Starting phenix.real_space_refine on Sat Sep 12 03:22:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7caf_30329/09_2026/7caf_30329.cif Found real_map, /net/cci-nas-00/data/ceres_data/7caf_30329/09_2026/7caf_30329.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7caf_30329/09_2026/7caf_30329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7caf_30329/09_2026/7caf_30329.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7caf_30329/09_2026/7caf_30329.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7caf_30329/09_2026/7caf_30329.cif" model { file = "/net/cci-nas-00/data/ceres_data/7caf_30329/09_2026/7caf_30329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7caf_30329/09_2026/7caf_30329.cif" } 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 8593 2.51 5 N 2255 2.21 5 O 2525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13414 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3382 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 31, 'TRANS': 411} Chain: "C" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2886 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2167 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 269} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2067 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.00, per 1000 atoms: 0.22 Number of scatterers: 13414 At special positions: 0 Unit cell: (82, 94.3, 164.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 2525 8.00 N 2255 7.00 C 8593 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 ALPHA1-1 " GLC F 1 " - " GLC F 2 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 581.2 milliseconds 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 16 sheets defined 49.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 44 through 53 removed outlier: 3.982A pdb=" N GLU E 53 " --> pdb=" O ASN E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 83 removed outlier: 3.635A pdb=" N GLY E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 104 Processing helix chain 'E' and resid 117 through 126 removed outlier: 4.539A pdb=" N ASN E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 192 through 207 removed outlier: 3.780A pdb=" N VAL E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.540A pdb=" N VAL E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.972A pdb=" N THR E 253 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 264 removed outlier: 3.523A pdb=" N ARG E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 286 removed outlier: 3.936A pdb=" N SER E 279 " --> pdb=" O TYR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.549A pdb=" N LEU E 300 " --> pdb=" O ASP E 297 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 297 through 301' Processing helix chain 'E' and resid 313 through 323 removed outlier: 3.929A pdb=" N ALA E 323 " --> pdb=" O ILE E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 370 Processing helix chain 'E' and resid 372 through 384 removed outlier: 6.207A pdb=" N TYR E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 402 Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.617A pdb=" N ILE E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 431 Processing helix chain 'E' and resid 444 through 460 removed outlier: 4.144A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 96 through 107 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.502A pdb=" N LEU C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 140 through 154 Processing helix chain 'C' and resid 172 through 189 removed outlier: 4.238A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.564A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 228 Processing helix chain 'C' and resid 232 through 239 removed outlier: 3.643A pdb=" N ALA C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 275 Processing helix chain 'C' and resid 287 through 291 removed outlier: 3.630A pdb=" N ILE C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 299 through 303 removed outlier: 3.771A pdb=" N ILE C 303 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 96 through 108 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 128 through 132 removed outlier: 4.101A pdb=" N LEU D 132 " --> pdb=" O SER D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 154 removed outlier: 3.561A pdb=" N VAL D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 168 removed outlier: 4.296A pdb=" N ASN D 168 " --> pdb=" O PRO D 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 165 through 168' Processing helix chain 'D' and resid 172 through 189 removed outlier: 4.536A pdb=" N GLN D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 4.104A pdb=" N ALA D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 337 through 345 removed outlier: 4.078A pdb=" N ASP D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 38 Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.934A pdb=" N ILE A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 76 through 110 removed outlier: 3.761A pdb=" N TRP A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 128 Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 161 through 190 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.783A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.526A pdb=" N ARG A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 212 " --> pdb=" O TRP A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 212' Processing helix chain 'A' and resid 219 through 236 removed outlier: 3.783A pdb=" N ILE A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.946A pdb=" N ASP A 250 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 267 through 292 removed outlier: 3.695A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.593A pdb=" N SER B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.970A pdb=" N VAL B 42 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 93 removed outlier: 3.647A pdb=" N LEU B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.700A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 127 through 132 removed outlier: 5.826A pdb=" N ARG B 130 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 163 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix removed outlier: 4.259A pdb=" N GLU B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.751A pdb=" N LYS B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 187 through 206 Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 241 through 263 Proline residue: B 255 - end of helix removed outlier: 4.260A pdb=" N PHE B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.587A pdb=" N ALA B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 30 through 31 removed outlier: 6.475A pdb=" N ILE E 30 " --> pdb=" O GLN E 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 64 through 66 removed outlier: 5.319A pdb=" N TYR E 34 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU E 66 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR E 36 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR E 35 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU E 349 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 9 removed outlier: 5.878A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.620A pdb=" N VAL C 85 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 195 " --> pdb=" O MET C 162 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 196 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 36 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL C 210 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE C 38 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET C 212 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 40 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL C 209 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE C 220 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C 211 " --> pdb=" O GLN C 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 245 through 249 removed outlier: 3.513A pdb=" N ILE C 282 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 311 removed outlier: 3.653A pdb=" N VAL C 310 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 315 through 317 Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 31 removed outlier: 5.186A pdb=" N PHE D 27 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 159 through 163 removed outlier: 3.555A pdb=" N VAL D 193 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 195 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE D 37 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE D 36 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL D 210 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 38 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N MET D 212 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 40 " --> pdb=" O MET D 212 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 245 through 248 removed outlier: 3.743A pdb=" N ASN D 245 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 250 through 251 Processing sheet with id=AB5, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.798A pdb=" N LEU D 306 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 310 through 311 removed outlier: 3.517A pdb=" N VAL D 310 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 314 through 317 removed outlier: 4.186A pdb=" N ILE D 314 " --> pdb=" O HIS D 325 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1683 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: 2.10 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3457 1.33 - 1.45: 2361 1.45 - 1.57: 7783 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 13678 Sorted by residual: bond pdb=" C1 GLC F 1 " pdb=" O5 GLC F 1 " ideal model delta sigma weight residual 1.410 1.509 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C3 GLC F 2 " pdb=" O3 GLC F 2 " ideal model delta sigma weight residual 1.410 1.483 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C5 GLC F 1 " pdb=" O5 GLC F 1 " ideal model delta sigma weight residual 1.410 1.481 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C1 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.410 1.474 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C5 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.410 1.473 -0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 13673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 18027 1.85 - 3.70: 515 3.70 - 5.56: 74 5.56 - 7.41: 23 7.41 - 9.26: 6 Bond angle restraints: 18645 Sorted by residual: angle pdb=" N VAL B 28 " pdb=" CA VAL B 28 " pdb=" C VAL B 28 " ideal model delta sigma weight residual 112.96 107.42 5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" N PRO D 242 " pdb=" CA PRO D 242 " pdb=" C PRO D 242 " ideal model delta sigma weight residual 112.47 104.05 8.42 2.06e+00 2.36e-01 1.67e+01 angle pdb=" C GLY C 221 " pdb=" N THR C 222 " pdb=" CA THR C 222 " ideal model delta sigma weight residual 120.51 126.37 -5.86 1.45e+00 4.76e-01 1.63e+01 angle pdb=" N ASP E 138 " pdb=" CA ASP E 138 " pdb=" C ASP E 138 " ideal model delta sigma weight residual 114.75 109.79 4.96 1.26e+00 6.30e-01 1.55e+01 angle pdb=" N SER D 241 " pdb=" CA SER D 241 " pdb=" CB SER D 241 " ideal model delta sigma weight residual 110.37 116.33 -5.96 1.78e+00 3.16e-01 1.12e+01 ... (remaining 18640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 7295 17.64 - 35.28: 749 35.28 - 52.92: 119 52.92 - 70.55: 29 70.55 - 88.19: 9 Dihedral angle restraints: 8201 sinusoidal: 3126 harmonic: 5075 Sorted by residual: dihedral pdb=" CA LYS E 360 " pdb=" C LYS E 360 " pdb=" N ALA E 361 " pdb=" CA ALA E 361 " ideal model delta harmonic sigma weight residual 180.00 154.80 25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ILE C 291 " pdb=" C ILE C 291 " pdb=" N GLU C 292 " pdb=" CA GLU C 292 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA VAL E 373 " pdb=" C VAL E 373 " pdb=" N GLU E 374 " pdb=" CA GLU E 374 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 8198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.964: 2220 0.964 - 1.927: 0 1.927 - 2.891: 0 2.891 - 3.854: 0 3.854 - 4.817: 1 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C1 GLC F 2 " pdb=" C2 GLC F 2 " pdb=" O1 GLC F 2 " pdb=" O5 GLC F 2 " both_signs ideal model delta sigma weight residual False 2.33 -2.48 4.82 2.00e-01 2.50e+01 5.80e+02 chirality pdb=" CA PRO D 242 " pdb=" N PRO D 242 " pdb=" C PRO D 242 " pdb=" CB PRO D 242 " both_signs ideal model delta sigma weight residual False 2.72 2.92 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CB ILE C 4 " pdb=" CA ILE C 4 " pdb=" CG1 ILE C 4 " pdb=" CG2 ILE C 4 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 2218 not shown) Planarity restraints: 2394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 375 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ASN E 375 " -0.060 2.00e-02 2.50e+03 pdb=" O ASN E 375 " 0.022 2.00e-02 2.50e+03 pdb=" N GLN E 376 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 266 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO D 267 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 267 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 267 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 113 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO E 114 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " 0.034 5.00e-02 4.00e+02 ... (remaining 2391 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 119 2.57 - 3.15: 11488 3.15 - 3.73: 20079 3.73 - 4.32: 27645 4.32 - 4.90: 47383 Nonbonded interactions: 106714 Sorted by model distance: nonbonded pdb=" O PRO D 242 " pdb=" O ALA D 243 " model vdw 1.987 3.040 nonbonded pdb=" O ARG B 130 " pdb=" NH1 ARG B 130 " model vdw 2.092 3.120 nonbonded pdb=" O ALA D 90 " pdb=" NH2 ARG D 151 " model vdw 2.197 3.120 nonbonded pdb=" OE2 GLU E 193 " pdb=" OH TYR E 424 " model vdw 2.224 3.040 nonbonded pdb=" O ALA D 2 " pdb=" OG1 THR D 191 " model vdw 2.236 3.040 ... (remaining 106709 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 'C' and (resid 2 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 391)) selection = (chain 'D' and (resid 2 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 391)) } 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=0.00 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.450 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.006 0.099 13679 Z= 0.253 Angle : 0.767 9.260 18648 Z= 0.422 Chirality : 0.113 4.817 2221 Planarity : 0.005 0.065 2394 Dihedral : 14.631 88.192 4929 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.01 % Favored : 90.70 % Rotamer: Outliers : 0.43 % Allowed : 8.71 % Favored : 90.86 % 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: -4.70 (0.16), residues: 1753 helix: -2.15 (0.15), residues: 816 sheet: -3.48 (0.31), residues: 174 loop : -4.16 (0.17), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 130 TYR 0.023 0.002 TYR E 34 PHE 0.010 0.001 PHE E 291 TRP 0.033 0.002 TRP E 136 HIS 0.002 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (13678) covalent geometry : angle 0.76580 / 0.42 (18645) hydrogen bonds : bond 0.14854 / 10.05 ( 590) hydrogen bonds : angle 6.77038 / 4.70 ( 1683) glycosidic custom : bond 0.06476 / 3.41 ( 1) glycosidic custom : angle 2.92094 / 1.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 204 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 169 MET cc_start: 0.8551 (ttt) cc_final: 0.8349 (ttt) REVERT: E 177 TYR cc_start: 0.8184 (t80) cc_final: 0.7967 (t80) REVERT: E 410 GLN cc_start: 0.7909 (pt0) cc_final: 0.7549 (tm-30) REVERT: D 187 ARG cc_start: 0.7056 (ttm170) cc_final: 0.6438 (mtm180) outliers start: 6 outliers final: 4 residues processed: 210 average time/residue: 0.1328 time to fit residues: 39.3687 Evaluate side-chains 164 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 160 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 344 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 ASN E 200 ASN C 138 GLN C 143 GLN C 176 GLN C 325 HIS D 143 GLN B 72 ASN B 220 GLN B 231 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130061 restraints weight = 16673.166| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.61 r_work: 0.3211 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13679 Z= 0.144 Angle : 0.694 13.599 18648 Z= 0.336 Chirality : 0.047 0.535 2221 Planarity : 0.006 0.064 2394 Dihedral : 6.046 52.560 1911 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.42 % Favored : 92.53 % Rotamer: Outliers : 2.00 % Allowed : 14.85 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -3.23 (0.18), residues: 1753 helix: -0.78 (0.17), residues: 833 sheet: -3.02 (0.32), residues: 169 loop : -3.58 (0.18), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 130 TYR 0.016 0.001 TYR B 155 PHE 0.011 0.001 PHE C 160 TRP 0.009 0.001 TRP E 106 HIS 0.002 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (13678) covalent geometry : angle 0.68738 / 0.33 (18645) hydrogen bonds : bond 0.04374 / 2.95 ( 590) hydrogen bonds : angle 5.14961 / 3.65 ( 1683) glycosidic custom : bond 0.02049 / 1.08 ( 1) glycosidic custom : angle 7.28229 / 3.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 177 TYR cc_start: 0.8445 (t80) cc_final: 0.8124 (t80) REVERT: E 410 GLN cc_start: 0.8297 (pt0) cc_final: 0.7747 (tm-30) REVERT: C 29 MET cc_start: 0.7885 (ptm) cc_final: 0.7676 (ptp) REVERT: C 149 MET cc_start: 0.6725 (mtp) cc_final: 0.6367 (mtp) REVERT: C 310 VAL cc_start: 0.7260 (p) cc_final: 0.7057 (p) REVERT: C 316 GLU cc_start: 0.8030 (pm20) cc_final: 0.7618 (pm20) REVERT: D 187 ARG cc_start: 0.7738 (ttm170) cc_final: 0.6997 (mtm180) REVERT: D 304 ARG cc_start: 0.7284 (mmt90) cc_final: 0.7041 (tmt170) outliers start: 28 outliers final: 16 residues processed: 198 average time/residue: 0.1179 time to fit residues: 34.3552 Evaluate side-chains 180 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 125 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 146 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN D 197 HIS B 127 ASN B 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130436 restraints weight = 16924.469| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.69 r_work: 0.3213 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13679 Z= 0.148 Angle : 0.665 10.410 18648 Z= 0.322 Chirality : 0.045 0.295 2221 Planarity : 0.005 0.066 2394 Dihedral : 5.760 59.492 1908 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.58 % Rotamer: Outliers : 3.00 % Allowed : 15.63 % Favored : 81.37 % 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: -2.66 (0.19), residues: 1753 helix: -0.31 (0.18), residues: 838 sheet: -2.78 (0.32), residues: 169 loop : -3.28 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 53 TYR 0.022 0.001 TYR C 227 PHE 0.010 0.001 PHE E 199 TRP 0.007 0.001 TRP E 166 HIS 0.004 0.001 HIS D 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (13678) covalent geometry : angle 0.66169 / 0.32 (18645) hydrogen bonds : bond 0.04214 / 2.83 ( 590) hydrogen bonds : angle 4.88349 / 3.47 ( 1683) glycosidic custom : bond 0.01750 / 0.92 ( 1) glycosidic custom : angle 5.43427 / 2.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 177 TYR cc_start: 0.8425 (t80) cc_final: 0.8098 (t80) REVERT: E 410 GLN cc_start: 0.8324 (pt0) cc_final: 0.7800 (tm-30) REVERT: C 149 MET cc_start: 0.6764 (mtp) cc_final: 0.6514 (mtp) REVERT: C 316 GLU cc_start: 0.8181 (pm20) cc_final: 0.7729 (pm20) REVERT: D 107 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7709 (mp) REVERT: D 145 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7650 (tm-30) REVERT: D 187 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7117 (mtm180) REVERT: D 197 HIS cc_start: 0.8098 (t-90) cc_final: 0.7874 (t70) REVERT: D 212 MET cc_start: 0.8396 (mtp) cc_final: 0.8161 (mtt) REVERT: A 58 GLU cc_start: 0.8312 (mp0) cc_final: 0.8077 (pm20) outliers start: 42 outliers final: 27 residues processed: 204 average time/residue: 0.1154 time to fit residues: 34.9798 Evaluate side-chains 193 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 31 optimal weight: 0.0010 chunk 129 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 138 GLN D 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128278 restraints weight = 16931.416| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.59 r_work: 0.3245 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13679 Z= 0.122 Angle : 0.635 11.202 18648 Z= 0.308 Chirality : 0.043 0.150 2221 Planarity : 0.005 0.069 2394 Dihedral : 5.458 58.124 1908 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.07 % Favored : 92.87 % Rotamer: Outliers : 3.21 % Allowed : 16.77 % Favored : 80.01 % 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: -2.28 (0.19), residues: 1753 helix: -0.03 (0.18), residues: 834 sheet: -2.51 (0.33), residues: 169 loop : -3.07 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 97 TYR 0.015 0.001 TYR E 424 PHE 0.015 0.001 PHE D 234 TRP 0.007 0.001 TRP B 138 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (13678) covalent geometry : angle 0.63349 / 0.31 (18645) hydrogen bonds : bond 0.03899 / 2.61 ( 590) hydrogen bonds : angle 4.70143 / 3.34 ( 1683) glycosidic custom : bond 0.00467 / 0.25 ( 1) glycosidic custom : angle 3.15809 / 1.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 138 ASP cc_start: 0.8373 (m-30) cc_final: 0.7590 (t0) REVERT: E 177 TYR cc_start: 0.8290 (t80) cc_final: 0.7959 (t80) REVERT: E 410 GLN cc_start: 0.8243 (pt0) cc_final: 0.7541 (tm-30) REVERT: C 29 MET cc_start: 0.7886 (ptm) cc_final: 0.7550 (ptp) REVERT: C 316 GLU cc_start: 0.7802 (pm20) cc_final: 0.7277 (pm20) REVERT: D 145 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 187 ARG cc_start: 0.7782 (ttm170) cc_final: 0.7080 (mtm180) REVERT: D 197 HIS cc_start: 0.7986 (t-90) cc_final: 0.7776 (t70) REVERT: D 212 MET cc_start: 0.8494 (mtp) cc_final: 0.8155 (mtt) REVERT: A 58 GLU cc_start: 0.8107 (mp0) cc_final: 0.7773 (pm20) outliers start: 45 outliers final: 34 residues processed: 212 average time/residue: 0.1165 time to fit residues: 36.2435 Evaluate side-chains 203 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 0.0770 chunk 164 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.168846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128363 restraints weight = 17137.426| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.54 r_work: 0.3252 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13679 Z= 0.136 Angle : 0.621 9.243 18648 Z= 0.306 Chirality : 0.044 0.162 2221 Planarity : 0.005 0.067 2394 Dihedral : 4.855 52.364 1906 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.13 % Favored : 92.81 % Rotamer: Outliers : 3.50 % Allowed : 17.63 % Favored : 78.87 % 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: -2.04 (0.20), residues: 1753 helix: 0.11 (0.19), residues: 837 sheet: -2.31 (0.34), residues: 168 loop : -2.89 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.016 0.001 TYR E 424 PHE 0.024 0.001 PHE D 234 TRP 0.007 0.001 TRP B 207 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (13678) covalent geometry : angle 0.62064 / 0.31 (18645) hydrogen bonds : bond 0.03933 / 2.63 ( 590) hydrogen bonds : angle 4.58969 / 3.27 ( 1683) glycosidic custom : bond 0.00602 / 0.32 ( 1) glycosidic custom : angle 2.26623 / 1.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 138 ASP cc_start: 0.8490 (m-30) cc_final: 0.7641 (t0) REVERT: E 410 GLN cc_start: 0.8274 (pt0) cc_final: 0.7602 (tm-30) REVERT: C 29 MET cc_start: 0.7958 (ptm) cc_final: 0.7574 (ptp) REVERT: C 316 GLU cc_start: 0.7879 (pm20) cc_final: 0.7348 (pm20) REVERT: D 187 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7175 (mtm180) REVERT: D 197 HIS cc_start: 0.8082 (t-90) cc_final: 0.7881 (t70) REVERT: D 212 MET cc_start: 0.8626 (mtp) cc_final: 0.8298 (mtt) REVERT: A 58 GLU cc_start: 0.8152 (mp0) cc_final: 0.7831 (pm20) outliers start: 49 outliers final: 40 residues processed: 211 average time/residue: 0.1189 time to fit residues: 36.7371 Evaluate side-chains 207 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 43 optimal weight: 0.4980 chunk 138 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.0040 chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 overall best weight: 0.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 411 GLN C 218 GLN B 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.170627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131144 restraints weight = 16849.808| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.77 r_work: 0.3264 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13679 Z= 0.113 Angle : 0.602 9.037 18648 Z= 0.296 Chirality : 0.043 0.154 2221 Planarity : 0.005 0.064 2394 Dihedral : 4.671 51.292 1906 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 3.07 % Allowed : 19.13 % Favored : 77.80 % 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: -1.78 (0.20), residues: 1753 helix: 0.27 (0.19), residues: 839 sheet: -2.08 (0.35), residues: 168 loop : -2.73 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 8 TYR 0.015 0.001 TYR E 424 PHE 0.037 0.001 PHE D 234 TRP 0.007 0.001 TRP B 207 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (13678) covalent geometry : angle 0.60131 / 0.30 (18645) hydrogen bonds : bond 0.03615 / 2.42 ( 590) hydrogen bonds : angle 4.49200 / 3.20 ( 1683) glycosidic custom : bond 0.00277 / 0.15 ( 1) glycosidic custom : angle 1.68890 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 138 ASP cc_start: 0.8366 (m-30) cc_final: 0.7604 (t0) REVERT: E 410 GLN cc_start: 0.8179 (pt0) cc_final: 0.7518 (tm-30) REVERT: C 29 MET cc_start: 0.7776 (ptm) cc_final: 0.7453 (ptp) REVERT: C 134 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7641 (mtm-85) REVERT: C 216 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7730 (pm20) REVERT: C 316 GLU cc_start: 0.7932 (pm20) cc_final: 0.7374 (pm20) REVERT: D 187 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7121 (mtm180) REVERT: D 212 MET cc_start: 0.8486 (mtp) cc_final: 0.8166 (mtt) REVERT: A 58 GLU cc_start: 0.8111 (mp0) cc_final: 0.7797 (pm20) REVERT: B 127 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7318 (t0) outliers start: 43 outliers final: 35 residues processed: 207 average time/residue: 0.1138 time to fit residues: 34.8190 Evaluate side-chains 206 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 261 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 77 optimal weight: 20.0000 chunk 135 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 337 ASN B 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.170480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129614 restraints weight = 16962.459| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.69 r_work: 0.3258 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13679 Z= 0.129 Angle : 0.609 8.443 18648 Z= 0.299 Chirality : 0.043 0.156 2221 Planarity : 0.005 0.063 2394 Dihedral : 4.626 50.885 1906 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.85 % Favored : 93.10 % Rotamer: Outliers : 3.50 % Allowed : 19.49 % Favored : 77.02 % 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: -1.68 (0.20), residues: 1753 helix: 0.29 (0.19), residues: 845 sheet: -2.02 (0.36), residues: 168 loop : -2.61 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 97 TYR 0.015 0.001 TYR E 424 PHE 0.028 0.001 PHE D 234 TRP 0.008 0.001 TRP B 207 HIS 0.002 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13678) covalent geometry : angle 0.60831 / 0.30 (18645) hydrogen bonds : bond 0.03728 / 2.50 ( 590) hydrogen bonds : angle 4.47512 / 3.19 ( 1683) glycosidic custom : bond 0.00250 / 0.13 ( 1) glycosidic custom : angle 2.09736 / 1.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 138 ASP cc_start: 0.8375 (m-30) cc_final: 0.7596 (t0) REVERT: E 410 GLN cc_start: 0.8156 (pt0) cc_final: 0.7475 (tm-30) REVERT: C 29 MET cc_start: 0.7744 (ptm) cc_final: 0.7376 (ptp) REVERT: C 134 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7693 (mtm-85) REVERT: C 216 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7711 (pm20) REVERT: C 316 GLU cc_start: 0.7856 (pm20) cc_final: 0.7323 (pm20) REVERT: D 158 LYS cc_start: 0.7847 (mmtt) cc_final: 0.6441 (mtpt) REVERT: D 187 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7119 (mtm180) REVERT: D 212 MET cc_start: 0.8469 (mtp) cc_final: 0.8150 (mtt) outliers start: 49 outliers final: 41 residues processed: 218 average time/residue: 0.1082 time to fit residues: 34.9812 Evaluate side-chains 216 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 261 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 0.0020 chunk 75 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127665 restraints weight = 16828.472| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.53 r_work: 0.3250 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13679 Z= 0.138 Angle : 0.616 8.388 18648 Z= 0.303 Chirality : 0.044 0.153 2221 Planarity : 0.005 0.063 2394 Dihedral : 4.656 50.503 1906 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.96 % Favored : 92.98 % Rotamer: Outliers : 3.28 % Allowed : 20.27 % Favored : 76.45 % 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: -1.58 (0.20), residues: 1753 helix: 0.33 (0.19), residues: 845 sheet: -1.88 (0.37), residues: 168 loop : -2.53 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 97 TYR 0.015 0.001 TYR E 424 PHE 0.023 0.001 PHE D 234 TRP 0.009 0.001 TRP B 207 HIS 0.002 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (13678) covalent geometry : angle 0.61538 / 0.30 (18645) hydrogen bonds : bond 0.03780 / 2.53 ( 590) hydrogen bonds : angle 4.47098 / 3.19 ( 1683) glycosidic custom : bond 0.00350 / 0.18 ( 1) glycosidic custom : angle 2.30272 / 1.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 138 ASP cc_start: 0.8360 (m-30) cc_final: 0.7590 (t0) REVERT: E 410 GLN cc_start: 0.8121 (pt0) cc_final: 0.7488 (tm-30) REVERT: C 29 MET cc_start: 0.7745 (ptm) cc_final: 0.7379 (ptp) REVERT: C 134 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7696 (mtm-85) REVERT: C 316 GLU cc_start: 0.7858 (pm20) cc_final: 0.7331 (pm20) REVERT: D 158 LYS cc_start: 0.7888 (mmtt) cc_final: 0.6491 (mtpt) REVERT: D 187 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7148 (mtm180) REVERT: D 212 MET cc_start: 0.8469 (mtp) cc_final: 0.8133 (mtt) REVERT: B 51 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8026 (pt0) outliers start: 46 outliers final: 41 residues processed: 212 average time/residue: 0.1096 time to fit residues: 34.3663 Evaluate side-chains 215 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 52 optimal weight: 0.0980 chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.170941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125854 restraints weight = 16857.368| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.26 r_work: 0.3291 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13679 Z= 0.118 Angle : 0.606 9.241 18648 Z= 0.296 Chirality : 0.043 0.150 2221 Planarity : 0.005 0.063 2394 Dihedral : 4.563 49.519 1906 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.67 % Favored : 93.27 % Rotamer: Outliers : 3.00 % Allowed : 21.13 % Favored : 75.87 % 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: -1.38 (0.20), residues: 1753 helix: 0.44 (0.19), residues: 844 sheet: -1.66 (0.38), residues: 161 loop : -2.38 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 97 TYR 0.017 0.001 TYR C 227 PHE 0.020 0.001 PHE D 234 TRP 0.008 0.001 TRP B 207 HIS 0.004 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (13678) covalent geometry : angle 0.60506 / 0.30 (18645) hydrogen bonds : bond 0.03571 / 2.39 ( 590) hydrogen bonds : angle 4.38627 / 3.12 ( 1683) glycosidic custom : bond 0.00160 / 0.08 ( 1) glycosidic custom : angle 2.04785 / 1.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 138 ASP cc_start: 0.8458 (m-30) cc_final: 0.7678 (t0) REVERT: E 410 GLN cc_start: 0.8244 (pt0) cc_final: 0.7577 (tm-30) REVERT: C 29 MET cc_start: 0.7888 (ptm) cc_final: 0.7545 (ptp) REVERT: C 134 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7803 (mtm-85) REVERT: C 216 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7750 (pm20) REVERT: C 316 GLU cc_start: 0.8022 (pm20) cc_final: 0.7531 (pm20) REVERT: D 124 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7886 (pttt) REVERT: D 158 LYS cc_start: 0.7918 (mmtt) cc_final: 0.6510 (mtpt) REVERT: D 187 ARG cc_start: 0.7913 (ttm170) cc_final: 0.7242 (mtm180) REVERT: D 212 MET cc_start: 0.8591 (mtp) cc_final: 0.8291 (mtt) REVERT: A 201 GLN cc_start: 0.7753 (tt0) cc_final: 0.7457 (tt0) REVERT: A 237 ILE cc_start: 0.7246 (pt) cc_final: 0.6971 (pt) outliers start: 42 outliers final: 39 residues processed: 213 average time/residue: 0.1232 time to fit residues: 38.5657 Evaluate side-chains 220 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 107 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 39 optimal weight: 0.0000 chunk 117 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.172546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132270 restraints weight = 16734.614| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.62 r_work: 0.3295 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13679 Z= 0.110 Angle : 0.602 9.707 18648 Z= 0.292 Chirality : 0.043 0.148 2221 Planarity : 0.005 0.063 2394 Dihedral : 4.448 47.822 1906 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.45 % Favored : 93.50 % Rotamer: Outliers : 2.71 % Allowed : 21.34 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.24 (0.20), residues: 1753 helix: 0.51 (0.19), residues: 851 sheet: -1.50 (0.38), residues: 161 loop : -2.30 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 97 TYR 0.026 0.001 TYR C 227 PHE 0.018 0.001 PHE D 234 TRP 0.007 0.001 TRP A 26 HIS 0.003 0.000 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (13678) covalent geometry : angle 0.60208 / 0.29 (18645) hydrogen bonds : bond 0.03397 / 2.27 ( 590) hydrogen bonds : angle 4.31612 / 3.07 ( 1683) glycosidic custom : bond 0.00098 / 0.05 ( 1) glycosidic custom : angle 1.80990 / 1.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 138 ASP cc_start: 0.8352 (m-30) cc_final: 0.7615 (t0) REVERT: E 410 GLN cc_start: 0.8071 (pt0) cc_final: 0.7445 (tm-30) REVERT: C 29 MET cc_start: 0.7673 (ptm) cc_final: 0.7352 (ptp) REVERT: C 134 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7722 (mtm-85) REVERT: C 216 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7685 (pm20) REVERT: C 316 GLU cc_start: 0.7894 (pm20) cc_final: 0.7377 (pm20) REVERT: D 124 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7849 (pttt) REVERT: D 158 LYS cc_start: 0.7802 (mmtt) cc_final: 0.6479 (mtpt) REVERT: D 187 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7059 (mtm180) REVERT: D 212 MET cc_start: 0.8449 (mtp) cc_final: 0.8124 (mtt) REVERT: D 244 MET cc_start: 0.7111 (tpp) cc_final: 0.6620 (ttm) REVERT: D 316 GLU cc_start: 0.7715 (pt0) cc_final: 0.7439 (pt0) REVERT: A 201 GLN cc_start: 0.7623 (tt0) cc_final: 0.7349 (tt0) REVERT: A 237 ILE cc_start: 0.6948 (pt) cc_final: 0.6723 (pt) REVERT: B 115 MET cc_start: 0.8154 (mmm) cc_final: 0.7863 (mmp) outliers start: 38 outliers final: 37 residues processed: 211 average time/residue: 0.1191 time to fit residues: 36.7699 Evaluate side-chains 214 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 96 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 305 ASN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130070 restraints weight = 16748.650| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.58 r_work: 0.3257 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13679 Z= 0.140 Angle : 0.634 8.258 18648 Z= 0.308 Chirality : 0.044 0.159 2221 Planarity : 0.005 0.063 2394 Dihedral : 4.533 47.505 1906 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.90 % Favored : 93.04 % Rotamer: Outliers : 2.86 % Allowed : 21.70 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.25 (0.20), residues: 1753 helix: 0.47 (0.19), residues: 846 sheet: -1.45 (0.39), residues: 161 loop : -2.25 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 97 TYR 0.022 0.001 TYR C 227 PHE 0.018 0.001 PHE D 234 TRP 0.009 0.001 TRP B 207 HIS 0.003 0.000 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (13678) covalent geometry : angle 0.63386 / 0.31 (18645) hydrogen bonds : bond 0.03665 / 2.46 ( 590) hydrogen bonds : angle 4.38035 / 3.11 ( 1683) glycosidic custom : bond 0.00424 / 0.22 ( 1) glycosidic custom : angle 2.26710 / 1.30 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3246.69 seconds wall clock time: 56 minutes 24.77 seconds (3384.77 seconds total)