Starting phenix.real_space_refine on Thu Jul 31 11:02:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7caf_30329/07_2025/7caf_30329.cif Found real_map, /net/cci-nas-00/data/ceres_data/7caf_30329/07_2025/7caf_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_30329/07_2025/7caf_30329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7caf_30329/07_2025/7caf_30329.map" model { file = "/net/cci-nas-00/data/ceres_data/7caf_30329/07_2025/7caf_30329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7caf_30329/07_2025/7caf_30329.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'ARG:plan': 4} 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: {'TYR:plan': 1, 'ARG:plan': 3, 'ASP: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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.61, per 1000 atoms: 0.72 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: 3.67 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.69 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: 4.03 Time building geometry restraints manager: 4.24 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 1.402 1.509 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C1 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.402 1.474 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C3 GLC F 2 " pdb=" O3 GLC F 2 " ideal model delta sigma weight residual 1.412 1.483 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C2 GLC F 2 " pdb=" C3 GLC F 2 " ideal model delta sigma weight residual 1.528 1.461 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C5 GLC F 1 " pdb=" O5 GLC F 1 " ideal model delta sigma weight residual 1.415 1.481 -0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 13673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 18017 1.85 - 3.70: 518 3.70 - 5.56: 80 5.56 - 7.41: 24 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 - 20.70: 7567 20.70 - 41.39: 565 41.39 - 62.09: 76 62.09 - 82.78: 12 82.78 - 103.48: 8 Dihedral angle restraints: 8228 sinusoidal: 3153 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 8225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2060 0.089 - 0.178: 159 0.178 - 0.267: 1 0.267 - 0.356: 0 0.356 - 0.444: 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 -2.04 -2.48 0.44 2.00e-01 2.50e+01 4.94e+00 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: 3.890 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 34.950 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 0.107 13679 Z= 0.254 Angle : 0.774 9.260 18648 Z= 0.423 Chirality : 0.048 0.444 2221 Planarity : 0.005 0.065 2394 Dihedral : 14.849 103.480 4956 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.002 TRP E 136 HIS 0.002 0.001 HIS C 94 PHE 0.010 0.001 PHE E 291 TYR 0.023 0.002 TYR E 34 ARG 0.007 0.000 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.14854 ( 590) hydrogen bonds : angle 6.77038 ( 1683) glycosidic custom : bond 0.06476 ( 1) glycosidic custom : angle 2.92094 ( 3) covalent geometry : bond 0.00553 (13678) covalent geometry : angle 0.77296 (18645) *********************** 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 : 1.561 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: 0.2794 time to fit residues: 82.2963 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 : 1.373 ------------------------------------------------------------------------------- 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 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.0970 chunk 73 optimal weight: 40.0000 chunk 45 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 ASN E 148 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.165792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128808 restraints weight = 16641.791| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.58 r_work: 0.3204 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13679 Z= 0.169 Angle : 0.691 10.370 18648 Z= 0.342 Chirality : 0.045 0.159 2221 Planarity : 0.006 0.060 2394 Dihedral : 6.375 65.549 1938 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.76 % Favored : 92.18 % Rotamer: Outliers : 2.07 % Allowed : 15.06 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.18), residues: 1753 helix: -0.87 (0.17), residues: 832 sheet: -3.06 (0.32), residues: 169 loop : -3.63 (0.18), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 106 HIS 0.003 0.001 HIS E 359 PHE 0.012 0.001 PHE C 160 TYR 0.018 0.002 TYR B 155 ARG 0.008 0.001 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 590) hydrogen bonds : angle 5.23799 ( 1683) glycosidic custom : bond 0.00871 ( 1) glycosidic custom : angle 2.50104 ( 3) covalent geometry : bond 0.00400 (13678) covalent geometry : angle 0.69049 (18645) *********************** 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 204 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 177 TYR cc_start: 0.8485 (t80) cc_final: 0.8186 (t80) REVERT: E 410 GLN cc_start: 0.8511 (pt0) cc_final: 0.7892 (tm-30) REVERT: C 29 MET cc_start: 0.8087 (ptm) cc_final: 0.7829 (ptp) REVERT: C 149 MET cc_start: 0.6915 (mtp) cc_final: 0.6619 (mtp) REVERT: C 310 VAL cc_start: 0.7322 (p) cc_final: 0.7111 (p) REVERT: C 316 GLU cc_start: 0.8039 (pm20) cc_final: 0.7637 (pm20) REVERT: D 187 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7097 (mtm180) REVERT: D 304 ARG cc_start: 0.7314 (mmt90) cc_final: 0.7084 (tmt170) outliers start: 29 outliers final: 18 residues processed: 196 average time/residue: 0.2760 time to fit residues: 78.6123 Evaluate side-chains 178 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 82 ILE 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 Chi-restraints excluded: chain B residue 127 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 41 optimal weight: 0.0070 chunk 92 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3911 r_free = 0.3911 target = 0.166787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129754 restraints weight = 16797.413| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.60 r_work: 0.3201 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13679 Z= 0.154 Angle : 0.645 10.338 18648 Z= 0.320 Chirality : 0.044 0.157 2221 Planarity : 0.005 0.066 2394 Dihedral : 5.266 54.202 1935 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.19 % Favored : 92.76 % Rotamer: Outliers : 3.50 % Allowed : 15.27 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.19), residues: 1753 helix: -0.32 (0.18), residues: 838 sheet: -2.78 (0.33), residues: 169 loop : -3.30 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 166 HIS 0.004 0.001 HIS D 197 PHE 0.009 0.001 PHE D 380 TYR 0.022 0.002 TYR C 227 ARG 0.007 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 590) hydrogen bonds : angle 4.91373 ( 1683) glycosidic custom : bond 0.00399 ( 1) glycosidic custom : angle 1.61317 ( 3) covalent geometry : bond 0.00367 (13678) covalent geometry : angle 0.64493 (18645) *********************** 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 224 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 177 TYR cc_start: 0.8428 (t80) cc_final: 0.8107 (t80) REVERT: E 410 GLN cc_start: 0.8312 (pt0) cc_final: 0.7794 (tm-30) REVERT: C 149 MET cc_start: 0.6816 (mtp) cc_final: 0.6540 (mtp) REVERT: C 310 VAL cc_start: 0.7282 (p) cc_final: 0.7080 (p) REVERT: C 316 GLU cc_start: 0.8167 (pm20) cc_final: 0.7711 (pm20) REVERT: D 107 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7707 (mp) REVERT: D 187 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7111 (mtm180) REVERT: D 212 MET cc_start: 0.8404 (mtp) cc_final: 0.8157 (mtt) REVERT: A 58 GLU cc_start: 0.8342 (mp0) cc_final: 0.8127 (pm20) outliers start: 49 outliers final: 33 residues processed: 210 average time/residue: 0.2625 time to fit residues: 82.2189 Evaluate side-chains 198 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 108 VAL Chi-restraints excluded: chain E residue 149 THR 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 367 ILE Chi-restraints excluded: chain C residue 4 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 Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 261 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 80 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 16 optimal weight: 0.4980 chunk 76 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 88 optimal weight: 0.0870 chunk 74 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3891 r_free = 0.3891 target = 0.164856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127797 restraints weight = 16810.153| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.72 r_work: 0.3167 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13679 Z= 0.221 Angle : 0.693 9.552 18648 Z= 0.343 Chirality : 0.047 0.167 2221 Planarity : 0.005 0.071 2394 Dihedral : 5.289 54.898 1933 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.04 % Favored : 91.90 % Rotamer: Outliers : 3.64 % Allowed : 17.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.19), residues: 1753 helix: -0.28 (0.18), residues: 839 sheet: -2.70 (0.33), residues: 176 loop : -3.20 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 207 HIS 0.002 0.001 HIS D 290 PHE 0.017 0.002 PHE D 234 TYR 0.018 0.002 TYR B 155 ARG 0.006 0.000 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 590) hydrogen bonds : angle 4.92824 ( 1683) glycosidic custom : bond 0.00167 ( 1) glycosidic custom : angle 1.04385 ( 3) covalent geometry : bond 0.00545 (13678) covalent geometry : angle 0.69257 (18645) *********************** 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 218 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 177 TYR cc_start: 0.8419 (t80) cc_final: 0.8126 (t80) REVERT: E 220 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8302 (mp) REVERT: E 410 GLN cc_start: 0.8302 (pt0) cc_final: 0.7848 (tm-30) REVERT: C 149 MET cc_start: 0.6868 (mtp) cc_final: 0.6576 (mtp) REVERT: C 161 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7742 (mp) REVERT: C 316 GLU cc_start: 0.8216 (pm20) cc_final: 0.7766 (pm20) REVERT: D 187 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7035 (mtm180) REVERT: D 212 MET cc_start: 0.8443 (mtp) cc_final: 0.8180 (mtt) REVERT: A 201 GLN cc_start: 0.8092 (tt0) cc_final: 0.7892 (tt0) outliers start: 51 outliers final: 39 residues processed: 203 average time/residue: 0.3157 time to fit residues: 94.6012 Evaluate side-chains 202 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 94 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 220 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 367 ILE 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 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 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 289 GLU 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 219 THR 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 42 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 0.0170 chunk 36 optimal weight: 0.0980 chunk 146 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 411 GLN C 138 GLN D 199 GLN B 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.169659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128954 restraints weight = 16940.171| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.87 r_work: 0.3226 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13679 Z= 0.120 Angle : 0.613 10.499 18648 Z= 0.303 Chirality : 0.043 0.152 2221 Planarity : 0.005 0.068 2394 Dihedral : 4.889 54.086 1933 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 3.43 % Allowed : 19.27 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.20), residues: 1753 helix: 0.06 (0.18), residues: 836 sheet: -2.40 (0.34), residues: 169 loop : -2.96 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 207 HIS 0.002 0.001 HIS C 94 PHE 0.024 0.001 PHE C 352 TYR 0.017 0.001 TYR E 424 ARG 0.004 0.000 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 590) hydrogen bonds : angle 4.65519 ( 1683) glycosidic custom : bond 0.00194 ( 1) glycosidic custom : angle 1.07347 ( 3) covalent geometry : bond 0.00263 (13678) covalent geometry : angle 0.61318 (18645) *********************** 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 234 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 410 GLN cc_start: 0.8223 (pt0) cc_final: 0.7560 (tm-30) REVERT: C 161 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7313 (mp) REVERT: C 316 GLU cc_start: 0.7828 (pm20) cc_final: 0.7285 (pm20) REVERT: D 107 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7361 (mp) REVERT: D 187 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7086 (mtm180) REVERT: D 212 MET cc_start: 0.8536 (mtp) cc_final: 0.8195 (mtt) REVERT: D 244 MET cc_start: 0.7028 (tpp) cc_final: 0.6713 (ttm) outliers start: 48 outliers final: 32 residues processed: 216 average time/residue: 0.2886 time to fit residues: 91.9005 Evaluate side-chains 201 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU 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 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 435 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 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 107 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 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 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 261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 66 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127743 restraints weight = 17020.531| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.95 r_work: 0.3200 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1940 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= 0.140 Angle : 0.627 9.208 18648 Z= 0.310 Chirality : 0.044 0.151 2221 Planarity : 0.005 0.064 2394 Dihedral : 4.827 54.053 1933 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.19 % Favored : 92.76 % Rotamer: Outliers : 3.78 % Allowed : 19.84 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.20), residues: 1753 helix: 0.15 (0.18), residues: 841 sheet: -2.22 (0.34), residues: 170 loop : -2.80 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 207 HIS 0.003 0.001 HIS C 197 PHE 0.014 0.001 PHE C 352 TYR 0.016 0.001 TYR E 424 ARG 0.004 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 590) hydrogen bonds : angle 4.58755 ( 1683) glycosidic custom : bond 0.00205 ( 1) glycosidic custom : angle 1.04660 ( 3) covalent geometry : bond 0.00331 (13678) covalent geometry : angle 0.62730 (18645) *********************** 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 225 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: E 410 GLN cc_start: 0.8233 (pt0) cc_final: 0.7563 (tm-30) REVERT: C 161 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7272 (mp) REVERT: C 316 GLU cc_start: 0.7853 (pm20) cc_final: 0.7303 (pm20) REVERT: D 187 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7001 (mtm180) REVERT: D 212 MET cc_start: 0.8557 (mtp) cc_final: 0.8218 (mtt) REVERT: D 244 MET cc_start: 0.7061 (tpp) cc_final: 0.6607 (ttm) REVERT: D 308 PHE cc_start: 0.7213 (p90) cc_final: 0.6939 (p90) outliers start: 53 outliers final: 43 residues processed: 207 average time/residue: 0.2455 time to fit residues: 75.9039 Evaluate side-chains 208 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 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 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 82 ILE Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 THR 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 36 LEU 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 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 261 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 174 optimal weight: 0.4980 chunk 165 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN B 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129518 restraints weight = 16929.947| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.86 r_work: 0.3243 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13679 Z= 0.123 Angle : 0.614 9.158 18648 Z= 0.303 Chirality : 0.043 0.170 2221 Planarity : 0.005 0.063 2394 Dihedral : 4.702 53.594 1933 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.90 % Favored : 93.04 % Rotamer: Outliers : 3.93 % Allowed : 20.77 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.20), residues: 1753 helix: 0.30 (0.19), residues: 837 sheet: -2.09 (0.35), residues: 170 loop : -2.72 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 207 HIS 0.003 0.001 HIS C 94 PHE 0.013 0.001 PHE C 27 TYR 0.016 0.001 TYR E 424 ARG 0.007 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 590) hydrogen bonds : angle 4.51707 ( 1683) glycosidic custom : bond 0.00171 ( 1) glycosidic custom : angle 1.01642 ( 3) covalent geometry : bond 0.00282 (13678) covalent geometry : angle 0.61366 (18645) *********************** 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 237 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 182 time to evaluate : 1.633 Fit side-chains revert: symmetry clash REVERT: E 410 GLN cc_start: 0.8194 (pt0) cc_final: 0.7537 (tm-30) REVERT: C 161 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7231 (mp) REVERT: C 216 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7698 (pm20) REVERT: C 316 GLU cc_start: 0.7868 (pm20) cc_final: 0.7322 (pm20) REVERT: D 158 LYS cc_start: 0.7861 (mmtt) cc_final: 0.6366 (mtpt) REVERT: D 187 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7135 (mtm180) REVERT: D 212 MET cc_start: 0.8481 (mtp) cc_final: 0.8159 (mtt) REVERT: D 244 MET cc_start: 0.7035 (tpp) cc_final: 0.6567 (ttm) REVERT: D 304 ARG cc_start: 0.6384 (tmt170) cc_final: 0.6000 (ptt180) REVERT: A 237 ILE cc_start: 0.7234 (pt) cc_final: 0.6962 (pt) outliers start: 55 outliers final: 43 residues processed: 220 average time/residue: 0.3032 time to fit residues: 98.7578 Evaluate side-chains 216 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU 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 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 40 VAL 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 193 VAL 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 82 ILE Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 THR 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 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 157 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 79 optimal weight: 0.0040 chunk 163 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 chunk 165 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3974 r_free = 0.3974 target = 0.171297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131151 restraints weight = 16978.350| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.86 r_work: 0.3256 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2383 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= 0.114 Angle : 0.600 8.813 18648 Z= 0.296 Chirality : 0.043 0.160 2221 Planarity : 0.005 0.061 2394 Dihedral : 4.566 52.646 1933 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.56 % Favored : 93.38 % Rotamer: Outliers : 3.14 % Allowed : 21.98 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.20), residues: 1753 helix: 0.43 (0.19), residues: 840 sheet: -1.93 (0.37), residues: 168 loop : -2.52 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 26 HIS 0.003 0.001 HIS C 94 PHE 0.016 0.001 PHE D 308 TYR 0.017 0.001 TYR E 424 ARG 0.006 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 590) hydrogen bonds : angle 4.41286 ( 1683) glycosidic custom : bond 0.00261 ( 1) glycosidic custom : angle 1.04914 ( 3) covalent geometry : bond 0.00254 (13678) covalent geometry : angle 0.59989 (18645) *********************** 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 229 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: E 410 GLN cc_start: 0.8115 (pt0) cc_final: 0.7431 (tm-30) REVERT: C 134 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7744 (mtm-85) REVERT: C 216 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7653 (pm20) REVERT: C 316 GLU cc_start: 0.7887 (pm20) cc_final: 0.7361 (pm20) REVERT: D 124 LYS cc_start: 0.8267 (ttmm) cc_final: 0.7870 (pttt) REVERT: D 158 LYS cc_start: 0.7778 (mmtt) cc_final: 0.6303 (mtpt) REVERT: D 187 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7146 (mtm180) REVERT: D 212 MET cc_start: 0.8506 (mtp) cc_final: 0.8179 (mtt) REVERT: D 244 MET cc_start: 0.7035 (tpp) cc_final: 0.6590 (ttm) REVERT: D 292 GLU cc_start: 0.7305 (tt0) cc_final: 0.7076 (tt0) REVERT: D 304 ARG cc_start: 0.6549 (tmt170) cc_final: 0.6307 (ptt180) REVERT: A 237 ILE cc_start: 0.7051 (pt) cc_final: 0.6792 (pt) outliers start: 44 outliers final: 38 residues processed: 213 average time/residue: 0.2477 time to fit residues: 77.1932 Evaluate side-chains 216 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 93 LEU 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 40 VAL 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 264 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 379 ILE 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 105 LEU 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 64 optimal weight: 0.0970 chunk 92 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 73 optimal weight: 40.0000 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.166846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125688 restraints weight = 16921.257| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.88 r_work: 0.3194 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13679 Z= 0.185 Angle : 0.661 9.052 18648 Z= 0.326 Chirality : 0.045 0.163 2221 Planarity : 0.005 0.062 2394 Dihedral : 4.835 53.833 1933 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 3.14 % Allowed : 21.98 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.20), residues: 1753 helix: 0.26 (0.18), residues: 849 sheet: -1.93 (0.36), residues: 175 loop : -2.55 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 207 HIS 0.002 0.001 HIS C 94 PHE 0.025 0.002 PHE C 27 TYR 0.017 0.002 TYR C 227 ARG 0.007 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 590) hydrogen bonds : angle 4.53617 ( 1683) glycosidic custom : bond 0.00159 ( 1) glycosidic custom : angle 1.04096 ( 3) covalent geometry : bond 0.00453 (13678) covalent geometry : angle 0.66074 (18645) *********************** 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 224 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: E 410 GLN cc_start: 0.8172 (pt0) cc_final: 0.7588 (tm-30) REVERT: C 316 GLU cc_start: 0.8031 (pm20) cc_final: 0.7486 (pm20) REVERT: D 124 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7848 (pttt) REVERT: D 158 LYS cc_start: 0.7961 (mmtt) cc_final: 0.6555 (mtpt) REVERT: D 187 ARG cc_start: 0.7863 (ttm170) cc_final: 0.7051 (mtm180) REVERT: D 212 MET cc_start: 0.8551 (mtp) cc_final: 0.8229 (mtt) REVERT: D 244 MET cc_start: 0.7229 (tpp) cc_final: 0.6710 (ttm) REVERT: D 304 ARG cc_start: 0.6634 (tmt170) cc_final: 0.6300 (ptt180) REVERT: B 250 MET cc_start: 0.8231 (mmt) cc_final: 0.7923 (tpp) outliers start: 44 outliers final: 43 residues processed: 209 average time/residue: 0.2505 time to fit residues: 78.2228 Evaluate side-chains 218 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 149 THR 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 40 VAL 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 193 VAL 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 173 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 THR 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 264 THR Chi-restraints excluded: chain D residue 289 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.170125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129414 restraints weight = 16882.778| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.92 r_work: 0.3237 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2418 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 : 0.620 9.506 18648 Z= 0.305 Chirality : 0.043 0.157 2221 Planarity : 0.005 0.061 2394 Dihedral : 4.658 53.298 1933 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 2.86 % Allowed : 22.56 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.20), residues: 1753 helix: 0.42 (0.19), residues: 846 sheet: -1.74 (0.37), residues: 168 loop : -2.41 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 207 HIS 0.003 0.000 HIS C 94 PHE 0.018 0.001 PHE C 27 TYR 0.025 0.001 TYR C 227 ARG 0.007 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 590) hydrogen bonds : angle 4.42781 ( 1683) glycosidic custom : bond 0.00193 ( 1) glycosidic custom : angle 1.03281 ( 3) covalent geometry : bond 0.00276 (13678) covalent geometry : angle 0.62032 (18645) ********************** 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 221 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 410 GLN cc_start: 0.8154 (pt0) cc_final: 0.7548 (tm-30) REVERT: C 216 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7546 (pm20) REVERT: C 316 GLU cc_start: 0.8022 (pm20) cc_final: 0.7503 (pm20) REVERT: D 124 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7803 (pttt) REVERT: D 158 LYS cc_start: 0.7884 (mmtt) cc_final: 0.6491 (mtpt) REVERT: D 187 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7062 (mtm180) REVERT: D 212 MET cc_start: 0.8553 (mtp) cc_final: 0.8241 (mtt) REVERT: D 244 MET cc_start: 0.7181 (tpp) cc_final: 0.6681 (ttm) REVERT: D 304 ARG cc_start: 0.6733 (tmt170) cc_final: 0.6492 (ptt180) REVERT: A 201 GLN cc_start: 0.7739 (tt0) cc_final: 0.7444 (tt0) REVERT: B 250 MET cc_start: 0.8131 (mmt) cc_final: 0.7909 (tpp) outliers start: 40 outliers final: 38 residues processed: 209 average time/residue: 0.2428 time to fit residues: 75.8238 Evaluate side-chains 214 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 149 THR 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 193 VAL 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 190 THR 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 100 optimal weight: 0.2980 chunk 9 optimal weight: 0.4980 chunk 170 optimal weight: 0.0670 chunk 164 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 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 = 0.170373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130168 restraints weight = 16883.534| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.64 r_work: 0.3259 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 13679 Z= 0.155 Angle : 0.835 59.190 18648 Z= 0.466 Chirality : 0.043 0.213 2221 Planarity : 0.005 0.062 2394 Dihedral : 4.669 53.301 1933 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 2.86 % Allowed : 22.27 % Favored : 74.88 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.20), residues: 1753 helix: 0.42 (0.19), residues: 846 sheet: -1.72 (0.37), residues: 168 loop : -2.40 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 207 HIS 0.003 0.001 HIS C 94 PHE 0.018 0.001 PHE C 27 TYR 0.022 0.001 TYR C 227 ARG 0.006 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 590) hydrogen bonds : angle 4.42707 ( 1683) glycosidic custom : bond 0.00093 ( 1) glycosidic custom : angle 1.03449 ( 3) covalent geometry : bond 0.00322 (13678) covalent geometry : angle 0.83500 (18645) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6631.06 seconds wall clock time: 117 minutes 56.66 seconds (7076.66 seconds total)