Starting phenix.real_space_refine on Sun Sep 13 08:20:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wsl_21893/09_2026/6wsl_21893.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wsl_21893/09_2026/6wsl_21893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wsl_21893/09_2026/6wsl_21893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wsl_21893/09_2026/6wsl_21893.map" model { file = "/net/cci-nas-00/data/ceres_data/6wsl_21893/09_2026/6wsl_21893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wsl_21893/09_2026/6wsl_21893.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wsl_21893/09_2026/6wsl_21893.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wsl_21893/09_2026/6wsl_21893.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4516 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 116 5.16 5 C 11490 2.51 5 N 3144 2.21 5 O 3442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18204 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3378 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain breaks: 1 Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3370 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Chain: "C" Number of atoms: 2026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2026 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 230} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 264 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3378 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain breaks: 1 Chain: "F" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3370 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Chain: "G" Number of atoms: 2026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2026 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 230} Chain: "H" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 264 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.24 Number of scatterers: 18204 At special positions: 0 Unit cell: (136.95, 146.91, 120.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 12 15.00 O 3442 8.00 N 3144 7.00 C 11490 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 917.7 milliseconds 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4244 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 16 sheets defined 41.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.779A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.764A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.679A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.484A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 removed outlier: 3.629A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.948A pdb=" N TYR A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 removed outlier: 4.013A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.844A pdb=" N ALA A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 386 removed outlier: 3.548A pdb=" N GLU A 386 " --> pdb=" O ALA A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 383 through 386' Processing helix chain 'A' and resid 387 through 400 removed outlier: 4.143A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.570A pdb=" N GLY A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.715A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 20 through 28 Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.622A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.660A pdb=" N VAL B 76 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 108 through 111 Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.594A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.962A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 removed outlier: 4.291A pdb=" N THR B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.161A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.607A pdb=" N TYR B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 212 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 235 removed outlier: 4.028A pdb=" N SER B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 257 Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.603A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 4.074A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 392 removed outlier: 3.518A pdb=" N ARG B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 405 through 423 removed outlier: 4.230A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 413 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.925A pdb=" N VAL C 81 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.644A pdb=" N GLN C 93 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 130 removed outlier: 3.555A pdb=" N GLU C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 150 through 155 Processing helix chain 'C' and resid 157 through 162 removed outlier: 3.874A pdb=" N THR C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 162' Processing helix chain 'C' and resid 168 through 179 removed outlier: 3.624A pdb=" N ALA C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 173 " --> pdb=" O CYS C 169 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.846A pdb=" N LEU C 226 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 250 removed outlier: 3.733A pdb=" N PHE C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 292 through 305 removed outlier: 4.292A pdb=" N ARG C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 305 " --> pdb=" O MET C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 35 Processing helix chain 'D' and resid 35 through 51 removed outlier: 3.562A pdb=" N ILE D 39 " --> pdb=" O GLN D 35 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 27 removed outlier: 3.505A pdb=" N VAL E 14 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN E 15 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS E 25 " --> pdb=" O TRP E 21 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 removed outlier: 3.794A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 110 through 124 removed outlier: 3.587A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.793A pdb=" N GLY E 146 " --> pdb=" O GLY E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.552A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP E 160 " --> pdb=" O ARG E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 195 removed outlier: 3.790A pdb=" N ILE E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU E 189 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 239 removed outlier: 3.616A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL E 235 " --> pdb=" O ILE E 231 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR E 239 " --> pdb=" O VAL E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 287 through 294 Processing helix chain 'E' and resid 295 through 297 No H-bonds generated for 'chain 'E' and resid 295 through 297' Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.634A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 387 removed outlier: 4.011A pdb=" N ILE E 384 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA E 385 " --> pdb=" O THR E 382 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 386 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 400 removed outlier: 4.535A pdb=" N LYS E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 3.664A pdb=" N GLY E 410 " --> pdb=" O HIS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 417 through 435 removed outlier: 3.815A pdb=" N GLU E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 Processing helix chain 'F' and resid 20 through 28 removed outlier: 3.500A pdb=" N ASP F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 4.189A pdb=" N LEU F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 78 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 109 through 126 removed outlier: 4.625A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 159 removed outlier: 3.532A pdb=" N LEU F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 158 " --> pdb=" O LYS F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 189 removed outlier: 4.304A pdb=" N THR F 186 " --> pdb=" O PRO F 182 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE F 189 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 194 removed outlier: 4.228A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 211 removed outlier: 3.608A pdb=" N TYR F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS F 211 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 235 removed outlier: 3.542A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER F 230 " --> pdb=" O ASN F 226 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 Processing helix chain 'F' and resid 289 through 294 Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 337 removed outlier: 3.799A pdb=" N GLN F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN F 337 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 392 removed outlier: 3.548A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG F 380 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG F 390 " --> pdb=" O THR F 386 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 405 through 423 removed outlier: 4.282A pdb=" N THR F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.656A pdb=" N VAL G 81 " --> pdb=" O MET G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 removed outlier: 3.607A pdb=" N GLN G 93 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 130 removed outlier: 3.558A pdb=" N GLU G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 133 No H-bonds generated for 'chain 'G' and resid 131 through 133' Processing helix chain 'G' and resid 149 through 162 removed outlier: 3.771A pdb=" N LEU G 156 " --> pdb=" O GLY G 152 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS G 162 " --> pdb=" O LYS G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 179 removed outlier: 3.609A pdb=" N ALA G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 227 removed outlier: 3.776A pdb=" N LEU G 226 " --> pdb=" O ARG G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 249 removed outlier: 3.633A pdb=" N LEU G 239 " --> pdb=" O THR G 235 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE G 243 " --> pdb=" O LEU G 239 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY G 248 " --> pdb=" O GLU G 244 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG G 249 " --> pdb=" O ALA G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 305 removed outlier: 3.769A pdb=" N LEU G 294 " --> pdb=" O PHE G 290 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU G 295 " --> pdb=" O ARG G 291 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG G 302 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE G 305 " --> pdb=" O MET G 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 35 Processing helix chain 'H' and resid 36 through 51 removed outlier: 3.546A pdb=" N ARG H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN H 51 " --> pdb=" O THR H 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 8.987A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.667A pdb=" N VAL A 62 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.528A pdb=" N SER A 379 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 320 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.736A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N ILE B 163 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'C' and resid 214 through 218 removed outlier: 3.574A pdb=" N GLY C 216 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 259 " --> pdb=" O PRO C 190 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER C 192 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL C 257 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS C 194 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 6 through 8 removed outlier: 7.102A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'E' and resid 134 through 137 removed outlier: 6.134A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 272 through 273 Processing sheet with id=AB3, first strand: chain 'E' and resid 316 through 317 removed outlier: 3.592A pdb=" N LEU E 317 " --> pdb=" O LYS E 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 90 through 92 removed outlier: 7.749A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N ILE F 163 " --> pdb=" O CYS F 129 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'F' and resid 267 through 271 removed outlier: 3.612A pdb=" N THR F 312 " --> pdb=" O ASN F 370 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 214 through 218 removed outlier: 3.776A pdb=" N GLY G 216 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU G 259 " --> pdb=" O PRO G 190 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER G 192 " --> pdb=" O VAL G 257 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL G 257 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS G 194 " --> pdb=" O LYS G 255 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3096 1.32 - 1.46: 7168 1.46 - 1.60: 8158 1.60 - 1.74: 12 1.74 - 1.89: 192 Bond restraints: 18626 Sorted by residual: bond pdb=" C2' G2P F 501 " pdb=" C3' G2P F 501 " ideal model delta sigma weight residual 1.528 1.232 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C2' G2P B 501 " pdb=" C3' G2P B 501 " ideal model delta sigma weight residual 1.528 1.232 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C4' G2P B 501 " pdb=" C5' G2P B 501 " ideal model delta sigma weight residual 1.518 1.388 0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C4' G2P F 501 " pdb=" C5' G2P F 501 " ideal model delta sigma weight residual 1.518 1.389 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C1' G2P F 501 " pdb=" C2' G2P F 501 " ideal model delta sigma weight residual 1.537 1.656 -0.119 2.00e-02 2.50e+03 3.52e+01 ... (remaining 18621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 25111 3.73 - 7.47: 115 7.47 - 11.20: 26 11.20 - 14.94: 2 14.94 - 18.67: 4 Bond angle restraints: 25258 Sorted by residual: angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C4 G2P B 501 " ideal model delta sigma weight residual 125.17 106.50 18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C1' G2P F 501 " pdb=" N9 G2P F 501 " pdb=" C4 G2P F 501 " ideal model delta sigma weight residual 125.17 108.06 17.11 3.00e+00 1.11e-01 3.25e+01 angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C8 G2P B 501 " ideal model delta sigma weight residual 127.92 144.90 -16.98 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C1' G2P F 501 " pdb=" N9 G2P F 501 " pdb=" C8 G2P F 501 " ideal model delta sigma weight residual 127.92 143.41 -15.49 3.00e+00 1.11e-01 2.67e+01 angle pdb=" C PRO G 117 " pdb=" N VAL G 118 " pdb=" CA VAL G 118 " ideal model delta sigma weight residual 120.33 124.36 -4.03 8.00e-01 1.56e+00 2.54e+01 ... (remaining 25253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.48: 10653 29.48 - 58.95: 450 58.95 - 88.43: 21 88.43 - 117.91: 2 117.91 - 147.39: 4 Dihedral angle restraints: 11130 sinusoidal: 4532 harmonic: 6598 Sorted by residual: dihedral pdb=" CA VAL B 286 " pdb=" C VAL B 286 " pdb=" N PRO B 287 " pdb=" CA PRO B 287 " ideal model delta harmonic sigma weight residual 180.00 139.75 40.25 0 5.00e+00 4.00e-02 6.48e+01 dihedral pdb=" CA VAL F 286 " pdb=" C VAL F 286 " pdb=" N PRO F 287 " pdb=" CA PRO F 287 " ideal model delta harmonic sigma weight residual 180.00 141.81 38.19 0 5.00e+00 4.00e-02 5.83e+01 dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -42.79 147.39 1 2.00e+01 2.50e-03 4.42e+01 ... (remaining 11127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2157 0.059 - 0.118: 532 0.118 - 0.177: 51 0.177 - 0.235: 4 0.235 - 0.294: 2 Chirality restraints: 2746 Sorted by residual: chirality pdb=" C3' G2P F 501 " pdb=" C2' G2P F 501 " pdb=" C4' G2P F 501 " pdb=" O3' G2P F 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" C4' G2P B 501 " pdb=" O3' G2P B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE A 114 " pdb=" CA ILE A 114 " pdb=" CG1 ILE A 114 " pdb=" CG2 ILE A 114 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2743 not shown) Planarity restraints: 3278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 286 " -0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO B 287 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 286 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.80e+00 pdb=" N PRO F 287 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 287 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 287 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 165 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO G 166 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO G 166 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 166 " -0.033 5.00e-02 4.00e+02 ... (remaining 3275 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5189 2.79 - 3.32: 15573 3.32 - 3.85: 30574 3.85 - 4.37: 35230 4.37 - 4.90: 59497 Nonbonded interactions: 146063 Sorted by model distance: nonbonded pdb=" OG SER B 278 " pdb=" OE1 GLN B 279 " model vdw 2.264 3.040 nonbonded pdb=" O SER B 382 " pdb=" OG1 THR B 386 " model vdw 2.283 3.040 nonbonded pdb=" OG SER G 269 " pdb=" OE1 GLU G 271 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR E 292 " pdb=" OH TYR E 319 " model vdw 2.306 3.040 nonbonded pdb=" O2' G2P B 501 " pdb=" O3' G2P B 501 " model vdw 2.307 2.432 ... (remaining 146058 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.160 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.007 0.296 18629 Z= 0.345 Angle : 0.823 18.673 25258 Z= 0.424 Chirality : 0.049 0.294 2746 Planarity : 0.006 0.088 3278 Dihedral : 15.242 147.387 6886 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 8.98 % Allowed : 12.24 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.33 (0.13), residues: 2258 helix: -4.51 (0.07), residues: 834 sheet: -3.27 (0.27), residues: 294 loop : -2.73 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 64 TYR 0.016 0.002 TYR B 310 PHE 0.018 0.002 PHE E 255 TRP 0.013 0.002 TRP C 275 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.34 (18626) covalent geometry : angle 0.82301 / 0.42 (25258) hydrogen bonds : bond 0.28860 / 19.00 ( 509) hydrogen bonds : angle 10.53333 / 7.38 ( 1446) Misc. bond : bond 0.00410 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 461 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9262 (mm) REVERT: A 90 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6827 (tp30) REVERT: A 97 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7866 (tp30) REVERT: A 152 LEU cc_start: 0.8794 (tp) cc_final: 0.8488 (tp) REVERT: A 155 GLU cc_start: 0.8774 (tt0) cc_final: 0.8570 (tt0) REVERT: A 192 HIS cc_start: 0.8092 (t-90) cc_final: 0.7696 (t-90) REVERT: A 258 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8683 (t0) REVERT: A 316 CYS cc_start: 0.8138 (t) cc_final: 0.7705 (t) REVERT: A 326 LYS cc_start: 0.8419 (tptp) cc_final: 0.8018 (mttt) REVERT: A 392 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7924 (t0) REVERT: A 396 ASP cc_start: 0.8783 (t70) cc_final: 0.8458 (t0) REVERT: A 432 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8281 (t80) REVERT: B 31 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8355 (t70) REVERT: B 68 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8502 (mt) REVERT: B 147 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8202 (tpp) REVERT: B 166 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 179 VAL cc_start: 0.9269 (t) cc_final: 0.9041 (p) REVERT: B 190 HIS cc_start: 0.8257 (t-90) cc_final: 0.8012 (t70) REVERT: B 280 GLN cc_start: 0.7704 (pt0) cc_final: 0.7339 (pm20) REVERT: B 363 MET cc_start: 0.7474 (mmt) cc_final: 0.6973 (mmt) REVERT: B 377 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9067 (tm) REVERT: C 145 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8059 (mmtt) REVERT: C 160 MET cc_start: 0.8096 (mmt) cc_final: 0.7701 (mmm) REVERT: C 180 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.7529 (p) REVERT: C 183 MET cc_start: 0.7814 (mtm) cc_final: 0.7537 (mpp) REVERT: C 187 GLU cc_start: 0.7559 (tt0) cc_final: 0.7346 (mp0) REVERT: C 215 TYR cc_start: 0.5042 (m-80) cc_final: 0.3637 (m-10) REVERT: C 275 TRP cc_start: 0.6973 (OUTLIER) cc_final: 0.5900 (m100) REVERT: C 291 ARG cc_start: 0.7223 (mtp-110) cc_final: 0.6576 (mtt90) REVERT: C 295 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5666 (tm-30) REVERT: C 296 ARG cc_start: 0.8449 (mmm160) cc_final: 0.8204 (tmm-80) REVERT: C 297 HIS cc_start: 0.5962 (t70) cc_final: 0.5548 (t70) REVERT: E 60 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8489 (tttm) REVERT: E 90 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7096 (mm-30) REVERT: E 171 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8202 (mp) REVERT: E 192 HIS cc_start: 0.8173 (t-90) cc_final: 0.7971 (t-90) REVERT: E 216 ASN cc_start: 0.9032 (m-40) cc_final: 0.8621 (m-40) REVERT: E 255 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8206 (t80) REVERT: E 316 CYS cc_start: 0.8053 (t) cc_final: 0.7068 (t) REVERT: E 411 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8099 (mm-30) REVERT: F 3 GLU cc_start: 0.5981 (mm-30) cc_final: 0.5689 (mm-30) REVERT: F 19 LYS cc_start: 0.8522 (tppt) cc_final: 0.8204 (tptm) REVERT: F 108 GLU cc_start: 0.8686 (tp30) cc_final: 0.8429 (tp30) REVERT: F 121 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8394 (mtm-85) REVERT: F 127 CYS cc_start: 0.6774 (m) cc_final: 0.5912 (m) REVERT: F 131 GLN cc_start: 0.8500 (tp40) cc_final: 0.7969 (tp40) REVERT: F 164 MET cc_start: 0.8509 (tpp) cc_final: 0.7877 (tpp) REVERT: F 166 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8514 (p) REVERT: F 190 HIS cc_start: 0.8234 (t-90) cc_final: 0.6657 (t70) REVERT: F 198 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7788 (pt0) REVERT: F 200 TYR cc_start: 0.8791 (m-80) cc_final: 0.8285 (m-80) REVERT: F 202 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8551 (mp) REVERT: F 213 ARG cc_start: 0.8354 (ttm110) cc_final: 0.8078 (mtm-85) REVERT: F 364 SER cc_start: 0.8735 (p) cc_final: 0.8533 (m) REVERT: G 145 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8051 (mmtm) REVERT: G 160 MET cc_start: 0.7979 (mmt) cc_final: 0.7741 (mmm) REVERT: G 180 THR cc_start: 0.8592 (p) cc_final: 0.7766 (p) REVERT: G 183 MET cc_start: 0.7704 (mtm) cc_final: 0.7465 (mpp) REVERT: G 202 PHE cc_start: 0.4974 (m-80) cc_final: 0.4647 (t80) REVERT: G 214 ARG cc_start: 0.7622 (mmt-90) cc_final: 0.7380 (mmp80) REVERT: G 215 TYR cc_start: 0.4647 (m-80) cc_final: 0.4194 (m-10) REVERT: G 234 ARG cc_start: 0.7696 (tpt90) cc_final: 0.7457 (mmm160) REVERT: G 249 ARG cc_start: 0.7633 (mtt180) cc_final: 0.7055 (ptp-170) REVERT: G 301 MET cc_start: 0.7315 (mtm) cc_final: 0.6947 (mmm) REVERT: H 44 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7960 (tpm170) outliers start: 176 outliers final: 66 residues processed: 591 average time/residue: 0.1548 time to fit residues: 134.2738 Evaluate side-chains 391 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 306 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 247 ASN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.1980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 50.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 15 GLN A 28 HIS A 88 HIS ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 186 ASN A 197 HIS A 266 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 94 GLN B 165 ASN B 190 HIS B 191 GLN B 195 ASN B 292 GLN B 334 GLN C 80 HIS ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 204 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN E 186 ASN E 197 HIS E 249 ASN E 256 GLN E 309 HIS E 329 ASN F 94 GLN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN F 292 GLN F 334 GLN F 370 ASN G 80 HIS G 277 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.131592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.089548 restraints weight = 33813.257| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.25 r_work: 0.3436 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18629 Z= 0.128 Angle : 0.611 9.024 25258 Z= 0.313 Chirality : 0.043 0.191 2746 Planarity : 0.005 0.070 3278 Dihedral : 10.621 146.453 2668 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.74 % Allowed : 17.24 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.15), residues: 2258 helix: -3.06 (0.12), residues: 864 sheet: -3.04 (0.27), residues: 312 loop : -2.25 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 262 TYR 0.019 0.001 TYR A 357 PHE 0.015 0.001 PHE A 255 TRP 0.014 0.002 TRP G 74 HIS 0.009 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (18626) covalent geometry : angle 0.61087 / 0.31 (25258) hydrogen bonds : bond 0.04072 / 2.67 ( 509) hydrogen bonds : angle 5.77530 / 4.04 ( 1446) Misc. bond : bond 0.00171 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 364 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 155 GLU cc_start: 0.9264 (tt0) cc_final: 0.8992 (tt0) REVERT: A 210 TYR cc_start: 0.8671 (m-80) cc_final: 0.8444 (m-80) REVERT: A 258 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8648 (t0) REVERT: A 326 LYS cc_start: 0.8515 (tptp) cc_final: 0.7919 (mttp) REVERT: A 396 ASP cc_start: 0.9211 (t70) cc_final: 0.8855 (t0) REVERT: A 432 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8180 (t80) REVERT: B 3 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: B 12 CYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7916 (t) REVERT: B 31 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8102 (t70) REVERT: B 166 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8459 (p) REVERT: B 191 GLN cc_start: 0.8669 (tp40) cc_final: 0.8421 (tp-100) REVERT: B 211 CYS cc_start: 0.9163 (m) cc_final: 0.8900 (m) REVERT: B 279 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8271 (mp10) REVERT: B 280 GLN cc_start: 0.8096 (pt0) cc_final: 0.7578 (pm20) REVERT: B 363 MET cc_start: 0.7926 (mmt) cc_final: 0.7544 (mmt) REVERT: B 405 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 412 GLU cc_start: 0.8656 (tp30) cc_final: 0.8282 (tp30) REVERT: C 123 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8043 (tm-30) REVERT: C 160 MET cc_start: 0.7973 (mmt) cc_final: 0.7644 (mmm) REVERT: C 180 THR cc_start: 0.8178 (p) cc_final: 0.6962 (t) REVERT: C 183 MET cc_start: 0.7776 (mtm) cc_final: 0.7299 (mpp) REVERT: C 186 LEU cc_start: 0.7217 (tp) cc_final: 0.6924 (tp) REVERT: C 275 TRP cc_start: 0.6704 (OUTLIER) cc_final: 0.5600 (m100) REVERT: E 216 ASN cc_start: 0.9257 (m-40) cc_final: 0.8946 (m-40) REVERT: E 255 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.7766 (t80) REVERT: E 271 THR cc_start: 0.8924 (m) cc_final: 0.8660 (m) REVERT: E 316 CYS cc_start: 0.8658 (t) cc_final: 0.7738 (t) REVERT: E 377 MET cc_start: 0.8654 (ppp) cc_final: 0.8359 (ppp) REVERT: E 411 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8428 (mm-30) REVERT: E 413 MET cc_start: 0.8574 (ttm) cc_final: 0.8374 (ttm) REVERT: F 3 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6327 (mp0) REVERT: F 19 LYS cc_start: 0.8716 (tppt) cc_final: 0.8264 (tptp) REVERT: F 125 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8324 (mm-30) REVERT: F 164 MET cc_start: 0.8663 (tpp) cc_final: 0.8156 (tpp) REVERT: F 166 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8747 (p) REVERT: F 190 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.7835 (t70) REVERT: F 191 GLN cc_start: 0.8368 (mm110) cc_final: 0.7910 (mm110) REVERT: F 198 GLU cc_start: 0.8589 (pt0) cc_final: 0.8296 (pt0) REVERT: F 202 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8558 (mp) REVERT: F 280 GLN cc_start: 0.8557 (pt0) cc_final: 0.8131 (pm20) REVERT: F 362 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9063 (ttpp) REVERT: G 145 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7781 (mttm) REVERT: G 180 THR cc_start: 0.8340 (p) cc_final: 0.7637 (p) REVERT: G 183 MET cc_start: 0.7707 (mtm) cc_final: 0.7498 (mpp) REVERT: G 202 PHE cc_start: 0.4788 (m-80) cc_final: 0.4406 (t80) REVERT: G 234 ARG cc_start: 0.7648 (tpt90) cc_final: 0.7398 (mmm160) REVERT: G 249 ARG cc_start: 0.7719 (mtt180) cc_final: 0.7385 (ptp90) REVERT: H 44 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7952 (tpm170) outliers start: 93 outliers final: 52 residues processed: 431 average time/residue: 0.1263 time to fit residues: 84.2175 Evaluate side-chains 351 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 286 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 390 ARG Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 115 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 169 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 202 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN B 131 GLN B 137 HIS ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS E 329 ASN F 137 HIS ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.132408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.090175 restraints weight = 33917.139| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.30 r_work: 0.3425 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18629 Z= 0.174 Angle : 0.592 8.230 25258 Z= 0.302 Chirality : 0.044 0.196 2746 Planarity : 0.005 0.099 3278 Dihedral : 9.866 146.670 2594 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.82 % Allowed : 18.32 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.16), residues: 2258 helix: -2.15 (0.15), residues: 882 sheet: -2.89 (0.27), residues: 312 loop : -1.98 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 291 TYR 0.019 0.001 TYR A 357 PHE 0.016 0.001 PHE A 255 TRP 0.014 0.002 TRP G 74 HIS 0.010 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (18626) covalent geometry : angle 0.59152 / 0.30 (25258) hydrogen bonds : bond 0.03633 / 2.38 ( 509) hydrogen bonds : angle 5.25687 / 3.67 ( 1446) Misc. bond : bond 0.00217 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 308 time to evaluate : 0.697 Fit side-chains REVERT: A 90 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 114 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8689 (tp) REVERT: A 155 GLU cc_start: 0.9288 (tt0) cc_final: 0.9040 (tt0) REVERT: A 203 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8046 (mtm) REVERT: A 396 ASP cc_start: 0.9284 (t70) cc_final: 0.9022 (t0) REVERT: A 432 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8216 (t80) REVERT: B 22 GLU cc_start: 0.8421 (tt0) cc_final: 0.8127 (tm-30) REVERT: B 31 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8684 (t70) REVERT: B 50 TYR cc_start: 0.8851 (m-80) cc_final: 0.8273 (m-10) REVERT: B 166 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8507 (p) REVERT: B 211 CYS cc_start: 0.9198 (m) cc_final: 0.8911 (m) REVERT: B 279 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8291 (mp10) REVERT: B 280 GLN cc_start: 0.8178 (pt0) cc_final: 0.7638 (pm20) REVERT: B 363 MET cc_start: 0.7907 (mmt) cc_final: 0.7629 (mmt) REVERT: B 405 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 412 GLU cc_start: 0.8738 (tp30) cc_final: 0.8385 (tp30) REVERT: C 123 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8052 (tm-30) REVERT: C 160 MET cc_start: 0.7899 (mmt) cc_final: 0.7617 (mmm) REVERT: C 180 THR cc_start: 0.8042 (p) cc_final: 0.7266 (p) REVERT: C 183 MET cc_start: 0.7751 (mtm) cc_final: 0.7356 (mpp) REVERT: C 275 TRP cc_start: 0.6657 (OUTLIER) cc_final: 0.5591 (m100) REVERT: E 90 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7909 (mm-30) REVERT: E 216 ASN cc_start: 0.9315 (m-40) cc_final: 0.9023 (m-40) REVERT: E 377 MET cc_start: 0.8810 (ppp) cc_final: 0.8410 (ppp) REVERT: E 411 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8555 (mm-30) REVERT: F 19 LYS cc_start: 0.8845 (tppt) cc_final: 0.8381 (tptm) REVERT: F 22 GLU cc_start: 0.8625 (tt0) cc_final: 0.8171 (tm-30) REVERT: F 125 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8381 (mm-30) REVERT: F 164 MET cc_start: 0.8719 (tpp) cc_final: 0.8150 (tpp) REVERT: F 166 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8823 (p) REVERT: F 198 GLU cc_start: 0.8622 (pt0) cc_final: 0.8208 (pt0) REVERT: F 202 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8665 (mp) REVERT: F 280 GLN cc_start: 0.8615 (pt0) cc_final: 0.8112 (pm20) REVERT: G 145 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7672 (mttm) REVERT: G 180 THR cc_start: 0.8152 (p) cc_final: 0.7416 (p) REVERT: G 183 MET cc_start: 0.7561 (mtm) cc_final: 0.7319 (mpp) REVERT: G 202 PHE cc_start: 0.4773 (m-80) cc_final: 0.4299 (t80) REVERT: G 228 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6644 (p90) REVERT: G 249 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7411 (ptp90) REVERT: G 296 ARG cc_start: 0.6414 (tmm160) cc_final: 0.5614 (tpt90) REVERT: H 44 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7913 (tpm170) outliers start: 114 outliers final: 63 residues processed: 386 average time/residue: 0.1329 time to fit residues: 79.1923 Evaluate side-chains 351 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 278 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 390 ARG Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 95 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 70 optimal weight: 0.0270 chunk 197 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 106 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 57 HIS F 195 ASN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.135037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.092794 restraints weight = 33686.677| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.31 r_work: 0.3494 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18629 Z= 0.101 Angle : 0.564 8.666 25258 Z= 0.280 Chirality : 0.043 0.280 2746 Planarity : 0.005 0.098 3278 Dihedral : 9.351 144.873 2585 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.74 % Allowed : 19.85 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.17), residues: 2258 helix: -1.41 (0.16), residues: 876 sheet: -2.71 (0.27), residues: 310 loop : -1.86 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 214 TYR 0.020 0.001 TYR A 24 PHE 0.015 0.001 PHE A 255 TRP 0.014 0.001 TRP B 344 HIS 0.007 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (18626) covalent geometry : angle 0.56354 / 0.28 (25258) hydrogen bonds : bond 0.03097 / 2.04 ( 509) hydrogen bonds : angle 4.79116 / 3.35 ( 1446) Misc. bond : bond 0.00144 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 327 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7622 (mm-30) REVERT: A 155 GLU cc_start: 0.9263 (tt0) cc_final: 0.9015 (tt0) REVERT: A 326 LYS cc_start: 0.8327 (tptp) cc_final: 0.7698 (mttt) REVERT: A 396 ASP cc_start: 0.9215 (t70) cc_final: 0.8959 (t0) REVERT: A 432 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8092 (t80) REVERT: B 12 CYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7895 (t) REVERT: B 19 LYS cc_start: 0.8772 (tppt) cc_final: 0.8166 (tptp) REVERT: B 22 GLU cc_start: 0.8317 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 31 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8629 (t70) REVERT: B 50 TYR cc_start: 0.8724 (m-80) cc_final: 0.8143 (m-10) REVERT: B 111 GLU cc_start: 0.7883 (mp0) cc_final: 0.7536 (mp0) REVERT: B 166 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8362 (p) REVERT: B 191 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8615 (tp-100) REVERT: B 211 CYS cc_start: 0.9179 (m) cc_final: 0.8895 (m) REVERT: B 279 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: B 280 GLN cc_start: 0.8095 (pt0) cc_final: 0.7648 (pm20) REVERT: B 405 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8143 (tm-30) REVERT: B 412 GLU cc_start: 0.8724 (tp30) cc_final: 0.8426 (tp30) REVERT: C 123 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7981 (tm-30) REVERT: C 160 MET cc_start: 0.7909 (mmt) cc_final: 0.7606 (mmm) REVERT: C 180 THR cc_start: 0.8137 (p) cc_final: 0.7335 (p) REVERT: C 183 MET cc_start: 0.7753 (mtm) cc_final: 0.7372 (mpp) REVERT: C 275 TRP cc_start: 0.6699 (OUTLIER) cc_final: 0.5579 (m100) REVERT: D 44 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7857 (tpm170) REVERT: E 90 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7860 (mm-30) REVERT: E 216 ASN cc_start: 0.9301 (m-40) cc_final: 0.9045 (m-40) REVERT: E 377 MET cc_start: 0.8603 (ppp) cc_final: 0.8307 (ppp) REVERT: E 432 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.7906 (t80) REVERT: F 12 CYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8131 (t) REVERT: F 19 LYS cc_start: 0.8865 (tppt) cc_final: 0.8375 (tptm) REVERT: F 22 GLU cc_start: 0.8535 (tt0) cc_final: 0.8087 (tm-30) REVERT: F 125 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8408 (mm-30) REVERT: F 164 MET cc_start: 0.8677 (tpp) cc_final: 0.8267 (tpp) REVERT: F 191 GLN cc_start: 0.8691 (tp40) cc_final: 0.8339 (tp-100) REVERT: F 198 GLU cc_start: 0.8617 (pt0) cc_final: 0.8359 (pt0) REVERT: F 202 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8597 (mp) REVERT: F 252 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8266 (mmtp) REVERT: F 280 GLN cc_start: 0.8595 (pt0) cc_final: 0.8133 (pm20) REVERT: G 74 TRP cc_start: 0.6959 (t-100) cc_final: 0.6759 (t-100) REVERT: G 123 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8299 (mm-30) REVERT: G 127 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8207 (mmp-170) REVERT: G 145 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7624 (mttm) REVERT: G 180 THR cc_start: 0.8245 (p) cc_final: 0.7496 (p) REVERT: G 183 MET cc_start: 0.7585 (mtm) cc_final: 0.7369 (mpp) REVERT: G 220 MET cc_start: 0.5188 (ptp) cc_final: 0.4981 (ptt) REVERT: G 249 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7405 (ptp90) REVERT: H 43 ASN cc_start: 0.6749 (OUTLIER) cc_final: 0.5960 (t0) outliers start: 93 outliers final: 56 residues processed: 391 average time/residue: 0.1310 time to fit residues: 79.2837 Evaluate side-chains 347 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 280 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 43 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 46 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN C 80 HIS ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN G 277 HIS G 297 HIS ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.131184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.088584 restraints weight = 34189.952| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.32 r_work: 0.3415 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 18629 Z= 0.219 Angle : 0.618 10.753 25258 Z= 0.309 Chirality : 0.045 0.251 2746 Planarity : 0.005 0.086 3278 Dihedral : 9.300 145.343 2573 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.20 % Allowed : 20.36 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.17), residues: 2258 helix: -1.09 (0.17), residues: 860 sheet: -2.72 (0.27), residues: 310 loop : -1.77 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 264 TYR 0.020 0.001 TYR A 357 PHE 0.016 0.001 PHE A 255 TRP 0.011 0.002 TRP A 21 HIS 0.009 0.001 HIS G 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (18626) covalent geometry : angle 0.61787 / 0.31 (25258) hydrogen bonds : bond 0.03346 / 2.20 ( 509) hydrogen bonds : angle 4.89136 / 3.44 ( 1446) Misc. bond : bond 0.00222 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 289 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9233 (mm) REVERT: A 90 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 114 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8674 (tp) REVERT: A 155 GLU cc_start: 0.9293 (tt0) cc_final: 0.9041 (tt0) REVERT: A 396 ASP cc_start: 0.9288 (t70) cc_final: 0.9039 (t0) REVERT: A 432 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8200 (t80) REVERT: B 22 GLU cc_start: 0.8452 (tt0) cc_final: 0.8234 (tm-30) REVERT: B 111 GLU cc_start: 0.8017 (mp0) cc_final: 0.7658 (mp0) REVERT: B 166 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8501 (p) REVERT: B 191 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8295 (tp-100) REVERT: B 200 TYR cc_start: 0.8987 (m-80) cc_final: 0.8751 (m-80) REVERT: B 211 CYS cc_start: 0.9208 (m) cc_final: 0.8930 (m) REVERT: B 267 MET cc_start: 0.9030 (ptp) cc_final: 0.8766 (ptm) REVERT: B 279 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8333 (mp10) REVERT: B 280 GLN cc_start: 0.8240 (pt0) cc_final: 0.7662 (pm20) REVERT: B 299 MET cc_start: 0.9142 (mmt) cc_final: 0.8599 (mmt) REVERT: B 412 GLU cc_start: 0.8774 (tp30) cc_final: 0.8480 (tp30) REVERT: C 123 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8072 (tm-30) REVERT: C 160 MET cc_start: 0.7920 (mmt) cc_final: 0.7600 (mmm) REVERT: C 180 THR cc_start: 0.8046 (p) cc_final: 0.7295 (p) REVERT: C 183 MET cc_start: 0.7746 (mtm) cc_final: 0.7321 (mpp) REVERT: C 275 TRP cc_start: 0.6755 (OUTLIER) cc_final: 0.5644 (m100) REVERT: D 44 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.7889 (tpm170) REVERT: E 216 ASN cc_start: 0.9350 (m-40) cc_final: 0.9062 (m-40) REVERT: E 255 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.7933 (t80) REVERT: E 377 MET cc_start: 0.8836 (ppp) cc_final: 0.8566 (ppp) REVERT: E 432 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.7857 (t80) REVERT: F 19 LYS cc_start: 0.8934 (tppt) cc_final: 0.8321 (tptp) REVERT: F 22 GLU cc_start: 0.8623 (tt0) cc_final: 0.8207 (tm-30) REVERT: F 125 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8413 (mm-30) REVERT: F 164 MET cc_start: 0.8776 (tpp) cc_final: 0.8302 (tpp) REVERT: F 191 GLN cc_start: 0.8731 (tp40) cc_final: 0.8378 (tp-100) REVERT: F 198 GLU cc_start: 0.8575 (pt0) cc_final: 0.8164 (pt0) REVERT: F 202 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8706 (mp) REVERT: F 252 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8688 (mmtp) REVERT: F 280 GLN cc_start: 0.8608 (pt0) cc_final: 0.8390 (pp30) REVERT: F 359 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7657 (mtm110) REVERT: G 127 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8208 (mmp-170) REVERT: G 145 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7611 (mttm) REVERT: G 180 THR cc_start: 0.8149 (p) cc_final: 0.7440 (p) REVERT: G 183 MET cc_start: 0.7551 (mtm) cc_final: 0.7302 (mpp) outliers start: 102 outliers final: 73 residues processed: 359 average time/residue: 0.1212 time to fit residues: 68.9590 Evaluate side-chains 353 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 270 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 247 ASN Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 13 optimal weight: 6.9990 chunk 102 optimal weight: 40.0000 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.130396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.087999 restraints weight = 33895.011| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.28 r_work: 0.3404 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18629 Z= 0.173 Angle : 0.589 9.200 25258 Z= 0.295 Chirality : 0.045 0.264 2746 Planarity : 0.004 0.084 3278 Dihedral : 9.133 145.202 2569 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.46 % Allowed : 19.74 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.17), residues: 2258 helix: -0.84 (0.18), residues: 868 sheet: -2.68 (0.27), residues: 310 loop : -1.72 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.015 0.001 TYR F 50 PHE 0.020 0.001 PHE A 52 TRP 0.010 0.001 TRP B 344 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (18626) covalent geometry : angle 0.58917 / 0.30 (25258) hydrogen bonds : bond 0.03141 / 2.08 ( 509) hydrogen bonds : angle 4.77976 / 3.35 ( 1446) Misc. bond : bond 0.00187 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 292 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7670 (mm-30) REVERT: A 114 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 155 GLU cc_start: 0.9266 (tt0) cc_final: 0.9009 (tt0) REVERT: A 396 ASP cc_start: 0.9262 (t70) cc_final: 0.9022 (t0) REVERT: A 425 MET cc_start: 0.9069 (tpt) cc_final: 0.8661 (tpt) REVERT: A 432 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8176 (t80) REVERT: B 12 CYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7994 (t) REVERT: B 19 LYS cc_start: 0.8856 (tppt) cc_final: 0.8388 (tptp) REVERT: B 50 TYR cc_start: 0.8855 (m-80) cc_final: 0.8394 (m-10) REVERT: B 147 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8372 (ttm) REVERT: B 166 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8503 (p) REVERT: B 191 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8287 (tp-100) REVERT: B 211 CYS cc_start: 0.9219 (m) cc_final: 0.8941 (m) REVERT: B 267 MET cc_start: 0.9045 (ptp) cc_final: 0.8720 (ptm) REVERT: B 279 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8330 (mp10) REVERT: B 299 MET cc_start: 0.9081 (mmt) cc_final: 0.8544 (mmt) REVERT: B 412 GLU cc_start: 0.8724 (tp30) cc_final: 0.8466 (tp30) REVERT: C 70 ASP cc_start: 0.4105 (p0) cc_final: 0.3845 (p0) REVERT: C 123 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8056 (tm-30) REVERT: C 160 MET cc_start: 0.7943 (mmt) cc_final: 0.7595 (mmm) REVERT: C 180 THR cc_start: 0.8138 (p) cc_final: 0.7326 (p) REVERT: C 183 MET cc_start: 0.7807 (mtm) cc_final: 0.7310 (mpp) REVERT: C 275 TRP cc_start: 0.6865 (OUTLIER) cc_final: 0.5829 (m100) REVERT: D 44 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7879 (tpm170) REVERT: E 90 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7945 (mm-30) REVERT: E 216 ASN cc_start: 0.9292 (m-40) cc_final: 0.9003 (m-40) REVERT: E 377 MET cc_start: 0.8787 (ppp) cc_final: 0.8501 (ppp) REVERT: E 396 ASP cc_start: 0.8815 (m-30) cc_final: 0.8451 (m-30) REVERT: E 432 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.7840 (t80) REVERT: F 19 LYS cc_start: 0.8907 (tppt) cc_final: 0.8334 (tptp) REVERT: F 22 GLU cc_start: 0.8574 (tt0) cc_final: 0.8214 (tm-30) REVERT: F 50 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8591 (m-10) REVERT: F 125 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8449 (mm-30) REVERT: F 191 GLN cc_start: 0.8611 (tp40) cc_final: 0.8187 (tp-100) REVERT: F 198 GLU cc_start: 0.8534 (pt0) cc_final: 0.8070 (pt0) REVERT: F 200 TYR cc_start: 0.9020 (m-80) cc_final: 0.8608 (m-80) REVERT: F 202 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8717 (mp) REVERT: F 252 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8657 (mmtp) REVERT: F 280 GLN cc_start: 0.8581 (pt0) cc_final: 0.8369 (pp30) REVERT: F 359 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7653 (mtm110) REVERT: G 145 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7712 (mttm) REVERT: G 180 THR cc_start: 0.8191 (p) cc_final: 0.7437 (p) REVERT: G 183 MET cc_start: 0.7603 (mtm) cc_final: 0.7315 (mpp) outliers start: 107 outliers final: 73 residues processed: 371 average time/residue: 0.1333 time to fit residues: 76.9087 Evaluate side-chains 362 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 278 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 36 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.132538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.090099 restraints weight = 33942.075| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.32 r_work: 0.3451 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18629 Z= 0.113 Angle : 0.581 11.220 25258 Z= 0.285 Chirality : 0.044 0.315 2746 Planarity : 0.004 0.077 3278 Dihedral : 8.884 144.422 2569 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.90 % Allowed : 20.56 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.18), residues: 2258 helix: -0.60 (0.18), residues: 866 sheet: -2.52 (0.28), residues: 310 loop : -1.63 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 291 TYR 0.021 0.001 TYR B 200 PHE 0.020 0.001 PHE A 255 TRP 0.019 0.001 TRP C 74 HIS 0.006 0.001 HIS F 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (18626) covalent geometry : angle 0.58054 / 0.28 (25258) hydrogen bonds : bond 0.02879 / 1.92 ( 509) hydrogen bonds : angle 4.58078 / 3.20 ( 1446) Misc. bond : bond 0.00140 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 312 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9278 (mm) REVERT: A 90 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7703 (mm-30) REVERT: A 114 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8681 (tp) REVERT: A 155 GLU cc_start: 0.9252 (tt0) cc_final: 0.8987 (tt0) REVERT: A 326 LYS cc_start: 0.8372 (tptp) cc_final: 0.7755 (mttt) REVERT: A 396 ASP cc_start: 0.9225 (t70) cc_final: 0.8986 (t0) REVERT: A 425 MET cc_start: 0.9065 (tpt) cc_final: 0.8630 (tpt) REVERT: A 432 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8127 (t80) REVERT: B 12 CYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7886 (t) REVERT: B 19 LYS cc_start: 0.8763 (tppt) cc_final: 0.8273 (mmmm) REVERT: B 50 TYR cc_start: 0.8792 (m-80) cc_final: 0.8356 (m-10) REVERT: B 147 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8386 (ttm) REVERT: B 166 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8541 (p) REVERT: B 191 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8275 (tp-100) REVERT: B 211 CYS cc_start: 0.9165 (m) cc_final: 0.8889 (m) REVERT: B 267 MET cc_start: 0.9019 (ptp) cc_final: 0.8707 (ptm) REVERT: B 279 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: B 280 GLN cc_start: 0.8104 (pt0) cc_final: 0.7670 (pm20) REVERT: B 299 MET cc_start: 0.9071 (mmt) cc_final: 0.8582 (mmt) REVERT: B 363 MET cc_start: 0.8145 (mtm) cc_final: 0.7883 (mtm) REVERT: B 412 GLU cc_start: 0.8730 (tp30) cc_final: 0.8503 (tp30) REVERT: C 70 ASP cc_start: 0.4212 (p0) cc_final: 0.4005 (p0) REVERT: C 123 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7989 (tm-30) REVERT: C 160 MET cc_start: 0.7874 (mmt) cc_final: 0.7531 (mmm) REVERT: C 180 THR cc_start: 0.8089 (p) cc_final: 0.6947 (t) REVERT: C 183 MET cc_start: 0.7779 (mtm) cc_final: 0.7177 (mpp) REVERT: C 275 TRP cc_start: 0.6698 (OUTLIER) cc_final: 0.5603 (m100) REVERT: D 44 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7866 (tpm170) REVERT: E 64 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7975 (ttm110) REVERT: E 90 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7878 (mm-30) REVERT: E 216 ASN cc_start: 0.9264 (m-40) cc_final: 0.8988 (m-40) REVERT: E 432 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7834 (t80) REVERT: F 12 CYS cc_start: 0.8571 (t) cc_final: 0.8113 (t) REVERT: F 19 LYS cc_start: 0.8890 (tppt) cc_final: 0.8386 (tptp) REVERT: F 22 GLU cc_start: 0.8529 (tt0) cc_final: 0.8178 (tm-30) REVERT: F 73 MET cc_start: 0.8773 (mmm) cc_final: 0.8505 (mmm) REVERT: F 125 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8412 (mm-30) REVERT: F 191 GLN cc_start: 0.8608 (tp40) cc_final: 0.8150 (tp-100) REVERT: F 198 GLU cc_start: 0.8505 (pt0) cc_final: 0.8157 (pt0) REVERT: F 202 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8718 (mp) REVERT: F 252 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8305 (mmtp) REVERT: F 359 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7608 (mtm110) REVERT: G 145 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7638 (mttm) REVERT: G 180 THR cc_start: 0.8083 (p) cc_final: 0.7410 (p) REVERT: G 183 MET cc_start: 0.7525 (mtm) cc_final: 0.7281 (mpp) outliers start: 96 outliers final: 66 residues processed: 382 average time/residue: 0.1330 time to fit residues: 78.7662 Evaluate side-chains 359 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 281 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 247 ASN Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 82 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 95 optimal weight: 50.0000 chunk 131 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.129194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.086840 restraints weight = 34413.051| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.33 r_work: 0.3385 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 18629 Z= 0.244 Angle : 0.658 12.505 25258 Z= 0.327 Chirality : 0.047 0.308 2746 Planarity : 0.005 0.114 3278 Dihedral : 9.108 145.245 2565 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 5.00 % Allowed : 21.38 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.18), residues: 2258 helix: -0.67 (0.18), residues: 866 sheet: -2.54 (0.27), residues: 326 loop : -1.61 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 214 TYR 0.023 0.002 TYR B 200 PHE 0.049 0.002 PHE F 20 TRP 0.014 0.002 TRP G 74 HIS 0.009 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (18626) covalent geometry : angle 0.65777 / 0.33 (25258) hydrogen bonds : bond 0.03283 / 2.17 ( 509) hydrogen bonds : angle 4.90309 / 3.43 ( 1446) Misc. bond : bond 0.00259 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 280 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7421 (tp30) REVERT: A 114 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8712 (tp) REVERT: A 155 GLU cc_start: 0.9261 (tt0) cc_final: 0.9048 (tt0) REVERT: A 357 TYR cc_start: 0.8759 (m-80) cc_final: 0.8488 (m-80) REVERT: A 432 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8172 (t80) REVERT: B 19 LYS cc_start: 0.8849 (tppt) cc_final: 0.8477 (tptp) REVERT: B 166 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8668 (p) REVERT: B 191 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8366 (tp-100) REVERT: B 211 CYS cc_start: 0.9205 (m) cc_final: 0.8923 (m) REVERT: B 279 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8420 (mp10) REVERT: B 280 GLN cc_start: 0.8184 (pt0) cc_final: 0.7645 (pm20) REVERT: B 299 MET cc_start: 0.9128 (mmt) cc_final: 0.8740 (mmt) REVERT: B 363 MET cc_start: 0.8480 (mtm) cc_final: 0.8149 (mtm) REVERT: B 412 GLU cc_start: 0.8773 (tp30) cc_final: 0.8536 (tp30) REVERT: C 123 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8039 (tm-30) REVERT: C 160 MET cc_start: 0.7854 (mmt) cc_final: 0.7533 (mmm) REVERT: C 180 THR cc_start: 0.8016 (p) cc_final: 0.7350 (p) REVERT: C 183 MET cc_start: 0.7761 (mtm) cc_final: 0.7244 (mpp) REVERT: C 275 TRP cc_start: 0.6651 (OUTLIER) cc_final: 0.5589 (m100) REVERT: D 44 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7921 (tpm170) REVERT: E 64 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7985 (ttm110) REVERT: E 90 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8026 (tp30) REVERT: E 216 ASN cc_start: 0.9306 (m-40) cc_final: 0.8991 (m-40) REVERT: E 377 MET cc_start: 0.8643 (ppp) cc_final: 0.8418 (tmm) REVERT: E 432 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.7734 (t80) REVERT: F 19 LYS cc_start: 0.8984 (tppt) cc_final: 0.8439 (tptp) REVERT: F 22 GLU cc_start: 0.8655 (tt0) cc_final: 0.8275 (tm-30) REVERT: F 125 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8446 (mm-30) REVERT: F 131 GLN cc_start: 0.8700 (tp40) cc_final: 0.8110 (tp40) REVERT: F 191 GLN cc_start: 0.8634 (tp40) cc_final: 0.8195 (tp-100) REVERT: F 198 GLU cc_start: 0.8556 (pt0) cc_final: 0.7989 (pt0) REVERT: F 200 TYR cc_start: 0.9018 (m-80) cc_final: 0.8613 (m-80) REVERT: F 202 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8771 (mp) REVERT: F 252 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8722 (mmtp) REVERT: F 279 GLN cc_start: 0.8124 (mm110) cc_final: 0.7348 (mt0) REVERT: G 145 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7613 (mttm) REVERT: G 180 THR cc_start: 0.7984 (p) cc_final: 0.7355 (p) REVERT: G 183 MET cc_start: 0.7559 (mtm) cc_final: 0.7298 (mpp) outliers start: 98 outliers final: 74 residues processed: 359 average time/residue: 0.1293 time to fit residues: 72.7733 Evaluate side-chains 354 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 271 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 247 ASN Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 111 optimal weight: 9.9990 chunk 105 optimal weight: 40.0000 chunk 153 optimal weight: 9.9990 chunk 110 optimal weight: 40.0000 chunk 20 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 211 optimal weight: 30.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN C 140 GLN C 210 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.131129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.088888 restraints weight = 34020.899| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.29 r_work: 0.3423 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18629 Z= 0.149 Angle : 0.617 11.127 25258 Z= 0.303 Chirality : 0.045 0.299 2746 Planarity : 0.005 0.106 3278 Dihedral : 8.857 144.701 2562 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.34 % Allowed : 22.09 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.18), residues: 2258 helix: -0.54 (0.18), residues: 862 sheet: -2.48 (0.27), residues: 326 loop : -1.51 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 214 TYR 0.013 0.001 TYR G 178 PHE 0.045 0.001 PHE F 20 TRP 0.017 0.002 TRP G 74 HIS 0.009 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (18626) covalent geometry : angle 0.61675 / 0.30 (25258) hydrogen bonds : bond 0.02998 / 1.99 ( 509) hydrogen bonds : angle 4.72321 / 3.31 ( 1446) Misc. bond : bond 0.00187 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 282 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9249 (mm) REVERT: A 90 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7394 (tp30) REVERT: A 114 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8725 (tp) REVERT: A 155 GLU cc_start: 0.9238 (tt0) cc_final: 0.8998 (tt0) REVERT: A 357 TYR cc_start: 0.8748 (m-80) cc_final: 0.8442 (m-80) REVERT: A 396 ASP cc_start: 0.9250 (t70) cc_final: 0.9016 (t0) REVERT: A 432 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8062 (t80) REVERT: B 12 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7945 (t) REVERT: B 19 LYS cc_start: 0.8793 (tppt) cc_final: 0.8413 (tptp) REVERT: B 50 TYR cc_start: 0.8851 (m-80) cc_final: 0.8442 (m-10) REVERT: B 166 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8653 (p) REVERT: B 191 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8403 (tp-100) REVERT: B 211 CYS cc_start: 0.9202 (m) cc_final: 0.8925 (m) REVERT: B 280 GLN cc_start: 0.8123 (pt0) cc_final: 0.7710 (pm20) REVERT: B 299 MET cc_start: 0.8995 (mmt) cc_final: 0.8766 (mmt) REVERT: B 363 MET cc_start: 0.8335 (mtm) cc_final: 0.8067 (mtm) REVERT: B 412 GLU cc_start: 0.8750 (tp30) cc_final: 0.8511 (tp30) REVERT: C 123 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8027 (tm-30) REVERT: C 160 MET cc_start: 0.7861 (mmt) cc_final: 0.7544 (mmm) REVERT: C 180 THR cc_start: 0.8010 (p) cc_final: 0.6898 (t) REVERT: C 183 MET cc_start: 0.7716 (mtm) cc_final: 0.7088 (mpp) REVERT: C 275 TRP cc_start: 0.6692 (OUTLIER) cc_final: 0.5626 (m100) REVERT: C 291 ARG cc_start: 0.6767 (tpm170) cc_final: 0.6304 (mmt-90) REVERT: D 44 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7920 (tpm170) REVERT: E 64 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7996 (ttm110) REVERT: E 90 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7956 (mm-30) REVERT: E 216 ASN cc_start: 0.9269 (m-40) cc_final: 0.8950 (m-40) REVERT: E 432 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.7746 (t80) REVERT: F 73 MET cc_start: 0.8785 (mmm) cc_final: 0.8482 (mmm) REVERT: F 121 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8625 (mtm-85) REVERT: F 125 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8455 (mm-30) REVERT: F 191 GLN cc_start: 0.8604 (tp40) cc_final: 0.8198 (tp40) REVERT: F 198 GLU cc_start: 0.8588 (pt0) cc_final: 0.8068 (pt0) REVERT: F 200 TYR cc_start: 0.8993 (m-80) cc_final: 0.8584 (m-80) REVERT: F 202 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8735 (mp) REVERT: F 252 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8655 (mmtp) REVERT: F 279 GLN cc_start: 0.8092 (mm110) cc_final: 0.7356 (mt0) REVERT: G 145 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7619 (mttm) REVERT: G 180 THR cc_start: 0.7989 (p) cc_final: 0.7372 (p) REVERT: G 183 MET cc_start: 0.7527 (mtm) cc_final: 0.7274 (mpp) outliers start: 85 outliers final: 66 residues processed: 349 average time/residue: 0.1299 time to fit residues: 70.5972 Evaluate side-chains 347 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 270 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 247 ASN Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 15 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 90 optimal weight: 0.0050 chunk 64 optimal weight: 3.9990 chunk 161 optimal weight: 0.0980 chunk 30 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 24 optimal weight: 0.0470 chunk 20 optimal weight: 8.9990 chunk 148 optimal weight: 0.5980 overall best weight: 0.7494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.134869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.092741 restraints weight = 33630.702| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.30 r_work: 0.3495 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18629 Z= 0.101 Angle : 0.606 12.292 25258 Z= 0.295 Chirality : 0.044 0.397 2746 Planarity : 0.004 0.099 3278 Dihedral : 8.530 144.135 2562 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.27 % Allowed : 22.96 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 2258 helix: -0.34 (0.18), residues: 864 sheet: -2.40 (0.27), residues: 342 loop : -1.52 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 264 TYR 0.015 0.001 TYR B 200 PHE 0.043 0.001 PHE F 20 TRP 0.020 0.002 TRP C 74 HIS 0.009 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (18626) covalent geometry : angle 0.60603 / 0.30 (25258) hydrogen bonds : bond 0.02723 / 1.81 ( 509) hydrogen bonds : angle 4.51082 / 3.16 ( 1446) Misc. bond : bond 0.00136 / 0.07 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 315 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7295 (tp30) REVERT: A 114 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8678 (tp) REVERT: A 155 GLU cc_start: 0.9246 (tt0) cc_final: 0.8961 (tt0) REVERT: A 297 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8166 (mt-10) REVERT: A 326 LYS cc_start: 0.8323 (tptp) cc_final: 0.7705 (mttt) REVERT: A 357 TYR cc_start: 0.8647 (m-80) cc_final: 0.8371 (m-80) REVERT: A 396 ASP cc_start: 0.9190 (t70) cc_final: 0.8960 (t0) REVERT: A 398 MET cc_start: 0.9234 (ttm) cc_final: 0.8644 (ttm) REVERT: A 432 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.7921 (t80) REVERT: A 434 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8632 (pt0) REVERT: B 12 CYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8045 (t) REVERT: B 19 LYS cc_start: 0.8726 (tppt) cc_final: 0.8213 (mmmm) REVERT: B 50 TYR cc_start: 0.8709 (m-80) cc_final: 0.8253 (m-10) REVERT: B 166 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8508 (p) REVERT: B 191 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8393 (tp-100) REVERT: B 211 CYS cc_start: 0.9163 (m) cc_final: 0.8878 (m) REVERT: B 280 GLN cc_start: 0.8198 (pt0) cc_final: 0.7900 (pt0) REVERT: B 363 MET cc_start: 0.8076 (mtm) cc_final: 0.7830 (mtm) REVERT: B 412 GLU cc_start: 0.8777 (tp30) cc_final: 0.8551 (tp30) REVERT: C 123 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7904 (tm-30) REVERT: C 160 MET cc_start: 0.7783 (mmt) cc_final: 0.7483 (mmm) REVERT: C 180 THR cc_start: 0.8066 (p) cc_final: 0.6903 (t) REVERT: C 183 MET cc_start: 0.7734 (mtm) cc_final: 0.7157 (mpp) REVERT: C 275 TRP cc_start: 0.6818 (OUTLIER) cc_final: 0.5621 (m100) REVERT: D 44 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7895 (tpm170) REVERT: E 50 ASN cc_start: 0.8430 (m-40) cc_final: 0.8092 (m-40) REVERT: E 90 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7857 (mm-30) REVERT: E 216 ASN cc_start: 0.9248 (m-40) cc_final: 0.8966 (m-40) REVERT: E 432 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.7743 (t80) REVERT: F 22 GLU cc_start: 0.8393 (tt0) cc_final: 0.7870 (tm-30) REVERT: F 73 MET cc_start: 0.8715 (mmm) cc_final: 0.8404 (mmm) REVERT: F 125 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8454 (mm-30) REVERT: F 147 MET cc_start: 0.8701 (ttm) cc_final: 0.8396 (ttm) REVERT: F 174 LYS cc_start: 0.9379 (mtmt) cc_final: 0.9178 (mtmm) REVERT: F 191 GLN cc_start: 0.8531 (tp40) cc_final: 0.8164 (tp40) REVERT: F 198 GLU cc_start: 0.8538 (pt0) cc_final: 0.8087 (pt0) REVERT: F 200 TYR cc_start: 0.8929 (m-80) cc_final: 0.8479 (m-80) REVERT: F 202 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8690 (mp) REVERT: F 252 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8236 (mmtp) REVERT: F 279 GLN cc_start: 0.8076 (mm110) cc_final: 0.7332 (mt0) REVERT: F 359 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7518 (mtm110) REVERT: F 405 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8003 (tm-30) REVERT: G 145 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7713 (mttm) REVERT: G 180 THR cc_start: 0.8104 (p) cc_final: 0.7437 (p) REVERT: G 183 MET cc_start: 0.7565 (mtm) cc_final: 0.7301 (mpp) outliers start: 64 outliers final: 47 residues processed: 364 average time/residue: 0.1269 time to fit residues: 71.9261 Evaluate side-chains 352 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 122 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.134420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.091936 restraints weight = 34059.113| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.36 r_work: 0.3481 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18629 Z= 0.111 Angle : 0.622 12.388 25258 Z= 0.300 Chirality : 0.044 0.353 2746 Planarity : 0.004 0.098 3278 Dihedral : 8.454 144.683 2562 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.76 % Allowed : 23.67 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.18), residues: 2258 helix: -0.28 (0.18), residues: 870 sheet: -2.41 (0.27), residues: 334 loop : -1.52 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 64 TYR 0.018 0.001 TYR A 24 PHE 0.022 0.001 PHE F 20 TRP 0.016 0.001 TRP G 74 HIS 0.008 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (18626) covalent geometry : angle 0.62229 / 0.30 (25258) hydrogen bonds : bond 0.02707 / 1.80 ( 509) hydrogen bonds : angle 4.52932 / 3.17 ( 1446) Misc. bond : bond 0.00141 / 0.07 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4760.94 seconds wall clock time: 82 minutes 27.02 seconds (4947.02 seconds total)