Starting phenix.real_space_refine on Wed Mar 4 09:52:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnc_27563/03_2026/8dnc_27563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnc_27563/03_2026/8dnc_27563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dnc_27563/03_2026/8dnc_27563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnc_27563/03_2026/8dnc_27563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dnc_27563/03_2026/8dnc_27563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnc_27563/03_2026/8dnc_27563.map" } resolution = 3.3 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= 0.000 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2340 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 7099 2.51 5 N 1671 2.21 5 O 1867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10672 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "C" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {'UBH': 1, 'UBO': 1, 'XXR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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} Time building chain proxies: 2.53, per 1000 atoms: 0.24 Number of scatterers: 10672 At special positions: 0 Unit cell: (91.8, 100.44, 142.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 2 15.00 Mg 1 11.99 O 1867 8.00 N 1671 7.00 C 7099 6.00 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=0, symmetry=0 Links applied ?1-2 " XXR E 1 " - " UBO E 2 " ?1-3 " UBO E 2 " - " UBH E 3 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 455.4 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 13 sheets defined 51.8% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 removed outlier: 4.186A pdb=" N LEU A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.888A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.561A pdb=" N ASN A 136 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.558A pdb=" N THR A 141 " --> pdb=" O PRO A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.892A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.878A pdb=" N VAL A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 190 removed outlier: 3.746A pdb=" N GLN A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.683A pdb=" N VAL A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 20 through 26 Processing helix chain 'B' and resid 30 through 48 removed outlier: 3.853A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 80 removed outlier: 3.672A pdb=" N TYR B 60 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 101 through 129 removed outlier: 3.779A pdb=" N ASN B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.690A pdb=" N ILE B 134 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 3.612A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.560A pdb=" N GLN B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.654A pdb=" N THR B 183 " --> pdb=" O PHE B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.730A pdb=" N ILE B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 192 " --> pdb=" O LEU B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 188 through 192' Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 223 through 254 Proline residue: B 235 - end of helix removed outlier: 4.665A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 114 through 130 removed outlier: 5.056A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.577A pdb=" N THR C 141 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 167 through 171 removed outlier: 4.202A pdb=" N ALA C 170 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'C' and resid 173 through 191 removed outlier: 3.573A pdb=" N GLN C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 removed outlier: 4.242A pdb=" N LYS C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 207' Processing helix chain 'C' and resid 224 through 240 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 22 through 43 removed outlier: 3.729A pdb=" N TRP D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Proline residue: D 32 - end of helix Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.722A pdb=" N LEU D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.741A pdb=" N GLY D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 80 through 88 removed outlier: 4.455A pdb=" N PHE D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N THR D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.075A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 101 through 129 removed outlier: 4.362A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 139 through 165 removed outlier: 4.184A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 removed outlier: 3.969A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.760A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 226 through 254 Proline residue: D 235 - end of helix removed outlier: 4.806A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 removed outlier: 4.316A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.771A pdb=" N GLU A 32 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.340A pdb=" N PHE A 163 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 197 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 165 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLU A 48 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE A 196 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU A 221 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS A 215 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 257 through 265 removed outlier: 5.516A pdb=" N ILE A 259 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU A 287 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU A 261 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN C 390 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 333 " --> pdb=" O GLU C 388 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 276 removed outlier: 6.149A pdb=" N PHE A 274 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY A 373 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A 345 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS A 367 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR A 343 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE A 369 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY A 341 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA A 297 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN A 313 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A 299 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY A 311 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A 301 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA7, first strand: chain 'A' and resid 380 through 381 removed outlier: 6.777A pdb=" N ILE C 301 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY C 311 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 299 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN C 313 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 297 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 392 removed outlier: 3.804A pdb=" N ASN A 390 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU C 261 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLU C 287 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE C 259 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 392 removed outlier: 3.804A pdb=" N ASN A 390 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 288 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 326 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'C' and resid 84 through 86 removed outlier: 3.687A pdb=" N VAL C 85 " --> pdb=" O CYS C 162 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 195 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE C 212 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU C 221 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 341 through 342 499 hydrogen bonds defined for protein. 1419 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: 1.36 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3196 1.34 - 1.46: 2700 1.46 - 1.58: 5000 1.58 - 1.70: 3 1.70 - 1.82: 52 Bond restraints: 10951 Sorted by residual: bond pdb=" N PRO D 103 " pdb=" CD PRO D 103 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" N GLY C 326 " pdb=" CA GLY C 326 " ideal model delta sigma weight residual 1.447 1.475 -0.028 9.20e-03 1.18e+04 9.24e+00 bond pdb=" N LYS C 325 " pdb=" CA LYS C 325 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.28e-02 6.10e+03 7.37e+00 bond pdb=" N LYS C 327 " pdb=" CA LYS C 327 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.22e-02 6.72e+03 6.17e+00 bond pdb=" C5 UBH E 3 " pdb=" O5 UBH E 3 " ideal model delta sigma weight residual 1.438 1.396 0.042 2.00e-02 2.50e+03 4.34e+00 ... (remaining 10946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 14563 2.09 - 4.18: 211 4.18 - 6.27: 33 6.27 - 8.36: 10 8.36 - 10.46: 1 Bond angle restraints: 14818 Sorted by residual: angle pdb=" C LEU B 91 " pdb=" N PHE B 92 " pdb=" CA PHE B 92 " ideal model delta sigma weight residual 122.38 115.50 6.88 1.81e+00 3.05e-01 1.44e+01 angle pdb=" CA GLY C 326 " pdb=" C GLY C 326 " pdb=" O GLY C 326 " ideal model delta sigma weight residual 121.48 118.50 2.98 9.90e-01 1.02e+00 9.07e+00 angle pdb=" CB ARG B 11 " pdb=" CG ARG B 11 " pdb=" CD ARG B 11 " ideal model delta sigma weight residual 111.30 118.18 -6.88 2.30e+00 1.89e-01 8.95e+00 angle pdb=" CA LEU A 90 " pdb=" CB LEU A 90 " pdb=" CG LEU A 90 " ideal model delta sigma weight residual 116.30 126.76 -10.46 3.50e+00 8.16e-02 8.92e+00 angle pdb=" CG ARG B 11 " pdb=" CD ARG B 11 " pdb=" NE ARG B 11 " ideal model delta sigma weight residual 112.00 118.54 -6.54 2.20e+00 2.07e-01 8.83e+00 ... (remaining 14813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.91: 5856 19.91 - 39.81: 506 39.81 - 59.72: 62 59.72 - 79.62: 10 79.62 - 99.53: 7 Dihedral angle restraints: 6441 sinusoidal: 2661 harmonic: 3780 Sorted by residual: dihedral pdb=" O1B ADP A 502 " pdb=" O3A ADP A 502 " pdb=" PB ADP A 502 " pdb=" PA ADP A 502 " ideal model delta sinusoidal sigma weight residual -60.00 -159.53 99.53 1 2.00e+01 2.50e-03 2.80e+01 dihedral pdb=" CA TRP B 26 " pdb=" C TRP B 26 " pdb=" N TRP B 27 " pdb=" CA TRP B 27 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LEU C 87 " pdb=" C LEU C 87 " pdb=" N LEU C 88 " pdb=" CA LEU C 88 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 6438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 966 0.031 - 0.061: 461 0.061 - 0.092: 147 0.092 - 0.122: 74 0.122 - 0.153: 15 Chirality restraints: 1663 Sorted by residual: chirality pdb=" CG LEU A 64 " pdb=" CB LEU A 64 " pdb=" CD1 LEU A 64 " pdb=" CD2 LEU A 64 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ASP C 354 " pdb=" N ASP C 354 " pdb=" C ASP C 354 " pdb=" CB ASP C 354 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA PHE A 134 " pdb=" N PHE A 134 " pdb=" C PHE A 134 " pdb=" CB PHE A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1660 not shown) Planarity restraints: 1815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 362 " -0.010 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C TRP C 362 " 0.033 2.00e-02 2.50e+03 pdb=" O TRP C 362 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE C 363 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 102 " 0.032 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO D 103 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 324 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C LYS C 324 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS C 324 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS C 325 " 0.010 2.00e-02 2.50e+03 ... (remaining 1812 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 70 2.57 - 3.15: 8647 3.15 - 3.74: 15996 3.74 - 4.32: 21911 4.32 - 4.90: 37776 Nonbonded interactions: 84400 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O2B ADP A 502 " model vdw 1.989 2.170 nonbonded pdb=" O LYS B 89 " pdb=" OG1 THR B 93 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR B 60 " pdb=" O VAL B 186 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR A 331 " pdb=" OD1 ASN C 390 " model vdw 2.244 3.040 nonbonded pdb=" O SER A 99 " pdb=" ND2 ASN A 103 " model vdw 2.247 3.120 ... (remaining 84395 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 1 through 395) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 individual isotropic 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.130 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.004 0.057 10953 Z= 0.174 Angle : 0.655 10.455 14824 Z= 0.347 Chirality : 0.043 0.153 1663 Planarity : 0.004 0.047 1815 Dihedral : 14.468 99.531 4025 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.24), residues: 1292 helix: 0.46 (0.22), residues: 616 sheet: -0.93 (0.40), residues: 186 loop : -1.96 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 11 TYR 0.019 0.001 TYR A 315 PHE 0.023 0.002 PHE D 126 TRP 0.016 0.002 TRP B 26 HIS 0.006 0.001 HIS C 361 Details of bonding type rmsd covalent geometry : bond 0.00366 (10951) covalent geometry : angle 0.65392 (14818) hydrogen bonds : bond 0.15673 ( 490) hydrogen bonds : angle 6.07800 ( 1419) glycosidic custom : bond 0.04038 ( 2) glycosidic custom : angle 1.82970 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: C 23 GLU cc_start: 0.7467 (tm-30) cc_final: 0.6773 (tt0) REVERT: C 131 LEU cc_start: 0.3642 (mp) cc_final: 0.3387 (mp) REVERT: C 261 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6339 (mm-30) REVERT: D 110 GLU cc_start: 0.6757 (tp30) cc_final: 0.6462 (tp30) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0910 time to fit residues: 27.9465 Evaluate side-chains 160 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.179952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133221 restraints weight = 14463.817| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.40 r_work: 0.3399 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10953 Z= 0.204 Angle : 0.652 10.264 14824 Z= 0.331 Chirality : 0.045 0.175 1663 Planarity : 0.004 0.035 1815 Dihedral : 5.741 102.186 1467 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.64 % Allowed : 9.83 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.24), residues: 1292 helix: 0.46 (0.22), residues: 614 sheet: -0.87 (0.41), residues: 189 loop : -1.95 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.022 0.002 TYR D 63 PHE 0.029 0.002 PHE B 92 TRP 0.019 0.003 TRP B 26 HIS 0.005 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00500 (10951) covalent geometry : angle 0.65155 (14818) hydrogen bonds : bond 0.05169 ( 490) hydrogen bonds : angle 4.95947 ( 1419) glycosidic custom : bond 0.00566 ( 2) glycosidic custom : angle 1.74860 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 104 ILE cc_start: 0.8983 (mt) cc_final: 0.8741 (mt) REVERT: A 119 ASP cc_start: 0.7878 (m-30) cc_final: 0.7651 (m-30) REVERT: A 140 LYS cc_start: 0.9203 (mttt) cc_final: 0.8985 (mtpt) REVERT: A 322 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6968 (mp0) REVERT: B 221 ASP cc_start: 0.8242 (p0) cc_final: 0.7946 (p0) REVERT: C 23 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6602 (tt0) REVERT: C 353 MET cc_start: 0.6013 (ptp) cc_final: 0.5278 (ptm) REVERT: D 12 GLN cc_start: 0.7777 (mp10) cc_final: 0.7370 (mp10) REVERT: D 124 ILE cc_start: 0.7913 (mm) cc_final: 0.7695 (mt) outliers start: 19 outliers final: 13 residues processed: 186 average time/residue: 0.0839 time to fit residues: 23.0986 Evaluate side-chains 173 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.177697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130519 restraints weight = 14597.963| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.42 r_work: 0.3364 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 10953 Z= 0.233 Angle : 0.658 9.094 14824 Z= 0.332 Chirality : 0.046 0.223 1663 Planarity : 0.004 0.039 1815 Dihedral : 5.897 106.846 1467 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.41 % Allowed : 13.62 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1292 helix: 0.26 (0.21), residues: 619 sheet: -0.80 (0.41), residues: 185 loop : -2.02 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 11 TYR 0.023 0.002 TYR D 63 PHE 0.026 0.002 PHE B 92 TRP 0.019 0.003 TRP B 26 HIS 0.005 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00574 (10951) covalent geometry : angle 0.65703 (14818) hydrogen bonds : bond 0.05262 ( 490) hydrogen bonds : angle 4.86933 ( 1419) glycosidic custom : bond 0.00493 ( 2) glycosidic custom : angle 1.65280 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.396 Fit side-chains REVERT: A 119 ASP cc_start: 0.7818 (m-30) cc_final: 0.7544 (m-30) REVERT: A 140 LYS cc_start: 0.9270 (mttt) cc_final: 0.9068 (mtpt) REVERT: B 23 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7676 (tt) REVERT: B 68 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8811 (tt) REVERT: B 118 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.7889 (tp) REVERT: B 144 LEU cc_start: 0.8330 (tp) cc_final: 0.8119 (mp) REVERT: B 205 MET cc_start: 0.8268 (mmm) cc_final: 0.8043 (tpp) REVERT: C 205 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8090 (mmmm) REVERT: C 249 GLN cc_start: 0.7227 (tt0) cc_final: 0.6868 (mp10) REVERT: C 353 MET cc_start: 0.5752 (ptp) cc_final: 0.5318 (ptm) REVERT: C 360 TYR cc_start: 0.7733 (m-80) cc_final: 0.7278 (m-80) REVERT: D 124 ILE cc_start: 0.8055 (mm) cc_final: 0.7852 (mt) outliers start: 28 outliers final: 18 residues processed: 186 average time/residue: 0.0905 time to fit residues: 24.6869 Evaluate side-chains 179 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.181559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143662 restraints weight = 14668.967| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.75 r_work: 0.3358 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10953 Z= 0.125 Angle : 0.570 9.609 14824 Z= 0.289 Chirality : 0.042 0.160 1663 Planarity : 0.004 0.036 1815 Dihedral : 5.599 102.836 1467 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.33 % Allowed : 16.38 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.24), residues: 1292 helix: 0.54 (0.22), residues: 619 sheet: -0.81 (0.41), residues: 188 loop : -1.99 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.018 0.001 TYR C 252 PHE 0.025 0.001 PHE B 92 TRP 0.015 0.002 TRP B 181 HIS 0.004 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00291 (10951) covalent geometry : angle 0.56949 (14818) hydrogen bonds : bond 0.04085 ( 490) hydrogen bonds : angle 4.59713 ( 1419) glycosidic custom : bond 0.00178 ( 2) glycosidic custom : angle 1.17853 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.311 Fit side-chains REVERT: A 87 LEU cc_start: 0.8017 (mt) cc_final: 0.7799 (mt) REVERT: A 119 ASP cc_start: 0.7703 (m-30) cc_final: 0.7487 (m-30) REVERT: A 129 SER cc_start: 0.8407 (t) cc_final: 0.8137 (p) REVERT: A 133 ASP cc_start: 0.8768 (p0) cc_final: 0.8536 (p0) REVERT: A 140 LYS cc_start: 0.9206 (tttt) cc_final: 0.9000 (mtpt) REVERT: B 23 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7833 (tt) REVERT: B 118 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7711 (tp) REVERT: B 205 MET cc_start: 0.8149 (mmm) cc_final: 0.7873 (mmm) REVERT: B 221 ASP cc_start: 0.7922 (p0) cc_final: 0.7646 (p0) REVERT: C 23 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6573 (tt0) REVERT: C 205 LYS cc_start: 0.8714 (ptpp) cc_final: 0.8164 (mmmm) REVERT: C 249 GLN cc_start: 0.7101 (tt0) cc_final: 0.6756 (mp10) REVERT: C 250 ASN cc_start: 0.7418 (m-40) cc_final: 0.7200 (m110) REVERT: C 323 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8047 (mm) REVERT: C 353 MET cc_start: 0.5528 (ptp) cc_final: 0.5313 (ptm) REVERT: C 360 TYR cc_start: 0.7695 (m-80) cc_final: 0.7264 (m-80) REVERT: D 3 LEU cc_start: 0.7669 (tt) cc_final: 0.7447 (tt) REVERT: D 12 GLN cc_start: 0.7575 (mp10) cc_final: 0.7205 (mp10) outliers start: 27 outliers final: 14 residues processed: 173 average time/residue: 0.0933 time to fit residues: 23.5641 Evaluate side-chains 164 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 118 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.181067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143167 restraints weight = 14534.192| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.76 r_work: 0.3342 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10953 Z= 0.141 Angle : 0.568 9.607 14824 Z= 0.289 Chirality : 0.043 0.156 1663 Planarity : 0.004 0.036 1815 Dihedral : 5.542 101.221 1467 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.59 % Allowed : 17.76 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.24), residues: 1292 helix: 0.61 (0.22), residues: 620 sheet: -0.69 (0.39), residues: 199 loop : -1.85 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.015 0.001 TYR D 63 PHE 0.024 0.001 PHE B 92 TRP 0.015 0.002 TRP B 181 HIS 0.004 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00338 (10951) covalent geometry : angle 0.56800 (14818) hydrogen bonds : bond 0.04141 ( 490) hydrogen bonds : angle 4.53449 ( 1419) glycosidic custom : bond 0.00243 ( 2) glycosidic custom : angle 1.23946 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.435 Fit side-chains REVERT: A 104 ILE cc_start: 0.8957 (mt) cc_final: 0.8640 (mt) REVERT: A 119 ASP cc_start: 0.7677 (m-30) cc_final: 0.7470 (m-30) REVERT: A 133 ASP cc_start: 0.8823 (p0) cc_final: 0.8546 (p0) REVERT: A 140 LYS cc_start: 0.9212 (tttt) cc_final: 0.8998 (mtpt) REVERT: B 23 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7766 (tt) REVERT: B 68 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8734 (tt) REVERT: B 118 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7726 (tp) REVERT: B 177 GLN cc_start: 0.8950 (mp10) cc_final: 0.8669 (mt0) REVERT: B 205 MET cc_start: 0.8206 (mmm) cc_final: 0.7912 (mmm) REVERT: C 23 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6607 (tt0) REVERT: C 87 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.5154 (tt) REVERT: C 90 LEU cc_start: 0.4815 (mt) cc_final: 0.3901 (pp) REVERT: C 146 MET cc_start: 0.5382 (mtp) cc_final: 0.3988 (tpt) REVERT: C 205 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8157 (mmmm) REVERT: C 323 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8026 (mm) REVERT: C 353 MET cc_start: 0.5520 (ptp) cc_final: 0.5286 (ptm) REVERT: C 360 TYR cc_start: 0.7771 (m-80) cc_final: 0.7322 (m-80) REVERT: D 3 LEU cc_start: 0.7687 (tt) cc_final: 0.7455 (tt) outliers start: 30 outliers final: 17 residues processed: 177 average time/residue: 0.0907 time to fit residues: 23.4974 Evaluate side-chains 171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 0.0270 chunk 114 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 ASN C 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.182883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145176 restraints weight = 14635.752| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.79 r_work: 0.3384 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10953 Z= 0.115 Angle : 0.555 10.012 14824 Z= 0.281 Chirality : 0.042 0.155 1663 Planarity : 0.003 0.035 1815 Dihedral : 5.353 97.379 1467 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.41 % Allowed : 17.93 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.24), residues: 1292 helix: 0.78 (0.22), residues: 620 sheet: -0.80 (0.38), residues: 206 loop : -1.76 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.026 0.001 TYR C 252 PHE 0.023 0.001 PHE B 92 TRP 0.014 0.002 TRP B 181 HIS 0.003 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00266 (10951) covalent geometry : angle 0.55442 (14818) hydrogen bonds : bond 0.03734 ( 490) hydrogen bonds : angle 4.40600 ( 1419) glycosidic custom : bond 0.00125 ( 2) glycosidic custom : angle 1.02097 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.247 Fit side-chains REVERT: A 104 ILE cc_start: 0.8907 (mt) cc_final: 0.8593 (mt) REVERT: A 119 ASP cc_start: 0.7693 (m-30) cc_final: 0.7491 (m-30) REVERT: A 133 ASP cc_start: 0.8790 (p0) cc_final: 0.8508 (p0) REVERT: B 23 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7769 (tt) REVERT: B 118 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7671 (tp) REVERT: B 177 GLN cc_start: 0.8930 (mp10) cc_final: 0.8619 (mt0) REVERT: B 205 MET cc_start: 0.8126 (mmm) cc_final: 0.7806 (mmm) REVERT: C 23 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6664 (tt0) REVERT: C 90 LEU cc_start: 0.4939 (mt) cc_final: 0.4146 (pp) REVERT: C 205 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8287 (mttt) REVERT: C 323 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8046 (mm) REVERT: C 360 TYR cc_start: 0.7693 (m-80) cc_final: 0.7242 (m-80) REVERT: D 3 LEU cc_start: 0.7666 (tt) cc_final: 0.7442 (tt) REVERT: D 12 GLN cc_start: 0.7562 (mp10) cc_final: 0.7220 (mp10) REVERT: D 224 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8441 (tt) outliers start: 28 outliers final: 16 residues processed: 184 average time/residue: 0.0927 time to fit residues: 24.5703 Evaluate side-chains 170 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 224 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 GLN C 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143943 restraints weight = 14576.767| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.79 r_work: 0.3344 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10953 Z= 0.149 Angle : 0.578 9.989 14824 Z= 0.292 Chirality : 0.043 0.153 1663 Planarity : 0.004 0.036 1815 Dihedral : 5.395 96.512 1467 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.59 % Allowed : 18.71 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1292 helix: 0.76 (0.22), residues: 620 sheet: -0.57 (0.39), residues: 203 loop : -1.82 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 116 TYR 0.019 0.001 TYR C 252 PHE 0.027 0.002 PHE B 90 TRP 0.015 0.002 TRP B 181 HIS 0.003 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00360 (10951) covalent geometry : angle 0.57790 (14818) hydrogen bonds : bond 0.04050 ( 490) hydrogen bonds : angle 4.40894 ( 1419) glycosidic custom : bond 0.00257 ( 2) glycosidic custom : angle 1.16556 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.413 Fit side-chains REVERT: A 104 ILE cc_start: 0.8987 (mt) cc_final: 0.8672 (mt) REVERT: A 119 ASP cc_start: 0.7783 (m-30) cc_final: 0.7544 (m-30) REVERT: A 133 ASP cc_start: 0.8832 (p0) cc_final: 0.8549 (p0) REVERT: B 23 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7734 (tt) REVERT: B 68 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8728 (tt) REVERT: B 118 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7690 (tp) REVERT: B 177 GLN cc_start: 0.8923 (mp10) cc_final: 0.8630 (mt0) REVERT: B 205 MET cc_start: 0.8177 (mmm) cc_final: 0.7862 (mmm) REVERT: C 23 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6660 (tt0) REVERT: C 90 LEU cc_start: 0.4910 (mt) cc_final: 0.4082 (pp) REVERT: C 205 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8326 (mttt) REVERT: C 250 ASN cc_start: 0.7058 (m-40) cc_final: 0.6724 (m110) REVERT: C 323 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7946 (mm) REVERT: C 360 TYR cc_start: 0.7744 (m-80) cc_final: 0.7273 (m-80) REVERT: D 3 LEU cc_start: 0.7680 (tt) cc_final: 0.7446 (tt) outliers start: 30 outliers final: 22 residues processed: 179 average time/residue: 0.0930 time to fit residues: 24.4825 Evaluate side-chains 178 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 45 optimal weight: 0.3980 chunk 124 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.182649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144767 restraints weight = 14512.663| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.74 r_work: 0.3380 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10953 Z= 0.121 Angle : 0.566 10.349 14824 Z= 0.285 Chirality : 0.042 0.150 1663 Planarity : 0.003 0.034 1815 Dihedral : 5.247 92.645 1467 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.76 % Allowed : 18.88 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.24), residues: 1292 helix: 0.89 (0.22), residues: 620 sheet: -0.69 (0.39), residues: 207 loop : -1.76 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 116 TYR 0.019 0.001 TYR C 252 PHE 0.023 0.001 PHE B 92 TRP 0.014 0.002 TRP B 181 HIS 0.003 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00282 (10951) covalent geometry : angle 0.56599 (14818) hydrogen bonds : bond 0.03697 ( 490) hydrogen bonds : angle 4.34792 ( 1419) glycosidic custom : bond 0.00137 ( 2) glycosidic custom : angle 0.96451 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.418 Fit side-chains REVERT: A 104 ILE cc_start: 0.8944 (mt) cc_final: 0.8630 (mt) REVERT: A 119 ASP cc_start: 0.7759 (m-30) cc_final: 0.7548 (m-30) REVERT: A 133 ASP cc_start: 0.8807 (p0) cc_final: 0.8524 (p0) REVERT: B 23 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7745 (tt) REVERT: B 68 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8656 (tt) REVERT: B 118 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7682 (tp) REVERT: B 177 GLN cc_start: 0.8898 (mp10) cc_final: 0.8613 (mt0) REVERT: B 205 MET cc_start: 0.8135 (mmm) cc_final: 0.7801 (mmm) REVERT: C 23 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6657 (tt0) REVERT: C 90 LEU cc_start: 0.4904 (mt) cc_final: 0.4152 (pp) REVERT: C 131 LEU cc_start: 0.4193 (mt) cc_final: 0.3719 (mt) REVERT: C 201 MET cc_start: 0.5243 (ptp) cc_final: 0.4255 (ptp) REVERT: C 205 LYS cc_start: 0.8728 (ptpp) cc_final: 0.8375 (mttt) REVERT: C 323 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8083 (mm) REVERT: C 327 LYS cc_start: 0.7849 (mttt) cc_final: 0.7506 (ttpp) REVERT: C 360 TYR cc_start: 0.7677 (m-80) cc_final: 0.7249 (m-80) REVERT: D 3 LEU cc_start: 0.7676 (tt) cc_final: 0.7452 (tt) REVERT: D 12 GLN cc_start: 0.7544 (mp10) cc_final: 0.7229 (mp10) REVERT: D 146 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7754 (mp) REVERT: D 224 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8420 (tt) outliers start: 32 outliers final: 20 residues processed: 186 average time/residue: 0.0944 time to fit residues: 25.7114 Evaluate side-chains 180 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 224 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.180079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142354 restraints weight = 14584.497| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.75 r_work: 0.3328 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10953 Z= 0.175 Angle : 0.614 10.282 14824 Z= 0.312 Chirality : 0.044 0.150 1663 Planarity : 0.004 0.036 1815 Dihedral : 5.409 94.503 1467 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.76 % Allowed : 19.57 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1292 helix: 0.76 (0.22), residues: 620 sheet: -0.52 (0.39), residues: 202 loop : -1.86 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 11 TYR 0.025 0.001 TYR C 252 PHE 0.022 0.002 PHE B 92 TRP 0.014 0.002 TRP B 181 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00429 (10951) covalent geometry : angle 0.61385 (14818) hydrogen bonds : bond 0.04308 ( 490) hydrogen bonds : angle 4.41397 ( 1419) glycosidic custom : bond 0.00308 ( 2) glycosidic custom : angle 1.22507 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.358 Fit side-chains REVERT: A 104 ILE cc_start: 0.8936 (mt) cc_final: 0.8624 (mt) REVERT: A 119 ASP cc_start: 0.7812 (m-30) cc_final: 0.7591 (m-30) REVERT: B 68 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8736 (tt) REVERT: B 118 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.7812 (tp) REVERT: B 145 TYR cc_start: 0.8490 (t80) cc_final: 0.8173 (t80) REVERT: B 177 GLN cc_start: 0.8908 (mp10) cc_final: 0.8614 (mt0) REVERT: B 205 MET cc_start: 0.8222 (mmm) cc_final: 0.7886 (mmm) REVERT: C 23 GLU cc_start: 0.7432 (tm-30) cc_final: 0.6655 (tt0) REVERT: C 90 LEU cc_start: 0.5051 (mt) cc_final: 0.4269 (pp) REVERT: C 131 LEU cc_start: 0.4060 (mt) cc_final: 0.3590 (mt) REVERT: C 201 MET cc_start: 0.5338 (ptp) cc_final: 0.4330 (ptp) REVERT: C 205 LYS cc_start: 0.8726 (ptpp) cc_final: 0.8390 (mttt) REVERT: C 323 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7894 (mm) REVERT: C 327 LYS cc_start: 0.7881 (mttt) cc_final: 0.7536 (ttpp) REVERT: C 360 TYR cc_start: 0.7773 (m-80) cc_final: 0.7272 (m-80) REVERT: D 3 LEU cc_start: 0.7683 (tt) cc_final: 0.7456 (tt) REVERT: D 12 GLN cc_start: 0.7564 (mp10) cc_final: 0.7203 (mp10) REVERT: D 146 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7849 (mp) outliers start: 32 outliers final: 23 residues processed: 177 average time/residue: 0.0868 time to fit residues: 22.7368 Evaluate side-chains 184 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.181270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144052 restraints weight = 14301.817| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.65 r_work: 0.3368 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10953 Z= 0.130 Angle : 0.595 10.728 14824 Z= 0.300 Chirality : 0.042 0.148 1663 Planarity : 0.003 0.037 1815 Dihedral : 5.282 91.773 1467 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.33 % Allowed : 19.91 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1292 helix: 0.92 (0.22), residues: 620 sheet: -0.66 (0.39), residues: 207 loop : -1.79 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 116 TYR 0.023 0.001 TYR C 252 PHE 0.024 0.001 PHE B 175 TRP 0.015 0.002 TRP B 181 HIS 0.003 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00310 (10951) covalent geometry : angle 0.59455 (14818) hydrogen bonds : bond 0.03790 ( 490) hydrogen bonds : angle 4.34997 ( 1419) glycosidic custom : bond 0.00136 ( 2) glycosidic custom : angle 0.96771 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.409 Fit side-chains REVERT: A 19 ASP cc_start: 0.8321 (t0) cc_final: 0.7399 (m-30) REVERT: A 104 ILE cc_start: 0.8848 (mt) cc_final: 0.8540 (mt) REVERT: A 119 ASP cc_start: 0.7840 (m-30) cc_final: 0.7615 (m-30) REVERT: B 68 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8684 (tt) REVERT: B 118 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7715 (tp) REVERT: B 177 GLN cc_start: 0.8877 (mp10) cc_final: 0.8592 (mt0) REVERT: B 205 MET cc_start: 0.8177 (mmm) cc_final: 0.7836 (mmm) REVERT: C 23 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6649 (tt0) REVERT: C 90 LEU cc_start: 0.4917 (mt) cc_final: 0.4188 (pp) REVERT: C 131 LEU cc_start: 0.3984 (mt) cc_final: 0.3722 (mt) REVERT: C 146 MET cc_start: 0.5375 (mtp) cc_final: 0.3925 (tpt) REVERT: C 201 MET cc_start: 0.5276 (ptp) cc_final: 0.4387 (ptp) REVERT: C 205 LYS cc_start: 0.8746 (ptpp) cc_final: 0.8336 (mmmm) REVERT: C 249 GLN cc_start: 0.7543 (tm130) cc_final: 0.7065 (tm-30) REVERT: C 323 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7972 (mm) REVERT: C 327 LYS cc_start: 0.7920 (mttt) cc_final: 0.7587 (ttpp) REVERT: C 360 TYR cc_start: 0.7719 (m-80) cc_final: 0.7242 (m-80) REVERT: D 3 LEU cc_start: 0.7684 (tt) cc_final: 0.7454 (tt) REVERT: D 12 GLN cc_start: 0.7606 (mp10) cc_final: 0.7248 (mp10) outliers start: 27 outliers final: 21 residues processed: 179 average time/residue: 0.0995 time to fit residues: 25.7318 Evaluate side-chains 181 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.181559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142109 restraints weight = 14653.348| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 4.01 r_work: 0.3317 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10953 Z= 0.184 Angle : 0.631 10.568 14824 Z= 0.320 Chirality : 0.044 0.161 1663 Planarity : 0.004 0.038 1815 Dihedral : 5.444 94.223 1467 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.93 % Allowed : 19.48 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.24), residues: 1292 helix: 0.76 (0.22), residues: 620 sheet: -0.53 (0.39), residues: 202 loop : -1.86 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 11 TYR 0.023 0.001 TYR C 252 PHE 0.023 0.002 PHE B 175 TRP 0.014 0.002 TRP B 181 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00449 (10951) covalent geometry : angle 0.63076 (14818) hydrogen bonds : bond 0.04367 ( 490) hydrogen bonds : angle 4.44779 ( 1419) glycosidic custom : bond 0.00318 ( 2) glycosidic custom : angle 1.23797 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.07 seconds wall clock time: 42 minutes 33.20 seconds (2553.20 seconds total)