Starting phenix.real_space_refine on Sat Sep 12 18:56:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lar_23249/09_2026/7lar_23249_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lar_23249/09_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_23249/09_2026/7lar_23249_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lar_23249/09_2026/7lar_23249_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lar_23249/09_2026/7lar_23249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lar_23249/09_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-2.2.1-6174/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: 2.88, per 1000 atoms: 0.16 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: 1.37 Conformation dependent library (CDL) restraints added in 582.5 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 13 sheets defined 36.2% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 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: 3.43 Time building geometry restraints manager: 1.87 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.590 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: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- 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 1.20632 / 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 : 0.444 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: 0.7356 (t0) REVERT: B 283 PHE cc_start: 0.8032 (t80) cc_final: 0.7804 (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: 0.8132 (p0) REVERT: C 202 TRP cc_start: 0.8827 (OUTLIER) cc_final: 0.7941 (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: 0.7338 (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: 0.7673 (t70) REVERT: D 209 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6181 (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: 0.8295 (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: 0.6312 (mmmt) outliers start: 71 outliers final: 34 residues processed: 310 average time/residue: 0.2056 time to fit residues: 87.6162 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 : 0.471 ------------------------------------------------------------------------------- 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: 2.9990 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 F 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.107032 restraints weight = 40044.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.111450 restraints weight = 20815.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114534 restraints weight = 13380.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116396 restraints weight = 9719.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117933 restraints weight = 7797.503| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9297 Z= 0.135 Angle : 0.730 10.174 12755 Z= 0.360 Chirality : 0.044 0.267 1408 Planarity : 0.005 0.078 1558 Dihedral : 15.372 155.106 1374 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.73 % Favored : 92.17 % Rotamer: Outliers : 5.14 % Allowed : 17.61 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.78 % 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: -2.25 (0.25), residues: 1086 helix: -0.57 (0.28), residues: 303 sheet: -1.59 (0.39), residues: 168 loop : -1.99 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 E 220 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 9296) covalent geometry : angle 0.73044 / 0.36 (12755) hydrogen bonds : bond 0.05175 / 3.53 ( 216) hydrogen bonds : angle 6.19998 / 4.41 ( 594) Misc. bond : bond 0.00065 / 0.03 ( 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 251 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.398 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 293 GLU cc_start: 0.7211 (tp30) cc_final: 0.6940 (tp30) REVERT: C 139 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7057 (p90) REVERT: C 152 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: C 200 ASN cc_start: 0.8717 (p0) cc_final: 0.8451 (p0) REVERT: C 215 ASP cc_start: 0.8390 (t70) cc_final: 0.7992 (p0) REVERT: C 216 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7420 (t0) REVERT: C 276 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7788 (tpm170) REVERT: D 155 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7868 (mtpp) REVERT: D 244 VAL cc_start: 0.9553 (t) cc_final: 0.9279 (m) REVERT: D 250 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8784 (m) REVERT: E 167 THR cc_start: 0.9348 (m) cc_final: 0.9099 (p) REVERT: E 186 ASN cc_start: 0.8654 (t0) cc_final: 0.8389 (t0) REVERT: E 275 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.5832 (m-80) REVERT: E 276 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.6626 (tpp-160) REVERT: E 288 THR cc_start: 0.4605 (OUTLIER) cc_final: 0.4060 (m) REVERT: F 159 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6370 (mmmt) REVERT: F 256 ASN cc_start: 0.8070 (p0) cc_final: 0.6858 (t0) outliers start: 49 outliers final: 33 residues processed: 232 average time/residue: 0.1827 time to fit residues: 60.3312 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 : 0.444 ------------------------------------------------------------------------------- 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 264 SER 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 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: 0.8980 chunk 77 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 36 optimal weight: 0.0870 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 207 HIS D 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109934 restraints weight = 39940.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114471 restraints weight = 20746.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117508 restraints weight = 13163.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119596 restraints weight = 9487.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120908 restraints weight = 7451.409| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9297 Z= 0.164 Angle : 0.683 9.531 12755 Z= 0.336 Chirality : 0.044 0.203 1408 Planarity : 0.004 0.045 1558 Dihedral : 14.219 145.503 1348 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 5.87 % Allowed : 17.61 % Favored : 76.52 % 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: -0.20 (0.29), residues: 302 sheet: -1.81 (0.38), residues: 161 loop : -1.96 (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 0.015 0.001 PHE A 147 TRP 0.009 0.001 TRP E 223 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9296) covalent geometry : angle 0.68319 / 0.34 (12755) hydrogen bonds : bond 0.03791 / 2.57 ( 216) hydrogen bonds : angle 5.69725 / 4.04 ( 594) Misc. bond : bond 0.00049 / 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 261 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 0.469 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: 0.8519 (pttp) cc_final: 0.8259 (pttm) REVERT: B 250 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8237 (p) REVERT: C 139 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.6827 (p90) REVERT: C 152 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: C 200 ASN cc_start: 0.8741 (p0) cc_final: 0.8456 (p0) REVERT: C 215 ASP cc_start: 0.8389 (t70) cc_final: 0.7981 (p0) REVERT: C 216 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: C 276 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7783 (tpm170) REVERT: D 155 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7845 (mtpp) REVERT: D 209 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5936 (mm-30) REVERT: D 244 VAL cc_start: 0.9547 (t) cc_final: 0.9256 (m) REVERT: D 250 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8772 (m) REVERT: E 167 THR cc_start: 0.9363 (m) cc_final: 0.9163 (p) REVERT: E 186 ASN cc_start: 0.8628 (t0) cc_final: 0.8339 (t0) REVERT: E 261 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6888 (tm-30) REVERT: E 275 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: E 276 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.6680 (tpp-160) REVERT: E 288 THR cc_start: 0.4730 (OUTLIER) cc_final: 0.4176 (m) REVERT: F 159 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6347 (mmmt) REVERT: F 256 ASN cc_start: 0.8008 (p0) cc_final: 0.6829 (t0) outliers start: 56 outliers final: 36 residues processed: 239 average time/residue: 0.1835 time to fit residues: 62.7991 Evaluate side-chains 231 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 209 GLU 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 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 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: 0.0870 chunk 43 optimal weight: 0.0030 chunk 76 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 104 optimal weight: 0.2980 chunk 17 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.8570 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.142597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115897 restraints weight = 39668.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121571 restraints weight = 18839.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125189 restraints weight = 11480.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127525 restraints weight = 8161.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129094 restraints weight = 6387.012| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9297 Z= 0.105 Angle : 0.640 9.245 12755 Z= 0.307 Chirality : 0.043 0.177 1408 Planarity : 0.004 0.041 1558 Dihedral : 13.545 140.634 1343 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.72 % Allowed : 18.45 % Favored : 76.83 % 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: -1.81 (0.26), residues: 1086 helix: 0.16 (0.30), residues: 308 sheet: -1.68 (0.39), residues: 161 loop : -1.82 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 199 TYR 0.022 0.001 TYR F 218 PHE 0.016 0.001 PHE A 147 TRP 0.008 0.001 TRP E 223 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9296) covalent geometry : angle 0.63962 / 0.31 (12755) hydrogen bonds : bond 0.02975 / 1.98 ( 216) hydrogen bonds : angle 5.31595 / 3.77 ( 594) Misc. bond : bond 0.00064 / 0.03 ( 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 239 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.8587 (pttp) cc_final: 0.8238 (pttm) REVERT: B 250 SER cc_start: 0.8770 (m) cc_final: 0.8194 (p) REVERT: C 139 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.6673 (p90) REVERT: C 152 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: C 215 ASP cc_start: 0.8266 (t70) cc_final: 0.7967 (p0) REVERT: C 276 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7696 (tpm170) REVERT: D 155 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7800 (mtpp) REVERT: D 250 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8787 (m) REVERT: E 167 THR cc_start: 0.9373 (m) cc_final: 0.9170 (p) REVERT: E 186 ASN cc_start: 0.8614 (t0) cc_final: 0.8334 (t0) REVERT: E 276 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.6637 (tpp-160) REVERT: E 288 THR cc_start: 0.4687 (OUTLIER) cc_final: 0.4119 (m) REVERT: E 300 THR cc_start: 0.7975 (t) cc_final: 0.7766 (m) REVERT: F 159 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6301 (mmmt) REVERT: F 194 TYR cc_start: 0.7816 (t80) cc_final: 0.7556 (t80) REVERT: F 256 ASN cc_start: 0.7932 (p0) cc_final: 0.6843 (t0) outliers start: 45 outliers final: 31 residues processed: 220 average time/residue: 0.1803 time to fit residues: 56.6134 Evaluate side-chains 221 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 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 138 GLN Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 141 VAL 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 D residue 264 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 220 TRP Chi-restraints excluded: chain E residue 247 LEU 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: 9.9990 chunk 76 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.3392 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.147210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121533 restraints weight = 38753.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127159 restraints weight = 18257.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130668 restraints weight = 11089.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132970 restraints weight = 7854.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134417 restraints weight = 6130.962| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3094 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= 0.156 Angle : 0.643 8.944 12755 Z= 0.312 Chirality : 0.043 0.186 1408 Planarity : 0.004 0.040 1558 Dihedral : 13.015 136.935 1327 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 5.24 % Allowed : 18.34 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.26), residues: 1086 helix: 0.19 (0.29), residues: 308 sheet: -1.79 (0.39), residues: 161 loop : -1.83 (0.26), residues: 617 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 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9296) covalent geometry : angle 0.64306 / 0.31 (12755) hydrogen bonds : bond 0.02947 / 1.97 ( 216) hydrogen bonds : angle 5.24314 / 3.73 ( 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 235 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.454 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: A 201 LYS cc_start: 0.8507 (pttp) cc_final: 0.8235 (pttm) REVERT: B 250 SER cc_start: 0.8723 (m) cc_final: 0.8130 (p) REVERT: C 139 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.6581 (p90) REVERT: C 152 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: C 202 TRP cc_start: 0.8806 (OUTLIER) cc_final: 0.7651 (m-90) REVERT: C 215 ASP cc_start: 0.8284 (t70) cc_final: 0.7959 (p0) REVERT: C 276 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7753 (tpm170) REVERT: D 250 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8782 (m) REVERT: D 276 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7581 (tpt170) REVERT: E 186 ASN cc_start: 0.8640 (t0) cc_final: 0.8353 (t0) REVERT: E 261 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6938 (tm-30) REVERT: E 276 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.6710 (tpp-160) REVERT: E 288 THR cc_start: 0.4735 (OUTLIER) cc_final: 0.4146 (m) REVERT: F 159 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6311 (mmmt) REVERT: F 194 TYR cc_start: 0.7852 (t80) cc_final: 0.7610 (t80) REVERT: F 256 ASN cc_start: 0.7908 (p0) cc_final: 0.6807 (t0) outliers start: 50 outliers final: 38 residues processed: 216 average time/residue: 0.1896 time to fit residues: 57.6256 Evaluate side-chains 229 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 128 GLU 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 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 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: 4.9990 chunk 100 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.126869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.102804 restraints weight = 40284.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.106900 restraints weight = 21287.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109699 restraints weight = 13845.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111527 restraints weight = 10224.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.112929 restraints weight = 8255.725| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9297 Z= 0.216 Angle : 0.671 8.633 12755 Z= 0.332 Chirality : 0.045 0.190 1408 Planarity : 0.004 0.051 1558 Dihedral : 12.753 145.316 1327 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 5.77 % Allowed : 18.76 % Favored : 75.47 % 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: -2.16 (0.25), residues: 1086 helix: 0.02 (0.29), residues: 302 sheet: -2.34 (0.39), residues: 151 loop : -1.99 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.021 0.002 TYR F 218 PHE 0.018 0.002 PHE A 147 TRP 0.010 0.001 TRP B 202 HIS 0.003 0.001 HIS E 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 ( 9296) covalent geometry : angle 0.67127 / 0.33 (12755) hydrogen bonds : bond 0.03134 / 2.12 ( 216) hydrogen bonds : angle 5.33819 / 3.80 ( 594) Misc. bond : bond 0.00082 / 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 239 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 0.467 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 201 LYS cc_start: 0.8631 (pttp) cc_final: 0.8329 (pttm) REVERT: B 250 SER cc_start: 0.8768 (m) cc_final: 0.8179 (p) REVERT: C 152 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: C 200 ASN cc_start: 0.8761 (p0) cc_final: 0.8065 (p0) REVERT: C 202 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.7465 (m-90) REVERT: C 215 ASP cc_start: 0.8342 (t70) cc_final: 0.8057 (p0) REVERT: C 216 ASP cc_start: 0.8434 (m-30) cc_final: 0.8041 (m-30) REVERT: C 276 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7784 (tpm170) REVERT: D 244 VAL cc_start: 0.9540 (t) cc_final: 0.9267 (m) REVERT: D 250 SER cc_start: 0.9133 (OUTLIER) cc_final: 0.8777 (m) REVERT: D 276 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7615 (tpt170) REVERT: E 275 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: E 276 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.6698 (tpp-160) REVERT: E 288 THR cc_start: 0.4746 (OUTLIER) cc_final: 0.4182 (m) REVERT: F 159 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6339 (mmmt) REVERT: F 194 TYR cc_start: 0.7981 (t80) cc_final: 0.7557 (t80) outliers start: 55 outliers final: 39 residues processed: 218 average time/residue: 0.1963 time to fit residues: 60.2031 Evaluate side-chains 224 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 123 VAL 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 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 238 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 90 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.129438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.105473 restraints weight = 39895.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109733 restraints weight = 20805.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112616 restraints weight = 13405.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114479 restraints weight = 9830.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115889 restraints weight = 7887.210| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9297 Z= 0.112 Angle : 0.623 8.552 12755 Z= 0.300 Chirality : 0.042 0.143 1408 Planarity : 0.004 0.038 1558 Dihedral : 12.389 143.181 1327 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.98 % Allowed : 20.44 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.26), residues: 1086 helix: 0.35 (0.30), residues: 308 sheet: -2.12 (0.39), residues: 151 loop : -1.86 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 276 TYR 0.025 0.002 TYR A 206 PHE 0.017 0.001 PHE A 147 TRP 0.008 0.001 TRP E 223 HIS 0.008 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9296) covalent geometry : angle 0.62312 / 0.30 (12755) hydrogen bonds : bond 0.02605 / 1.73 ( 216) hydrogen bonds : angle 5.02398 / 3.60 ( 594) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 VAL cc_start: 0.9259 (t) cc_final: 0.8909 (m) REVERT: A 201 LYS cc_start: 0.8559 (pttp) cc_final: 0.8231 (pttm) REVERT: C 152 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: C 202 TRP cc_start: 0.8791 (OUTLIER) cc_final: 0.7571 (m-90) REVERT: C 276 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7746 (tpm170) REVERT: D 238 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7293 (mt-10) REVERT: D 250 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8797 (m) REVERT: E 186 ASN cc_start: 0.8698 (t0) cc_final: 0.8424 (t0) REVERT: E 261 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6936 (tm-30) REVERT: E 276 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.6687 (tpp-160) REVERT: F 159 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6335 (mmmt) REVERT: F 194 TYR cc_start: 0.7882 (t80) cc_final: 0.7591 (t80) outliers start: 38 outliers final: 31 residues processed: 201 average time/residue: 0.1932 time to fit residues: 55.0910 Evaluate side-chains 205 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.9980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.129989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.105864 restraints weight = 39825.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.110191 restraints weight = 20840.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113156 restraints weight = 13319.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114995 restraints weight = 9691.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116467 restraints weight = 7767.879| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9297 Z= 0.125 Angle : 0.621 8.407 12755 Z= 0.299 Chirality : 0.042 0.149 1408 Planarity : 0.004 0.041 1558 Dihedral : 12.098 140.880 1321 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 4.51 % Allowed : 19.92 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.26), residues: 1086 helix: 0.47 (0.30), residues: 308 sheet: -2.09 (0.39), residues: 150 loop : -1.82 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 228 TYR 0.021 0.002 TYR F 218 PHE 0.018 0.001 PHE A 147 TRP 0.009 0.001 TRP E 223 HIS 0.015 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9296) covalent geometry : angle 0.62090 / 0.30 (12755) hydrogen bonds : bond 0.02539 / 1.68 ( 216) hydrogen bonds : angle 4.93663 / 3.55 ( 594) Misc. bond : bond 0.00008 / 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 223 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.453 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: A 173 VAL cc_start: 0.9273 (t) cc_final: 0.8926 (m) REVERT: A 201 LYS cc_start: 0.8568 (pttp) cc_final: 0.8212 (pttm) REVERT: C 152 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: C 202 TRP cc_start: 0.8786 (OUTLIER) cc_final: 0.7525 (m-90) REVERT: C 276 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7827 (tpm170) REVERT: D 238 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: D 250 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8824 (m) REVERT: D 276 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7577 (tpt170) REVERT: E 186 ASN cc_start: 0.8688 (t0) cc_final: 0.8407 (t0) REVERT: E 261 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6939 (tm-30) REVERT: E 276 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.6718 (tpp-160) REVERT: F 159 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6338 (mmmt) REVERT: F 194 TYR cc_start: 0.7866 (t80) cc_final: 0.7585 (t80) outliers start: 43 outliers final: 31 residues processed: 204 average time/residue: 0.1999 time to fit residues: 57.7121 Evaluate side-chains 211 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 138 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 238 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 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: 3.9990 chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 15 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.4682 ------------------------------------------------------------------------------- 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 = 0.129377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104860 restraints weight = 39983.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.109176 restraints weight = 20968.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111978 restraints weight = 13501.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114111 restraints weight = 9932.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.115374 restraints weight = 7885.381| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9297 Z= 0.116 Angle : 0.611 8.369 12755 Z= 0.292 Chirality : 0.042 0.144 1408 Planarity : 0.004 0.038 1558 Dihedral : 11.828 139.192 1320 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.30 % Allowed : 19.81 % 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: -1.61 (0.26), residues: 1086 helix: 0.67 (0.30), residues: 308 sheet: -2.06 (0.39), residues: 150 loop : -1.77 (0.25), residues: 628 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 0.019 0.001 PHE A 147 TRP 0.009 0.001 TRP B 202 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9296) covalent geometry : angle 0.61061 / 0.29 (12755) hydrogen bonds : bond 0.02389 / 1.58 ( 216) hydrogen bonds : angle 4.83162 / 3.48 ( 594) Misc. bond : bond 0.00044 / 0.02 ( 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: 41 poor density : 177 time to evaluate : 0.454 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: 0.9272 (t) cc_final: 0.8919 (m) REVERT: A 201 LYS cc_start: 0.8520 (pttp) cc_final: 0.8203 (pttm) REVERT: C 152 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: C 202 TRP cc_start: 0.8775 (OUTLIER) cc_final: 0.7548 (m-90) REVERT: C 276 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7746 (tpm170) REVERT: D 238 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: D 244 VAL cc_start: 0.9473 (t) cc_final: 0.9224 (m) REVERT: D 250 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8825 (m) REVERT: E 186 ASN cc_start: 0.8672 (t0) cc_final: 0.8410 (t0) REVERT: E 261 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6960 (tm-30) REVERT: E 276 ARG cc_start: 0.7626 (ttm-80) cc_final: 0.6752 (tpp-160) REVERT: F 159 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6310 (mmmt) REVERT: F 194 TYR cc_start: 0.7848 (t80) cc_final: 0.7556 (t80) outliers start: 41 outliers final: 32 residues processed: 199 average time/residue: 0.1901 time to fit residues: 53.7956 Evaluate side-chains 213 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 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 138 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 264 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 220 TRP Chi-restraints excluded: chain E residue 221 LEU 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 33 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.130749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106421 restraints weight = 39819.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110797 restraints weight = 20676.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113756 restraints weight = 13194.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115606 restraints weight = 9635.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117104 restraints weight = 7733.706| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9297 Z= 0.104 Angle : 0.601 8.249 12755 Z= 0.286 Chirality : 0.042 0.139 1408 Planarity : 0.004 0.040 1558 Dihedral : 11.669 138.496 1320 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.88 % Allowed : 20.23 % 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: -1.44 (0.26), residues: 1086 helix: 0.88 (0.31), residues: 308 sheet: -2.05 (0.39), residues: 152 loop : -1.67 (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 0.019 0.001 PHE A 147 TRP 0.012 0.001 TRP B 220 HIS 0.006 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 9296) covalent geometry : angle 0.60105 / 0.29 (12755) hydrogen bonds : bond 0.02279 / 1.50 ( 216) hydrogen bonds : angle 4.70697 / 3.40 ( 594) Misc. bond : bond 0.00065 / 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 224 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.444 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: A 173 VAL cc_start: 0.9283 (t) cc_final: 0.8932 (m) REVERT: A 201 LYS cc_start: 0.8536 (pttp) cc_final: 0.8181 (pttm) REVERT: C 152 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: C 202 TRP cc_start: 0.8758 (OUTLIER) cc_final: 0.7482 (m-90) REVERT: C 276 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7761 (tpm170) REVERT: D 238 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7370 (mt-10) REVERT: D 244 VAL cc_start: 0.9498 (t) cc_final: 0.9240 (m) REVERT: D 250 SER cc_start: 0.9164 (OUTLIER) cc_final: 0.8826 (m) REVERT: E 186 ASN cc_start: 0.8652 (t0) cc_final: 0.8395 (t0) REVERT: E 261 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6958 (tm-30) REVERT: E 276 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.6715 (tpp-160) REVERT: F 159 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6347 (mmmt) REVERT: F 194 TYR cc_start: 0.7808 (t80) cc_final: 0.7534 (t80) REVERT: F 225 ASP cc_start: 0.8810 (t0) cc_final: 0.8407 (t0) outliers start: 37 outliers final: 30 residues processed: 206 average time/residue: 0.1867 time to fit residues: 54.6930 Evaluate side-chains 218 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 238 GLU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 264 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 220 TRP Chi-restraints excluded: chain E residue 221 LEU 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: 4.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 0.0670 overall best weight: 1.0300 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.130333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.106215 restraints weight = 39580.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110465 restraints weight = 20425.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113387 restraints weight = 13131.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.115283 restraints weight = 9598.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.116712 restraints weight = 7675.453| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3848 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= 0.104 Angle : 0.604 8.166 12755 Z= 0.287 Chirality : 0.042 0.137 1408 Planarity : 0.004 0.055 1558 Dihedral : 11.589 138.609 1320 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.67 % Allowed : 20.86 % Favored : 75.47 % 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: -1.38 (0.26), residues: 1086 helix: 0.96 (0.31), residues: 308 sheet: -2.02 (0.40), residues: 152 loop : -1.64 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 148 TYR 0.020 0.001 TYR A 206 PHE 0.021 0.001 PHE A 147 TRP 0.008 0.001 TRP E 223 HIS 0.006 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 9296) covalent geometry : angle 0.60354 / 0.29 (12755) hydrogen bonds : bond 0.02267 / 1.47 ( 216) hydrogen bonds : angle 4.70032 / 3.42 ( 594) Misc. bond : bond 0.00065 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2962.12 seconds wall clock time: 51 minutes 11.49 seconds (3071.49 seconds total)