Starting phenix.real_space_refine on Wed Feb 4 16:33:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ny1_49915/02_2026/9ny1_49915_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ny1_49915/02_2026/9ny1_49915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ny1_49915/02_2026/9ny1_49915_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ny1_49915/02_2026/9ny1_49915_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ny1_49915/02_2026/9ny1_49915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ny1_49915/02_2026/9ny1_49915.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 7281 2.51 5 N 1977 2.21 5 O 2224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11518 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2872 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 1 Chain: "B" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2859 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 7, 'TRANS': 342} Chain breaks: 1 Chain: "C" Number of atoms: 2905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2905 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 7, 'TRANS': 348} Chain breaks: 1 Chain: "D" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2882 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 1 Time building chain proxies: 2.59, per 1000 atoms: 0.22 Number of scatterers: 11518 At special positions: 0 Unit cell: (96.824, 128.744, 122.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2224 8.00 N 1977 7.00 C 7281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 411.4 milliseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 60.3% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 28 removed outlier: 3.698A pdb=" N GLU A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.642A pdb=" N ARG A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 210 removed outlier: 4.933A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 197 " --> pdb=" O MET A 193 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.723A pdb=" N TYR A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.661A pdb=" N THR A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 273 through 295 removed outlier: 4.532A pdb=" N GLU A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 325 removed outlier: 3.556A pdb=" N LEU A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 317 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 removed outlier: 3.802A pdb=" N TYR A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 347 removed outlier: 3.686A pdb=" N ARG A 347 " --> pdb=" O ASN A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 347' Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.675A pdb=" N ALA A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS A 365 " --> pdb=" O HIS A 361 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 removed outlier: 3.619A pdb=" N LYS A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 383' Processing helix chain 'B' and resid 19 through 28 removed outlier: 3.523A pdb=" N THR B 23 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 117 through 123 removed outlier: 3.568A pdb=" N SER B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.572A pdb=" N GLU B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.578A pdb=" N LYS B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 206 removed outlier: 3.716A pdb=" N ASP B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 203 " --> pdb=" O TRP B 199 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.552A pdb=" N ILE B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 removed outlier: 3.598A pdb=" N LYS B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 257 " --> pdb=" O ASN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.668A pdb=" N LEU B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 295 removed outlier: 4.125A pdb=" N GLU B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.547A pdb=" N GLN B 307 " --> pdb=" O TYR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 325 removed outlier: 3.669A pdb=" N HIS B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 343 removed outlier: 3.607A pdb=" N VAL B 333 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 367 removed outlier: 3.630A pdb=" N ALA B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS B 365 " --> pdb=" O HIS B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 29 removed outlier: 3.701A pdb=" N TYR C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 21 " --> pdb=" O ILE C 17 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 87 removed outlier: 4.217A pdb=" N TRP C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 83 " --> pdb=" O ASN C 79 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE C 84 " --> pdb=" O TRP C 80 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 85 " --> pdb=" O MET C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 removed outlier: 4.182A pdb=" N SER C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 133 removed outlier: 4.268A pdb=" N LYS C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 removed outlier: 3.649A pdb=" N ASN C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.872A pdb=" N SER C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 181 removed outlier: 3.570A pdb=" N LEU C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 181 " --> pdb=" O TYR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 207 removed outlier: 3.783A pdb=" N TYR C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 197 " --> pdb=" O MET C 193 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.613A pdb=" N GLY C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 258 removed outlier: 3.697A pdb=" N GLN C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 268 removed outlier: 4.155A pdb=" N ILE C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 287 Processing helix chain 'C' and resid 302 through 325 removed outlier: 3.832A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 345 removed outlier: 3.717A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'C' and resid 356 through 370 removed outlier: 3.623A pdb=" N ALA C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.750A pdb=" N LEU C 383 " --> pdb=" O PHE C 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.576A pdb=" N ARG D 21 " --> pdb=" O ILE D 17 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 removed outlier: 3.839A pdb=" N LYS D 75 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR D 76 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 83 " --> pdb=" O ASN D 79 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 84 " --> pdb=" O TRP D 80 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP D 85 " --> pdb=" O MET D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 115 removed outlier: 3.943A pdb=" N LEU D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 removed outlier: 4.103A pdb=" N ASP D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 147 removed outlier: 4.129A pdb=" N ASN D 141 " --> pdb=" O PRO D 137 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TYR D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 removed outlier: 3.687A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 removed outlier: 3.656A pdb=" N LEU D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 181 " --> pdb=" O TYR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 210 removed outlier: 4.139A pdb=" N TYR D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 230 removed outlier: 3.501A pdb=" N ARG D 224 " --> pdb=" O ASP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 removed outlier: 3.547A pdb=" N GLN D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 258 " --> pdb=" O THR D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 268 removed outlier: 3.898A pdb=" N ILE D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 294 removed outlier: 3.581A pdb=" N LEU D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 302 through 325 removed outlier: 3.695A pdb=" N GLN D 319 " --> pdb=" O GLY D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 345 Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'D' and resid 356 through 370 removed outlier: 3.716A pdb=" N ALA D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS D 365 " --> pdb=" O HIS D 361 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 3.516A pdb=" N LEU A 97 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR A 161 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 96 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE A 163 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 98 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 94 through 97 Processing sheet with id=AA4, first strand: chain 'C' and resid 163 through 164 removed outlier: 4.175A pdb=" N ILE C 163 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR C 100 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 160 through 164 removed outlier: 8.326A pdb=" N THR D 161 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE D 96 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE D 163 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU D 98 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER D 33 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N LEU D 97 " --> pdb=" O SER D 33 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.60: 11691 1.60 - 1.99: 51 1.99 - 2.37: 2 2.37 - 2.76: 0 2.76 - 3.15: 4 Bond restraints: 11748 Sorted by residual: bond pdb=" CE2 PHE A 125 " pdb=" CZ PHE A 125 " ideal model delta sigma weight residual 1.382 3.145 -1.763 3.00e-02 1.11e+03 3.46e+03 bond pdb=" CD2 PHE A 125 " pdb=" CE2 PHE A 125 " ideal model delta sigma weight residual 1.382 3.111 -1.729 3.00e-02 1.11e+03 3.32e+03 bond pdb=" CE1 PHE A 125 " pdb=" CZ PHE A 125 " ideal model delta sigma weight residual 1.382 3.103 -1.721 3.00e-02 1.11e+03 3.29e+03 bond pdb=" CD1 PHE A 125 " pdb=" CE1 PHE A 125 " ideal model delta sigma weight residual 1.382 3.048 -1.666 3.00e-02 1.11e+03 3.08e+03 bond pdb=" CG PHE A 125 " pdb=" CD1 PHE A 125 " ideal model delta sigma weight residual 1.384 2.210 -0.826 2.10e-02 2.27e+03 1.55e+03 ... (remaining 11743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.74: 15840 9.74 - 19.48: 24 19.48 - 29.22: 9 29.22 - 38.96: 4 38.96 - 48.70: 1 Bond angle restraints: 15878 Sorted by residual: angle pdb=" N THR A 114 " pdb=" CA THR A 114 " pdb=" C THR A 114 " ideal model delta sigma weight residual 111.14 146.14 -35.00 1.08e+00 8.57e-01 1.05e+03 angle pdb=" O CYS A 154 " pdb=" C CYS A 154 " pdb=" N ARG A 155 " ideal model delta sigma weight residual 122.59 91.38 31.21 1.33e+00 5.65e-01 5.51e+02 angle pdb=" N ILE B 39 " pdb=" CA ILE B 39 " pdb=" C ILE B 39 " ideal model delta sigma weight residual 109.34 158.04 -48.70 2.08e+00 2.31e-01 5.48e+02 angle pdb=" C CYS C 104 " pdb=" N HIS C 105 " pdb=" CA HIS C 105 " ideal model delta sigma weight residual 121.54 157.87 -36.33 1.91e+00 2.74e-01 3.62e+02 angle pdb=" N ASP B 152 " pdb=" CA ASP B 152 " pdb=" C ASP B 152 " ideal model delta sigma weight residual 110.28 137.43 -27.15 1.48e+00 4.57e-01 3.37e+02 ... (remaining 15873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5805 17.97 - 35.94: 914 35.94 - 53.90: 279 53.90 - 71.87: 40 71.87 - 89.84: 22 Dihedral angle restraints: 7060 sinusoidal: 2894 harmonic: 4166 Sorted by residual: dihedral pdb=" C CYS C 104 " pdb=" N CYS C 104 " pdb=" CA CYS C 104 " pdb=" CB CYS C 104 " ideal model delta harmonic sigma weight residual -122.60 -76.89 -45.71 0 2.50e+00 1.60e-01 3.34e+02 dihedral pdb=" C ILE B 39 " pdb=" N ILE B 39 " pdb=" CA ILE B 39 " pdb=" CB ILE B 39 " ideal model delta harmonic sigma weight residual -122.00 -95.97 -26.03 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" N SER A 115 " pdb=" C SER A 115 " pdb=" CA SER A 115 " pdb=" CB SER A 115 " ideal model delta harmonic sigma weight residual 122.80 96.82 25.98 0 2.50e+00 1.60e-01 1.08e+02 ... (remaining 7057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.266: 1722 0.266 - 0.533: 12 0.533 - 0.799: 2 0.799 - 1.066: 1 1.066 - 1.332: 2 Chirality restraints: 1739 Sorted by residual: chirality pdb=" CA THR A 114 " pdb=" N THR A 114 " pdb=" C THR A 114 " pdb=" CB THR A 114 " both_signs ideal model delta sigma weight residual False 2.53 1.19 1.33 2.00e-01 2.50e+01 4.44e+01 chirality pdb=" CA ILE B 39 " pdb=" N ILE B 39 " pdb=" C ILE B 39 " pdb=" CB ILE B 39 " both_signs ideal model delta sigma weight residual False 2.43 1.30 1.13 2.00e-01 2.50e+01 3.20e+01 chirality pdb=" CA LEU B 40 " pdb=" N LEU B 40 " pdb=" C LEU B 40 " pdb=" CB LEU B 40 " both_signs ideal model delta sigma weight residual False 2.51 3.35 -0.84 2.00e-01 2.50e+01 1.76e+01 ... (remaining 1736 not shown) Planarity restraints: 2039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 155 " 0.826 9.50e-02 1.11e+02 3.70e-01 8.32e+01 pdb=" NE ARG B 155 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG B 155 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 155 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 155 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 125 " 0.005 2.00e-02 2.50e+03 6.63e-02 7.70e+01 pdb=" CG PHE A 125 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 125 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 PHE A 125 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 PHE A 125 " -0.103 2.00e-02 2.50e+03 pdb=" CE2 PHE A 125 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE A 125 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 212 " 0.135 5.00e-02 4.00e+02 2.02e-01 6.51e+01 pdb=" N PRO A 213 " -0.348 5.00e-02 4.00e+02 pdb=" CA PRO A 213 " 0.127 5.00e-02 4.00e+02 pdb=" CD PRO A 213 " 0.085 5.00e-02 4.00e+02 ... (remaining 2036 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 3 1.97 - 2.70: 324 2.70 - 3.43: 15778 3.43 - 4.17: 25913 4.17 - 4.90: 47581 Nonbonded interactions: 89599 Sorted by model distance: nonbonded pdb=" O CYS C 104 " pdb=" SG CYS C 104 " model vdw 1.234 3.400 nonbonded pdb=" O ILE B 39 " pdb=" CG1 ILE B 39 " model vdw 1.759 3.440 nonbonded pdb=" O THR A 114 " pdb=" OE1 GLN A 116 " model vdw 1.790 3.040 nonbonded pdb=" C CYS C 104 " pdb=" SG CYS C 104 " model vdw 2.028 2.904 nonbonded pdb=" O CYS C 104 " pdb=" CB CYS C 104 " model vdw 2.053 2.752 ... (remaining 89594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 41 or resid 64 through 383)) selection = (chain 'B' and resid 13 through 383) selection = (chain 'C' and (resid 13 through 41 or resid 64 through 383)) selection = (chain 'D' and resid 13 through 383) } 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.610 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.034 1.763 11748 Z= 1.213 Angle : 1.340 48.696 15878 Z= 0.767 Chirality : 0.076 1.332 1739 Planarity : 0.011 0.370 2039 Dihedral : 19.180 89.841 4366 Min Nonbonded Distance : 1.234 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.17 % Favored : 91.76 % Rotamer: Outliers : 1.18 % Allowed : 33.44 % Favored : 65.38 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.11 (0.18), residues: 1396 helix: -2.79 (0.13), residues: 787 sheet: -0.84 (0.74), residues: 47 loop : -2.60 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 21 TYR 0.035 0.002 TYR D 240 PHE 0.103 0.004 PHE A 125 TRP 0.010 0.001 TRP B 12 HIS 0.022 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.03385 (11748) covalent geometry : angle 1.34000 (15878) hydrogen bonds : bond 0.25887 ( 471) hydrogen bonds : angle 8.10538 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: D 187 GLU cc_start: 0.7755 (pm20) cc_final: 0.7494 (pm20) REVERT: D 240 TYR cc_start: 0.8106 (t80) cc_final: 0.7893 (t80) outliers start: 15 outliers final: 5 residues processed: 116 average time/residue: 0.0833 time to fit residues: 14.5070 Evaluate side-chains 103 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.209880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146001 restraints weight = 15490.210| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.78 r_work: 0.3506 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.974 11748 Z= 0.714 Angle : 0.705 20.879 15878 Z= 0.381 Chirality : 0.042 0.200 1739 Planarity : 0.005 0.156 2039 Dihedral : 5.312 56.866 1554 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.09 % Favored : 92.84 % Rotamer: Outliers : 4.09 % Allowed : 28.40 % Favored : 67.51 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.21), residues: 1396 helix: -1.02 (0.17), residues: 797 sheet: -0.20 (0.86), residues: 36 loop : -2.44 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.014 0.001 TYR B 338 PHE 0.065 0.002 PHE A 125 TRP 0.008 0.001 TRP A 314 HIS 0.004 0.001 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.01902 (11748) covalent geometry : angle 0.70484 (15878) hydrogen bonds : bond 0.04717 ( 471) hydrogen bonds : angle 4.34178 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 116 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6232 (pt0) REVERT: A 367 MET cc_start: 0.8040 (mtt) cc_final: 0.7794 (mtt) REVERT: B 18 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: B 125 PHE cc_start: 0.6088 (OUTLIER) cc_final: 0.5586 (t80) REVERT: C 13 LEU cc_start: 0.4706 (OUTLIER) cc_final: 0.4219 (tt) REVERT: C 160 PHE cc_start: 0.7946 (t80) cc_final: 0.7258 (t80) REVERT: D 187 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7358 (pm20) outliers start: 52 outliers final: 27 residues processed: 153 average time/residue: 0.0874 time to fit residues: 20.0415 Evaluate side-chains 131 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 383 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 22 optimal weight: 0.0270 chunk 47 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.210856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.150723 restraints weight = 15487.305| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.91 r_work: 0.3547 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.969 11748 Z= 0.705 Angle : 0.650 21.113 15878 Z= 0.353 Chirality : 0.040 0.204 1739 Planarity : 0.005 0.142 2039 Dihedral : 4.893 57.348 1549 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 4.17 % Allowed : 28.95 % Favored : 66.88 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.22), residues: 1396 helix: -0.24 (0.18), residues: 799 sheet: 0.13 (0.88), residues: 36 loop : -2.24 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 21 TYR 0.015 0.001 TYR B 303 PHE 0.066 0.002 PHE A 125 TRP 0.010 0.001 TRP C 292 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.01883 (11748) covalent geometry : angle 0.65027 (15878) hydrogen bonds : bond 0.03896 ( 471) hydrogen bonds : angle 3.87545 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 116 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6446 (mp10) REVERT: B 125 PHE cc_start: 0.6381 (OUTLIER) cc_final: 0.5854 (t80) REVERT: B 194 TYR cc_start: 0.6508 (t80) cc_final: 0.6202 (t80) REVERT: B 307 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: C 160 PHE cc_start: 0.7916 (t80) cc_final: 0.7333 (t80) REVERT: C 299 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8329 (tm-30) REVERT: D 187 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7220 (pm20) outliers start: 53 outliers final: 33 residues processed: 144 average time/residue: 0.0868 time to fit residues: 18.8300 Evaluate side-chains 137 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS B 234 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.205717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142861 restraints weight = 15474.568| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.94 r_work: 0.3497 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.967 11748 Z= 0.741 Angle : 0.756 21.168 15878 Z= 0.404 Chirality : 0.045 0.221 1739 Planarity : 0.005 0.131 2039 Dihedral : 5.155 57.064 1548 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.95 % Favored : 91.98 % Rotamer: Outliers : 5.82 % Allowed : 27.69 % Favored : 66.48 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.22), residues: 1396 helix: -0.24 (0.18), residues: 805 sheet: -0.78 (0.71), residues: 53 loop : -2.25 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.020 0.002 TYR B 261 PHE 0.067 0.003 PHE A 125 TRP 0.031 0.002 TRP C 80 HIS 0.006 0.001 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.01960 (11748) covalent geometry : angle 0.75629 (15878) hydrogen bonds : bond 0.04833 ( 471) hydrogen bonds : angle 4.17533 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 111 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 116 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6308 (mp-120) REVERT: A 241 PHE cc_start: 0.7227 (m-80) cc_final: 0.6583 (m-80) REVERT: B 125 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.6126 (t80) REVERT: B 194 TYR cc_start: 0.6506 (t80) cc_final: 0.6183 (t80) REVERT: B 234 GLN cc_start: 0.5066 (OUTLIER) cc_final: 0.4848 (tp40) REVERT: B 307 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: C 13 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4276 (tt) REVERT: D 187 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7142 (pm20) outliers start: 74 outliers final: 44 residues processed: 169 average time/residue: 0.0841 time to fit residues: 21.4981 Evaluate side-chains 155 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 105 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 85 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 chunk 64 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN B 18 GLN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 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 = 0.4447 r_free = 0.4447 target = 0.211844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.150078 restraints weight = 15226.286| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.63 r_work: 0.3516 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.968 11748 Z= 0.703 Angle : 0.651 21.117 15878 Z= 0.351 Chirality : 0.040 0.261 1739 Planarity : 0.004 0.126 2039 Dihedral : 4.783 51.841 1548 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 3.78 % Allowed : 29.58 % Favored : 66.64 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.23), residues: 1396 helix: 0.29 (0.19), residues: 806 sheet: -0.81 (0.70), residues: 58 loop : -2.21 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 25 TYR 0.020 0.001 TYR B 261 PHE 0.067 0.002 PHE A 125 TRP 0.046 0.001 TRP C 80 HIS 0.002 0.000 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.01878 (11748) covalent geometry : angle 0.65078 (15878) hydrogen bonds : bond 0.03483 ( 471) hydrogen bonds : angle 3.68068 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 116 GLN cc_start: 0.6438 (OUTLIER) cc_final: 0.6159 (mp-120) REVERT: B 37 PHE cc_start: 0.7297 (t80) cc_final: 0.7079 (t80) REVERT: B 125 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.6049 (t80) REVERT: B 194 TYR cc_start: 0.6566 (t80) cc_final: 0.6281 (t80) REVERT: B 231 LYS cc_start: 0.6542 (tptt) cc_final: 0.6313 (tptt) REVERT: B 307 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: C 80 TRP cc_start: 0.8066 (m-10) cc_final: 0.7849 (m100) REVERT: D 13 LEU cc_start: 0.1022 (OUTLIER) cc_final: 0.0657 (pp) REVERT: D 187 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7143 (pm20) outliers start: 48 outliers final: 31 residues processed: 143 average time/residue: 0.0866 time to fit residues: 18.9885 Evaluate side-chains 137 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.0030 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 100 optimal weight: 0.0770 chunk 10 optimal weight: 10.0000 overall best weight: 0.7750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS C 79 ASN ** C 299 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 = 0.4422 r_free = 0.4422 target = 0.209444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.146412 restraints weight = 15622.414| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.93 r_work: 0.3502 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.967 11748 Z= 0.709 Angle : 0.671 21.148 15878 Z= 0.360 Chirality : 0.041 0.231 1739 Planarity : 0.004 0.121 2039 Dihedral : 4.760 49.945 1548 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.59 % Favored : 92.34 % Rotamer: Outliers : 4.09 % Allowed : 29.35 % Favored : 66.56 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.23), residues: 1396 helix: 0.40 (0.19), residues: 800 sheet: -0.77 (0.70), residues: 58 loop : -2.11 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 25 TYR 0.020 0.001 TYR B 261 PHE 0.068 0.002 PHE A 125 TRP 0.029 0.001 TRP C 80 HIS 0.003 0.001 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.01891 (11748) covalent geometry : angle 0.67126 (15878) hydrogen bonds : bond 0.03710 ( 471) hydrogen bonds : angle 3.72160 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 108 time to evaluate : 0.433 Fit side-chains REVERT: B 125 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.6170 (t80) REVERT: B 194 TYR cc_start: 0.6478 (t80) cc_final: 0.6189 (t80) REVERT: B 231 LYS cc_start: 0.6618 (tptt) cc_final: 0.6412 (tptt) REVERT: B 249 GLU cc_start: 0.8017 (pm20) cc_final: 0.7770 (pm20) REVERT: B 307 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: D 13 LEU cc_start: 0.0969 (OUTLIER) cc_final: 0.0642 (pp) REVERT: D 187 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7131 (pm20) outliers start: 52 outliers final: 35 residues processed: 146 average time/residue: 0.0838 time to fit residues: 18.5981 Evaluate side-chains 143 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 102 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** C 299 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 = 0.4424 r_free = 0.4424 target = 0.209740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.149198 restraints weight = 15685.501| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.81 r_work: 0.3502 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.968 11748 Z= 0.707 Angle : 0.657 21.146 15878 Z= 0.354 Chirality : 0.041 0.210 1739 Planarity : 0.004 0.117 2039 Dihedral : 4.685 47.383 1548 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.16 % Favored : 92.77 % Rotamer: Outliers : 3.86 % Allowed : 29.74 % Favored : 66.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1396 helix: 0.50 (0.19), residues: 804 sheet: -0.76 (0.71), residues: 58 loop : -2.13 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 25 TYR 0.021 0.001 TYR B 261 PHE 0.068 0.002 PHE A 125 TRP 0.054 0.001 TRP C 80 HIS 0.003 0.000 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.01886 (11748) covalent geometry : angle 0.65714 (15878) hydrogen bonds : bond 0.03563 ( 471) hydrogen bonds : angle 3.67333 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 106 time to evaluate : 0.413 Fit side-chains REVERT: B 18 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: B 125 PHE cc_start: 0.6345 (OUTLIER) cc_final: 0.6097 (t80) REVERT: B 194 TYR cc_start: 0.6578 (t80) cc_final: 0.6303 (t80) REVERT: B 249 GLU cc_start: 0.7997 (pm20) cc_final: 0.7703 (pm20) REVERT: B 307 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: C 335 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: D 13 LEU cc_start: 0.0846 (OUTLIER) cc_final: 0.0513 (pp) REVERT: D 187 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7102 (pm20) outliers start: 49 outliers final: 37 residues processed: 141 average time/residue: 0.0920 time to fit residues: 19.5935 Evaluate side-chains 147 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 95 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 86 optimal weight: 0.0870 chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** C 299 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 = 0.4439 r_free = 0.4439 target = 0.211179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.148920 restraints weight = 15684.371| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.78 r_work: 0.3496 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.968 11748 Z= 0.706 Angle : 0.668 21.154 15878 Z= 0.356 Chirality : 0.040 0.210 1739 Planarity : 0.004 0.114 2039 Dihedral : 4.632 44.174 1548 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.45 % Favored : 92.48 % Rotamer: Outliers : 3.93 % Allowed : 29.82 % Favored : 66.25 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.23), residues: 1396 helix: 0.61 (0.19), residues: 796 sheet: -0.67 (0.75), residues: 52 loop : -1.99 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 25 TYR 0.022 0.001 TYR B 261 PHE 0.068 0.002 PHE A 125 TRP 0.074 0.001 TRP C 80 HIS 0.003 0.000 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.01884 (11748) covalent geometry : angle 0.66818 (15878) hydrogen bonds : bond 0.03473 ( 471) hydrogen bonds : angle 3.66861 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 98 time to evaluate : 0.342 Fit side-chains REVERT: B 18 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: B 125 PHE cc_start: 0.6409 (OUTLIER) cc_final: 0.6163 (t80) REVERT: B 194 TYR cc_start: 0.6522 (t80) cc_final: 0.6263 (t80) REVERT: B 307 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: B 379 PHE cc_start: 0.6083 (p90) cc_final: 0.5737 (p90) REVERT: C 335 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: D 13 LEU cc_start: 0.1005 (OUTLIER) cc_final: 0.0658 (pp) REVERT: D 187 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7116 (pm20) outliers start: 50 outliers final: 37 residues processed: 137 average time/residue: 0.0890 time to fit residues: 18.5122 Evaluate side-chains 141 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 50.0000 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 93 optimal weight: 0.0970 chunk 120 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.210286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147133 restraints weight = 15515.028| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.66 r_work: 0.3478 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.968 11748 Z= 0.711 Angle : 0.681 21.163 15878 Z= 0.364 Chirality : 0.041 0.211 1739 Planarity : 0.004 0.111 2039 Dihedral : 4.666 41.387 1548 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.24 % Favored : 91.69 % Rotamer: Outliers : 4.01 % Allowed : 29.66 % Favored : 66.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.23), residues: 1396 helix: 0.53 (0.19), residues: 804 sheet: -0.69 (0.75), residues: 52 loop : -2.06 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 25 TYR 0.023 0.001 TYR B 261 PHE 0.068 0.002 PHE A 125 TRP 0.062 0.001 TRP C 80 HIS 0.003 0.001 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.01895 (11748) covalent geometry : angle 0.68076 (15878) hydrogen bonds : bond 0.03686 ( 471) hydrogen bonds : angle 3.73436 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.409 Fit side-chains REVERT: A 241 PHE cc_start: 0.7241 (m-80) cc_final: 0.6942 (m-80) REVERT: B 125 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.6038 (t80) REVERT: B 194 TYR cc_start: 0.6605 (t80) cc_final: 0.6364 (t80) REVERT: B 307 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: B 379 PHE cc_start: 0.6358 (p90) cc_final: 0.5977 (p90) REVERT: D 13 LEU cc_start: 0.0965 (OUTLIER) cc_final: 0.0653 (pp) REVERT: D 187 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7133 (pm20) outliers start: 51 outliers final: 40 residues processed: 137 average time/residue: 0.0821 time to fit residues: 17.2451 Evaluate side-chains 143 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 0.0970 chunk 7 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** C 299 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 = 0.4391 r_free = 0.4391 target = 0.205923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139181 restraints weight = 15615.742| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.73 r_work: 0.3469 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.967 11748 Z= 0.716 Angle : 0.719 21.162 15878 Z= 0.379 Chirality : 0.042 0.211 1739 Planarity : 0.004 0.109 2039 Dihedral : 4.777 37.668 1548 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.09 % Favored : 91.83 % Rotamer: Outliers : 3.86 % Allowed : 29.82 % Favored : 66.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1396 helix: 0.43 (0.19), residues: 808 sheet: -0.71 (0.76), residues: 52 loop : -2.14 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 25 TYR 0.023 0.002 TYR B 261 PHE 0.068 0.002 PHE A 125 TRP 0.068 0.002 TRP C 80 HIS 0.004 0.001 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.01907 (11748) covalent geometry : angle 0.71934 (15878) hydrogen bonds : bond 0.03941 ( 471) hydrogen bonds : angle 3.82422 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.439 Fit side-chains REVERT: B 125 PHE cc_start: 0.6281 (OUTLIER) cc_final: 0.6042 (t80) REVERT: B 194 TYR cc_start: 0.6630 (t80) cc_final: 0.6402 (t80) REVERT: B 307 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: D 187 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7145 (pm20) outliers start: 49 outliers final: 38 residues processed: 141 average time/residue: 0.0861 time to fit residues: 18.3539 Evaluate side-chains 145 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 371 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** C 299 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 = 0.4425 r_free = 0.4425 target = 0.209602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148935 restraints weight = 15670.970| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.95 r_work: 0.3484 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.968 11748 Z= 0.707 Angle : 0.685 21.144 15878 Z= 0.365 Chirality : 0.041 0.211 1739 Planarity : 0.004 0.108 2039 Dihedral : 4.647 28.172 1548 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.81 % Favored : 92.12 % Rotamer: Outliers : 3.30 % Allowed : 30.13 % Favored : 66.56 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.23), residues: 1396 helix: 0.54 (0.19), residues: 813 sheet: -0.76 (0.75), residues: 52 loop : -2.10 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 25 TYR 0.023 0.001 TYR B 261 PHE 0.068 0.002 PHE A 125 TRP 0.091 0.002 TRP C 80 HIS 0.002 0.000 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.01886 (11748) covalent geometry : angle 0.68473 (15878) hydrogen bonds : bond 0.03526 ( 471) hydrogen bonds : angle 3.71389 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.23 seconds wall clock time: 44 minutes 9.99 seconds (2649.99 seconds total)