0.299 Chirality : 0.043 0.149 1408 Planarity : 0.004 0.039 1558 Dihedral : 12.163 139.378 1323 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 5.03 % Allowed : 19.08 % Favored : 75.89 % 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: -1.80 (0.26), residues: 1086 helix: 0.44 (0.30), residues: 308 sheet: -2.08 (0.39), residues: 150 loop : -1.87 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 276 TYR 0.020 0.002 TYR A 206 PHE 0.018 0.001 PHE A 147 TRP 0.009 0.001 TRP E 223 HIS 0.006 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 9296) covalent geometry : angle 0.62112 / 0.30 (12755) hydrogen bonds : bond 0.02587 / 1.73 ( 216) hydrogen bonds : angle 5.04233 / 3.61 ( 594) Misc. bond : bond 0.00005 / 0.00 ( 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 233 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.517 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: A 173 VAL cc_start: 0.9286 (t) cc_final: 0.8918 (m) REVERT: A 201 LYS cc_start: 0.8589 (pttp) cc_final: 0.8248 (pttm) REVERT: C 152 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: C 202 TRP cc_start: 0.8867 (OUTLIER) cc_final: 0.7501 (m-90) REVERT: C 276 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7787 (tpm170) REVERT: D 244 VAL cc_start: 0.9482 (t) cc_final: 0.9242 (m) REVERT: D 250 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8835 (m) REVERT: D 276 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7578 (tpt170) REVERT: E 186 ASN cc_start: 0.8728 (t0) cc_final: 0.8455 (t0) REVERT: E 261 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6914 (tm-30) REVERT: E 276 ARG cc_start: 0.7646 (ttm-80) cc_final: 0.6696 (tpp-160) REVERT: F 159 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6270 (mmmt) REVERT: F 194 TYR cc_start: 0.7866 (t80) cc_final: 0.7622 (t80) outliers start: 48 outliers final: 36 residues processed: 214 average time/residue: 0.1902 time to fit residues: 57.7024 Evaluate side-chains 213 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 220 TRP Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 283 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105298 restraints weight = 39862.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109708 restraints weight = 20802.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112643 restraints weight = 13276.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114495 restraints weight = 9677.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115977 restraints weight = 7751.426| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9297 Z= 0.136 Angle : 0.621 8.435 12755 Z= 0.299 Chirality : 0.043 0.144 1408 Planarity : 0.004 0.042 1558 Dihedral : 11.958 138.428 1322 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.40 % Allowed : 19.60 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.75 (0.26), residues: 1086 helix: 0.52 (0.30), residues: 308 sheet: -2.10 (0.39), residues: 150 loop : -1.84 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 228 TYR 0.022 0.002 TYR A 206 PHE 0.019 0.001 PHE A 147 TRP 0.009 0.001 TRP E 223 HIS 0.006 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9296) covalent geometry : angle 0.62148 / 0.30 (12755) hydrogen bonds : bond 0.02497 / 1.66 ( 216) hydrogen bonds : angle 4.95162 / 3.56 ( 594) Misc. bond : bond 0.00025 / 0.01 ( 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 218 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 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: A 173 VAL cc_start: 0.9275 (t) cc_final: 0.8939 (m) REVERT: A 201 LYS cc_start: 0.8555 (pttp) cc_final: 0.8266 (pttm) REVERT: C 152 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: C 202 TRP cc_start: 0.8852 (OUTLIER) cc_final: 0.7494 (m-90) REVERT: C 276 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7800 (tpm170) REVERT: D 209 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6335 (mm-30) REVERT: D 244 VAL cc_start: 0.9505 (t) cc_final: 0.9260 (m) REVERT: D 250 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8851 (m) REVERT: D 276 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7604 (tpt170) REVERT: E 186 ASN cc_start: 0.8724 (t0) cc_final: 0.8459 (t0) REVERT: E 276 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.6767 (tpp-160) REVERT: F 159 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6301 (mmmt) REVERT: F 194 TYR cc_start: 0.7855 (t80) cc_final: 0.7612 (t80) outliers start: 42 outliers final: 34 residues processed: 200 average time/residue: 0.1986 time to fit residues: 55.7705 Evaluate side-chains 215 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 220 TRP Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 283 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107064 restraints weight = 39821.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111482 restraints weight = 20887.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114412 restraints weight = 13349.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.116340 restraints weight = 9759.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117712 restraints weight = 7783.816| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9297 Z= 0.098 Angle : 0.607 8.417 12755 Z= 0.289 Chirality : 0.042 0.140 1408 Planarity : 0.004 0.040 1558 Dihedral : 11.802 137.962 1322 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.88 % Allowed : 20.55 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.54 (0.26), residues: 1086 helix: 0.74 (0.31), residues: 308 sheet: -1.96 (0.40), residues: 150 loop : -1.75 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 228 TYR 0.021 0.001 TYR A 206 PHE 0.019 0.001 PHE A 147 TRP 0.009 0.001 TRP E 223 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9296) covalent geometry : angle 0.60724 / 0.29 (12755) hydrogen bonds : bond 0.02307 / 1.51 ( 216) hydrogen bonds : angle 4.78766 / 3.45 ( 594) Misc. bond : bond 0.00062 / 0.03 ( 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 228 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.461 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: A 173 VAL cc_start: 0.9282 (t) cc_final: 0.8942 (m) REVERT: A 201 LYS cc_start: 0.8528 (pttp) cc_final: 0.8185 (pttm) REVERT: C 152 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: C 202 TRP cc_start: 0.8778 (OUTLIER) cc_final: 0.7502 (m-90) REVERT: C 276 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7783 (tpm170) REVERT: D 238 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7239 (mt-10) REVERT: D 244 VAL cc_start: 0.9494 (t) cc_final: 0.9264 (m) REVERT: D 250 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8863 (m) REVERT: D 276 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7591 (tpt170) REVERT: E 186 ASN cc_start: 0.8617 (t0) cc_final: 0.8356 (t0) REVERT: E 276 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.6770 (tpp-160) REVERT: F 159 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6331 (mmmt) REVERT: F 170 HIS cc_start: 0.8156 (m-70) cc_final: 0.7899 (m170) REVERT: F 194 TYR cc_start: 0.7818 (t80) cc_final: 0.7532 (t80) outliers start: 37 outliers final: 29 residues processed: 212 average time/residue: 0.1908 time to fit residues: 56.6807 Evaluate side-chains 216 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 220 TRP Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 283 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107073 restraints weight = 39526.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111342 restraints weight = 20603.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114283 restraints weight = 13242.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116097 restraints weight = 9661.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.117518 restraints weight = 7755.003| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9297 Z= 0.102 Angle : 0.601 8.133 12755 Z= 0.285 Chirality : 0.042 0.140 1408 Planarity : 0.004 0.076 1558 Dihedral : 11.583 137.569 1320 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.46 % Allowed : 20.65 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.43 (0.26), residues: 1086 helix: 0.89 (0.31), residues: 308 sheet: -1.98 (0.40), residues: 152 loop : -1.68 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 228 TYR 0.021 0.001 TYR A 206 PHE 0.021 0.001 PHE A 147 TRP 0.009 0.001 TRP E 223 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 9296) covalent geometry : angle 0.60132 / 0.29 (12755) hydrogen bonds : bond 0.02214 / 1.45 ( 216) hydrogen bonds : angle 4.67520 / 3.38 ( 594) Misc. bond : bond 0.00072 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.40 seconds wall clock time: 52 minutes 6.61 seconds (3126.61 seconds total)