Starting phenix.real_space_refine on Wed Mar 4 21:41:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7anz_11835/03_2026/7anz_11835.cif Found real_map, /net/cci-nas-00/data/ceres_data/7anz_11835/03_2026/7anz_11835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7anz_11835/03_2026/7anz_11835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7anz_11835/03_2026/7anz_11835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7anz_11835/03_2026/7anz_11835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7anz_11835/03_2026/7anz_11835.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 56 5.16 5 C 10787 2.51 5 N 2772 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16751 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3269 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain breaks: 6 Chain: "A" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 16, 'TRANS': 383} Chain breaks: 6 Chain: "C" Number of atoms: 5142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5142 Classifications: {'peptide': 618} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 606} Chain breaks: 6 Chain: "D" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 5155 Classifications: {'peptide': 613} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 597} Chain breaks: 4 Time building chain proxies: 3.59, per 1000 atoms: 0.21 Number of scatterers: 16751 At special positions: 0 Unit cell: (176.55, 169.06, 86.67, 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 56 16.00 O 3136 8.00 N 2772 7.00 C 10787 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: 1.42 Conformation dependent library (CDL) restraints added in 698.9 milliseconds 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3922 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 8 sheets defined 59.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'B' and resid 11 through 30 removed outlier: 3.891A pdb=" N GLN B 16 " --> pdb=" O GLN B 12 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 removed outlier: 4.063A pdb=" N LEU B 79 " --> pdb=" O HIS B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.697A pdb=" N SER B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.791A pdb=" N GLU B 141 " --> pdb=" O TYR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.603A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 removed outlier: 3.531A pdb=" N LYS B 179 " --> pdb=" O GLY B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 189 removed outlier: 3.583A pdb=" N ASP B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 224 removed outlier: 3.657A pdb=" N THR B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 218 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.813A pdb=" N ILE B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 287 through 293 removed outlier: 3.572A pdb=" N ILE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 329 removed outlier: 3.702A pdb=" N LEU B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 371 removed outlier: 4.083A pdb=" N GLN B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 427 removed outlier: 3.973A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 422 " --> pdb=" O LYS B 418 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 463 removed outlier: 3.709A pdb=" N VAL B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.615A pdb=" N GLY A 14 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 removed outlier: 3.982A pdb=" N LEU A 79 " --> pdb=" O HIS A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 100 through 110 removed outlier: 3.723A pdb=" N ALA A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 removed outlier: 3.569A pdb=" N LYS A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.526A pdb=" N LEU A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 189 removed outlier: 4.131A pdb=" N VAL A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 184 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.824A pdb=" N ASN A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 removed outlier: 3.789A pdb=" N ASN A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.707A pdb=" N LYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.587A pdb=" N ASN A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.838A pdb=" N LEU A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 368 removed outlier: 3.590A pdb=" N LYS A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 427 removed outlier: 3.920A pdb=" N PHE A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.689A pdb=" N VAL A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.977A pdb=" N LEU C 154 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 187 removed outlier: 3.704A pdb=" N LYS C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 173 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 removed outlier: 3.617A pdb=" N PHE C 197 " --> pdb=" O HIS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.693A pdb=" N LEU C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 235 removed outlier: 4.391A pdb=" N HIS C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 222 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 234 " --> pdb=" O ARG C 230 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 290 removed outlier: 3.596A pdb=" N ILE C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 308 removed outlier: 3.910A pdb=" N ASP C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N PHE C 299 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 302 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.645A pdb=" N GLY C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 removed outlier: 4.174A pdb=" N LEU C 365 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 392 removed outlier: 3.554A pdb=" N LYS C 377 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 382 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE C 388 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR C 392 " --> pdb=" O PHE C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 436 removed outlier: 3.809A pdb=" N ASP C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 removed outlier: 3.570A pdb=" N ASN C 445 " --> pdb=" O PRO C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 451 Processing helix chain 'C' and resid 456 through 464 removed outlier: 3.504A pdb=" N ASN C 461 " --> pdb=" O PHE C 457 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.618A pdb=" N LYS C 471 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 491 removed outlier: 3.889A pdb=" N LEU C 482 " --> pdb=" O SER C 478 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 488 " --> pdb=" O LYS C 484 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 489 " --> pdb=" O GLN C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 removed outlier: 3.562A pdb=" N LEU C 508 " --> pdb=" O VAL C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.657A pdb=" N VAL C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU C 526 " --> pdb=" O TYR C 522 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 4.241A pdb=" N VAL C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 628 removed outlier: 3.741A pdb=" N GLN C 601 " --> pdb=" O GLN C 597 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N MET C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE C 606 " --> pdb=" O TYR C 602 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 627 " --> pdb=" O TRP C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 667 removed outlier: 3.767A pdb=" N TRP C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 657 " --> pdb=" O SER C 653 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 658 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 659 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN C 664 " --> pdb=" O HIS C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 690 removed outlier: 4.319A pdb=" N GLU C 677 " --> pdb=" O HIS C 673 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 678 " --> pdb=" O ASN C 674 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 683 " --> pdb=" O LYS C 679 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 684 " --> pdb=" O ASN C 680 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THR C 685 " --> pdb=" O LEU C 681 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN C 688 " --> pdb=" O THR C 684 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 690 " --> pdb=" O ALA C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 758 removed outlier: 3.540A pdb=" N ILE C 744 " --> pdb=" O VAL C 740 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 745 " --> pdb=" O GLU C 741 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 787 removed outlier: 3.555A pdb=" N LYS C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C 782 " --> pdb=" O HIS C 778 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 784 " --> pdb=" O ASN C 780 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN C 785 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 786 " --> pdb=" O TYR C 782 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 787 " --> pdb=" O ILE C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 801 removed outlier: 3.509A pdb=" N GLU C 800 " --> pdb=" O GLU C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 851 removed outlier: 3.673A pdb=" N GLN C 832 " --> pdb=" O THR C 828 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 841 " --> pdb=" O GLY C 837 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 842 " --> pdb=" O GLU C 838 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 848 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 869 removed outlier: 3.868A pdb=" N LEU C 859 " --> pdb=" O ASN C 855 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 860 " --> pdb=" O GLN C 856 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 866 " --> pdb=" O SER C 862 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 867 " --> pdb=" O ASN C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 removed outlier: 3.588A pdb=" N LEU D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 209 removed outlier: 4.562A pdb=" N LEU D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 196 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL D 205 " --> pdb=" O GLN D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 242 removed outlier: 3.996A pdb=" N TYR D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN D 238 " --> pdb=" O ASN D 234 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 255 removed outlier: 3.636A pdb=" N TYR D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 253 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 269 removed outlier: 3.838A pdb=" N PHE D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 4.239A pdb=" N LEU D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 301 removed outlier: 3.612A pdb=" N THR D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 removed outlier: 4.230A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 313 " --> pdb=" O TYR D 309 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS D 315 " --> pdb=" O ASN D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 351 Processing helix chain 'D' and resid 361 through 371 removed outlier: 4.603A pdb=" N THR D 367 " --> pdb=" O GLN D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 389 removed outlier: 3.662A pdb=" N SER D 389 " --> pdb=" O ASN D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 403 through 423 removed outlier: 3.505A pdb=" N SER D 413 " --> pdb=" O LYS D 409 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU D 417 " --> pdb=" O SER D 413 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.892A pdb=" N PHE D 442 " --> pdb=" O ASN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 457 removed outlier: 3.913A pdb=" N ILE D 451 " --> pdb=" O THR D 447 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET D 455 " --> pdb=" O ILE D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 486 through 489 removed outlier: 3.761A pdb=" N ASN D 489 " --> pdb=" O SER D 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 486 through 489' Processing helix chain 'D' and resid 529 through 532 Processing helix chain 'D' and resid 533 through 552 removed outlier: 3.767A pdb=" N MET D 539 " --> pdb=" O GLN D 535 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 546 " --> pdb=" O PHE D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 567 removed outlier: 4.117A pdb=" N GLU D 562 " --> pdb=" O GLU D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 571 removed outlier: 3.522A pdb=" N LEU D 571 " --> pdb=" O VAL D 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 568 through 571' Processing helix chain 'D' and resid 575 through 605 removed outlier: 3.687A pdb=" N LEU D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS D 581 " --> pdb=" O ARG D 577 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 586 " --> pdb=" O SER D 582 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE D 596 " --> pdb=" O HIS D 592 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN D 598 " --> pdb=" O THR D 594 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 599 " --> pdb=" O GLN D 595 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 602 " --> pdb=" O ASN D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 617 removed outlier: 3.622A pdb=" N ASN D 612 " --> pdb=" O VAL D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 623 Processing helix chain 'D' and resid 657 through 674 removed outlier: 3.878A pdb=" N GLU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS D 665 " --> pdb=" O LEU D 661 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 672 " --> pdb=" O TYR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 708 removed outlier: 3.627A pdb=" N ASN D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 725 removed outlier: 3.584A pdb=" N LEU D 715 " --> pdb=" O GLU D 711 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 717 " --> pdb=" O TYR D 713 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR D 718 " --> pdb=" O SER D 714 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 721 " --> pdb=" O VAL D 717 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL D 723 " --> pdb=" O PHE D 719 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 724 " --> pdb=" O GLY D 720 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER D 725 " --> pdb=" O LEU D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 768 removed outlier: 3.520A pdb=" N LYS D 749 " --> pdb=" O LEU D 745 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG D 750 " --> pdb=" O HIS D 746 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR D 757 " --> pdb=" O TYR D 753 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 765 " --> pdb=" O TYR D 761 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN D 766 " --> pdb=" O LYS D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 773 removed outlier: 3.795A pdb=" N ASN D 773 " --> pdb=" O LYS D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 784 removed outlier: 3.664A pdb=" N LYS D 783 " --> pdb=" O ASP D 780 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 784 " --> pdb=" O LEU D 781 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 118 through 119 removed outlier: 8.130A pdb=" N HIS B 119 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 95 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU B 4 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLN B 163 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 6 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE B 165 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 8 " --> pdb=" O PHE B 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.571A pdb=" N THR B 90 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 199 through 200 removed outlier: 4.702A pdb=" N SER B 306 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N HIS B 234 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 11.364A pdb=" N ILE B 308 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 383 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.886A pdb=" N GLU A 4 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLN A 163 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 6 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N PHE A 165 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 8 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER A 306 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N HIS A 234 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 11.121A pdb=" N ILE A 308 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE A 303 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN A 406 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 401 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN A 349 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A 403 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET A 347 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN A 405 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 383 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.878A pdb=" N THR A 90 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 334 through 335 removed outlier: 3.617A pdb=" N LEU C 359 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 331 through 332 removed outlier: 3.884A pdb=" N ILE D 332 " --> pdb=" O LYS D 345 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS D 345 " --> pdb=" O ILE D 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 496 through 500 removed outlier: 3.647A pdb=" N ARG D 499 " --> pdb=" O THR D 514 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5336 1.34 - 1.46: 3965 1.46 - 1.58: 7683 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 17082 Sorted by residual: bond pdb=" N CYS C 868 " pdb=" CA CYS C 868 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.45e+00 bond pdb=" N THR C 685 " pdb=" CA THR C 685 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.41e+00 bond pdb=" N ASP D 647 " pdb=" CA ASP D 647 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.54e+00 bond pdb=" N LEU D 522 " pdb=" CA LEU D 522 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" C LEU C 867 " pdb=" N CYS C 868 " ideal model delta sigma weight residual 1.332 1.355 -0.022 1.40e-02 5.10e+03 2.51e+00 ... (remaining 17077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 22636 2.37 - 4.74: 341 4.74 - 7.10: 61 7.10 - 9.47: 15 9.47 - 11.84: 9 Bond angle restraints: 23062 Sorted by residual: angle pdb=" C ASN D 626 " pdb=" N ASP D 627 " pdb=" CA ASP D 627 " ideal model delta sigma weight residual 121.70 131.97 -10.27 1.80e+00 3.09e-01 3.26e+01 angle pdb=" C ASP D 521 " pdb=" N LEU D 522 " pdb=" CA LEU D 522 " ideal model delta sigma weight residual 121.70 131.78 -10.08 1.80e+00 3.09e-01 3.14e+01 angle pdb=" N ILE B 44 " pdb=" CA ILE B 44 " pdb=" C ILE B 44 " ideal model delta sigma weight residual 111.91 106.97 4.94 8.90e-01 1.26e+00 3.08e+01 angle pdb=" C SER D 525 " pdb=" N TYR D 526 " pdb=" CA TYR D 526 " ideal model delta sigma weight residual 121.70 130.64 -8.94 1.80e+00 3.09e-01 2.47e+01 angle pdb=" N PHE D 636 " pdb=" CA PHE D 636 " pdb=" C PHE D 636 " ideal model delta sigma weight residual 114.75 108.49 6.26 1.26e+00 6.30e-01 2.46e+01 ... (remaining 23057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 8993 17.78 - 35.55: 1006 35.55 - 53.33: 212 53.33 - 71.11: 44 71.11 - 88.88: 20 Dihedral angle restraints: 10275 sinusoidal: 4241 harmonic: 6034 Sorted by residual: dihedral pdb=" CA ILE D 343 " pdb=" C ILE D 343 " pdb=" N ILE D 344 " pdb=" CA ILE D 344 " ideal model delta harmonic sigma weight residual -180.00 -138.21 -41.79 0 5.00e+00 4.00e-02 6.99e+01 dihedral pdb=" CA PHE D 329 " pdb=" C PHE D 329 " pdb=" N PHE D 330 " pdb=" CA PHE D 330 " ideal model delta harmonic sigma weight residual 180.00 -145.97 -34.03 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA ILE D 425 " pdb=" C ILE D 425 " pdb=" N ILE D 426 " pdb=" CA ILE D 426 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 ... (remaining 10272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2061 0.054 - 0.107: 464 0.107 - 0.161: 60 0.161 - 0.214: 10 0.214 - 0.268: 4 Chirality restraints: 2599 Sorted by residual: chirality pdb=" CB ILE C 107 " pdb=" CA ILE C 107 " pdb=" CG1 ILE C 107 " pdb=" CG2 ILE C 107 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE C 324 " pdb=" CA ILE C 324 " pdb=" CG1 ILE C 324 " pdb=" CG2 ILE C 324 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB THR C 408 " pdb=" CA THR C 408 " pdb=" OG1 THR C 408 " pdb=" CG2 THR C 408 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2596 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 867 " -0.031 2.00e-02 2.50e+03 6.01e-02 3.62e+01 pdb=" C LEU C 867 " 0.104 2.00e-02 2.50e+03 pdb=" O LEU C 867 " -0.039 2.00e-02 2.50e+03 pdb=" N CYS C 868 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 684 " -0.029 2.00e-02 2.50e+03 5.65e-02 3.20e+01 pdb=" C THR C 684 " 0.098 2.00e-02 2.50e+03 pdb=" O THR C 684 " -0.036 2.00e-02 2.50e+03 pdb=" N THR C 685 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 869 " -0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO C 870 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 870 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 870 " -0.045 5.00e-02 4.00e+02 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4750 2.80 - 3.33: 14918 3.33 - 3.85: 26469 3.85 - 4.38: 31679 4.38 - 4.90: 52932 Nonbonded interactions: 130748 Sorted by model distance: nonbonded pdb=" OG1 THR A 82 " pdb=" OG1 THR A 90 " model vdw 2.277 3.040 nonbonded pdb=" O LYS C 377 " pdb=" OG1 THR C 381 " model vdw 2.282 3.040 nonbonded pdb=" O LEU A 181 " pdb=" OG SER A 185 " model vdw 2.284 3.040 nonbonded pdb=" O HIS D 396 " pdb=" OG SER D 401 " model vdw 2.287 3.040 nonbonded pdb=" O TYR D 277 " pdb=" OG1 THR D 281 " model vdw 2.289 3.040 ... (remaining 130743 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 2 through 471) selection = (chain 'B' and (resid 2 through 42 or resid 72 through 471)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.630 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.003 0.043 17082 Z= 0.159 Angle : 0.775 11.841 23062 Z= 0.410 Chirality : 0.046 0.268 2599 Planarity : 0.005 0.080 2919 Dihedral : 15.891 88.882 6353 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.49 % Favored : 93.36 % Rotamer: Outliers : 0.31 % Allowed : 7.23 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.88 (0.12), residues: 1989 helix: -4.51 (0.05), residues: 1082 sheet: -1.96 (0.46), residues: 109 loop : -3.01 (0.18), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 92 TYR 0.022 0.001 TYR C 109 PHE 0.026 0.001 PHE D 636 TRP 0.008 0.001 TRP B 377 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00326 (17082) covalent geometry : angle 0.77527 (23062) hydrogen bonds : bond 0.33423 ( 671) hydrogen bonds : angle 10.07487 ( 1974) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 449 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7463 (tt0) cc_final: 0.6928 (mt-10) REVERT: B 135 TYR cc_start: 0.7828 (t80) cc_final: 0.7414 (t80) REVERT: B 137 TYR cc_start: 0.7911 (t80) cc_final: 0.7303 (t80) REVERT: B 159 LEU cc_start: 0.7572 (tp) cc_final: 0.7360 (tp) REVERT: B 241 ILE cc_start: 0.8206 (mm) cc_final: 0.8006 (mt) REVERT: B 409 MET cc_start: 0.7200 (mmm) cc_final: 0.6991 (mmm) REVERT: A 156 CYS cc_start: 0.6433 (m) cc_final: 0.6032 (m) REVERT: A 289 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6976 (mm-30) REVERT: A 355 ASN cc_start: 0.6429 (p0) cc_final: 0.6195 (p0) REVERT: A 441 ASN cc_start: 0.6812 (p0) cc_final: 0.6549 (p0) REVERT: C 99 LEU cc_start: 0.7724 (pt) cc_final: 0.7408 (pp) REVERT: C 365 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7286 (mm) REVERT: C 374 ILE cc_start: 0.8444 (tp) cc_final: 0.8077 (tt) REVERT: C 761 THR cc_start: 0.7936 (m) cc_final: 0.7662 (m) REVERT: C 844 LEU cc_start: 0.8213 (mt) cc_final: 0.7881 (mt) REVERT: D 202 LEU cc_start: 0.8338 (tp) cc_final: 0.8115 (tt) REVERT: D 356 LYS cc_start: 0.6438 (tppt) cc_final: 0.6237 (tppt) REVERT: D 375 CYS cc_start: 0.6877 (t) cc_final: 0.6520 (t) REVERT: D 424 GLN cc_start: 0.7575 (tp40) cc_final: 0.7252 (tt0) REVERT: D 445 MET cc_start: 0.8106 (mmt) cc_final: 0.7607 (mmt) REVERT: D 780 ASP cc_start: 0.5428 (p0) cc_final: 0.5096 (p0) REVERT: D 781 LEU cc_start: 0.8158 (tp) cc_final: 0.7957 (tp) outliers start: 6 outliers final: 1 residues processed: 455 average time/residue: 0.1405 time to fit residues: 92.3071 Evaluate side-chains 329 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 365 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN B 117 ASN B 195 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN A 16 GLN A 264 ASN A 294 ASN A 419 GLN C 159 GLN C 185 GLN C 200 ASN C 202 ASN C 223 GLN C 375 GLN C 483 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 HIS C 652 HIS C 660 HIS C 742 GLN D 234 ASN D 237 ASN D 252 ASN D 272 ASN D 341 ASN ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 ASN D 700 GLN D 766 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.157909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.130134 restraints weight = 26796.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.132120 restraints weight = 17911.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.132925 restraints weight = 15433.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.134330 restraints weight = 12379.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.134496 restraints weight = 10495.113| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17082 Z= 0.138 Angle : 0.631 9.416 23062 Z= 0.327 Chirality : 0.041 0.175 2599 Planarity : 0.004 0.065 2919 Dihedral : 4.940 43.510 2192 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.57 % Allowed : 14.08 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.15), residues: 1989 helix: -2.29 (0.12), residues: 1113 sheet: -1.54 (0.45), residues: 120 loop : -2.72 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 380 TYR 0.016 0.001 TYR A 226 PHE 0.023 0.002 PHE C 829 TRP 0.011 0.001 TRP D 544 HIS 0.004 0.001 HIS D 556 Details of bonding type rmsd covalent geometry : bond 0.00306 (17082) covalent geometry : angle 0.63068 (23062) hydrogen bonds : bond 0.05202 ( 671) hydrogen bonds : angle 5.05510 ( 1974) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 359 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 ILE cc_start: 0.6189 (OUTLIER) cc_final: 0.5630 (pt) REVERT: B 99 GLU cc_start: 0.7703 (pm20) cc_final: 0.7426 (pm20) REVERT: B 135 TYR cc_start: 0.7417 (t80) cc_final: 0.7107 (t80) REVERT: B 154 ASP cc_start: 0.5992 (m-30) cc_final: 0.5603 (m-30) REVERT: B 224 ILE cc_start: 0.8562 (pt) cc_final: 0.8252 (tt) REVERT: B 288 MET cc_start: 0.8598 (tpp) cc_final: 0.8338 (mtp) REVERT: B 380 ARG cc_start: 0.6162 (mtm-85) cc_final: 0.5849 (mtp85) REVERT: B 409 MET cc_start: 0.7481 (mmm) cc_final: 0.7035 (mmm) REVERT: A 97 ASP cc_start: 0.7677 (t70) cc_final: 0.7392 (t70) REVERT: A 99 GLU cc_start: 0.8033 (mp0) cc_final: 0.7727 (mm-30) REVERT: A 289 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7071 (mm-30) REVERT: A 367 LYS cc_start: 0.8461 (tppt) cc_final: 0.7893 (tptp) REVERT: A 441 ASN cc_start: 0.7387 (p0) cc_final: 0.7087 (p0) REVERT: A 458 ILE cc_start: 0.8660 (mm) cc_final: 0.8444 (mt) REVERT: C 180 PHE cc_start: 0.8457 (t80) cc_final: 0.8237 (t80) REVERT: C 192 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7591 (tm-30) REVERT: C 212 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7231 (tm-30) REVERT: C 361 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7625 (mtpt) REVERT: C 844 LEU cc_start: 0.8146 (mt) cc_final: 0.7936 (mt) REVERT: C 849 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 850 VAL cc_start: 0.8930 (m) cc_final: 0.8490 (t) REVERT: D 424 GLN cc_start: 0.8056 (tp40) cc_final: 0.7394 (tt0) REVERT: D 445 MET cc_start: 0.8066 (mmt) cc_final: 0.7436 (mmt) REVERT: D 452 ASP cc_start: 0.6299 (t0) cc_final: 0.5994 (t0) REVERT: D 550 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8204 (t0) REVERT: D 706 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7499 (tp) REVERT: D 711 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: D 722 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8693 (tt) REVERT: D 750 ARG cc_start: 0.7094 (tpp80) cc_final: 0.6712 (tpp80) outliers start: 49 outliers final: 28 residues processed: 385 average time/residue: 0.1201 time to fit residues: 70.9225 Evaluate side-chains 332 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 711 GLU Chi-restraints excluded: chain D residue 722 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 202 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 0.0070 overall best weight: 0.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN B 45 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN C 185 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 427 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.155463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.127790 restraints weight = 27159.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129334 restraints weight = 17535.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130120 restraints weight = 14205.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.131833 restraints weight = 12075.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.131928 restraints weight = 10931.326| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17082 Z= 0.148 Angle : 0.607 10.248 23062 Z= 0.309 Chirality : 0.041 0.187 2599 Planarity : 0.004 0.061 2919 Dihedral : 4.783 49.124 2190 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.35 % Allowed : 16.81 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.60 (0.17), residues: 1989 helix: -1.15 (0.14), residues: 1124 sheet: -1.43 (0.46), residues: 116 loop : -2.54 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 451 TYR 0.023 0.001 TYR A 226 PHE 0.029 0.002 PHE D 513 TRP 0.010 0.001 TRP C 318 HIS 0.011 0.001 HIS D 759 Details of bonding type rmsd covalent geometry : bond 0.00348 (17082) covalent geometry : angle 0.60673 (23062) hydrogen bonds : bond 0.04297 ( 671) hydrogen bonds : angle 4.58953 ( 1974) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 322 time to evaluate : 0.598 Fit side-chains REVERT: B 95 LEU cc_start: 0.8614 (mt) cc_final: 0.8215 (mt) REVERT: B 135 TYR cc_start: 0.7426 (t80) cc_final: 0.7120 (t80) REVERT: B 154 ASP cc_start: 0.5968 (m-30) cc_final: 0.5479 (m-30) REVERT: B 224 ILE cc_start: 0.8502 (pt) cc_final: 0.8249 (tt) REVERT: B 288 MET cc_start: 0.8716 (tpp) cc_final: 0.8359 (mtp) REVERT: B 354 TYR cc_start: 0.6145 (p90) cc_final: 0.5926 (p90) REVERT: B 355 ASN cc_start: 0.7649 (p0) cc_final: 0.7275 (p0) REVERT: A 99 GLU cc_start: 0.7979 (mp0) cc_final: 0.7685 (mm-30) REVERT: A 186 ASP cc_start: 0.6157 (p0) cc_final: 0.5868 (p0) REVERT: A 228 ASP cc_start: 0.7524 (m-30) cc_final: 0.6890 (m-30) REVERT: A 289 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7050 (mm-30) REVERT: A 367 LYS cc_start: 0.8396 (tppt) cc_final: 0.7874 (tptp) REVERT: A 458 ILE cc_start: 0.8845 (mm) cc_final: 0.8601 (mt) REVERT: C 192 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 212 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7237 (tm-30) REVERT: C 844 LEU cc_start: 0.8191 (mt) cc_final: 0.7969 (mt) REVERT: D 424 GLN cc_start: 0.8091 (tp40) cc_final: 0.7470 (tt0) REVERT: D 445 MET cc_start: 0.8155 (mmt) cc_final: 0.7470 (mmm) REVERT: D 452 ASP cc_start: 0.6145 (t0) cc_final: 0.5854 (t0) REVERT: D 706 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7446 (tp) REVERT: D 750 ARG cc_start: 0.7034 (tpp80) cc_final: 0.6727 (tpp80) outliers start: 64 outliers final: 42 residues processed: 359 average time/residue: 0.1172 time to fit residues: 65.1503 Evaluate side-chains 332 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 868 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 744 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 164 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN B 161 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN A 16 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.156093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.127499 restraints weight = 26744.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.130281 restraints weight = 17530.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.131221 restraints weight = 13738.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.131818 restraints weight = 11956.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.132019 restraints weight = 11142.653| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17082 Z= 0.130 Angle : 0.581 9.509 23062 Z= 0.296 Chirality : 0.041 0.179 2599 Planarity : 0.003 0.055 2919 Dihedral : 4.695 55.182 2190 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.19 % Allowed : 18.59 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.93 (0.18), residues: 1989 helix: -0.52 (0.15), residues: 1126 sheet: -1.55 (0.42), residues: 130 loop : -2.34 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 222 TYR 0.022 0.001 TYR D 536 PHE 0.020 0.001 PHE D 513 TRP 0.015 0.001 TRP D 544 HIS 0.011 0.001 HIS D 759 Details of bonding type rmsd covalent geometry : bond 0.00302 (17082) covalent geometry : angle 0.58146 (23062) hydrogen bonds : bond 0.03726 ( 671) hydrogen bonds : angle 4.33089 ( 1974) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 317 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 ILE cc_start: 0.6434 (OUTLIER) cc_final: 0.5835 (pt) REVERT: B 95 LEU cc_start: 0.8654 (mt) cc_final: 0.8305 (mt) REVERT: B 135 TYR cc_start: 0.7476 (t80) cc_final: 0.7135 (t80) REVERT: B 224 ILE cc_start: 0.8483 (pt) cc_final: 0.8221 (tt) REVERT: B 288 MET cc_start: 0.8674 (tpp) cc_final: 0.8372 (mtp) REVERT: B 355 ASN cc_start: 0.7703 (p0) cc_final: 0.7423 (p0) REVERT: A 4 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 228 ASP cc_start: 0.7593 (m-30) cc_final: 0.7000 (m-30) REVERT: A 289 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7070 (mm-30) REVERT: A 367 LYS cc_start: 0.8312 (tppt) cc_final: 0.7853 (tptp) REVERT: C 192 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7656 (tm-30) REVERT: C 212 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7253 (tm-30) REVERT: C 218 MET cc_start: 0.7675 (tpt) cc_final: 0.6844 (tpt) REVERT: C 591 ASN cc_start: 0.8083 (p0) cc_final: 0.7734 (p0) REVERT: C 844 LEU cc_start: 0.8203 (mt) cc_final: 0.7983 (mt) REVERT: D 424 GLN cc_start: 0.8133 (tp40) cc_final: 0.7459 (tt0) REVERT: D 445 MET cc_start: 0.8083 (mmt) cc_final: 0.7363 (mmm) REVERT: D 452 ASP cc_start: 0.6066 (t0) cc_final: 0.5828 (t0) REVERT: D 536 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7079 (t80) REVERT: D 706 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7428 (tp) outliers start: 61 outliers final: 41 residues processed: 357 average time/residue: 0.1157 time to fit residues: 65.3512 Evaluate side-chains 327 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 868 CYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 721 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 52 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 186 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN B 212 GLN B 294 ASN A 16 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 634 ASN C 794 ASN D 238 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.154082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124847 restraints weight = 26793.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.127613 restraints weight = 17852.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.129489 restraints weight = 13645.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.130142 restraints weight = 12294.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130426 restraints weight = 10769.589| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17082 Z= 0.150 Angle : 0.609 9.411 23062 Z= 0.309 Chirality : 0.042 0.215 2599 Planarity : 0.003 0.053 2919 Dihedral : 4.587 38.496 2188 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.77 % Allowed : 19.58 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.18), residues: 1989 helix: -0.15 (0.15), residues: 1116 sheet: -1.43 (0.42), residues: 134 loop : -2.32 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 750 TYR 0.026 0.001 TYR D 536 PHE 0.016 0.001 PHE C 457 TRP 0.018 0.001 TRP C 318 HIS 0.010 0.001 HIS D 759 Details of bonding type rmsd covalent geometry : bond 0.00358 (17082) covalent geometry : angle 0.60928 (23062) hydrogen bonds : bond 0.03707 ( 671) hydrogen bonds : angle 4.30026 ( 1974) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 312 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6398 (mt) REVERT: B 95 LEU cc_start: 0.8686 (mt) cc_final: 0.8357 (mt) REVERT: B 135 TYR cc_start: 0.7485 (t80) cc_final: 0.7079 (t80) REVERT: B 288 MET cc_start: 0.8758 (tpp) cc_final: 0.8404 (mtp) REVERT: B 355 ASN cc_start: 0.7686 (p0) cc_final: 0.7447 (p0) REVERT: A 89 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7476 (m-10) REVERT: A 367 LYS cc_start: 0.8304 (tppt) cc_final: 0.7841 (tptp) REVERT: C 192 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 212 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7441 (tm-30) REVERT: C 591 ASN cc_start: 0.8219 (p0) cc_final: 0.7958 (p0) REVERT: C 782 TYR cc_start: 0.7787 (t80) cc_final: 0.7577 (t80) REVERT: C 844 LEU cc_start: 0.8202 (mt) cc_final: 0.7941 (mt) REVERT: D 328 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6491 (tt0) REVERT: D 424 GLN cc_start: 0.8147 (tp40) cc_final: 0.7422 (tt0) REVERT: D 452 ASP cc_start: 0.6407 (t0) cc_final: 0.6057 (t0) REVERT: D 455 MET cc_start: 0.7553 (mtp) cc_final: 0.7326 (mtm) REVERT: D 536 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7367 (t80) REVERT: D 706 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7427 (tp) outliers start: 72 outliers final: 50 residues processed: 357 average time/residue: 0.1140 time to fit residues: 64.1714 Evaluate side-chains 345 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 868 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 722 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 1 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 51 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN B 294 ASN A 16 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS D 238 ASN D 252 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.155673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.127300 restraints weight = 26919.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129584 restraints weight = 18350.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.130389 restraints weight = 14874.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.130797 restraints weight = 12648.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.132037 restraints weight = 11784.681| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17082 Z= 0.119 Angle : 0.586 9.345 23062 Z= 0.297 Chirality : 0.041 0.218 2599 Planarity : 0.003 0.050 2919 Dihedral : 4.483 39.049 2188 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.66 % Allowed : 20.42 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.28 (0.19), residues: 1989 helix: 0.14 (0.16), residues: 1117 sheet: -1.39 (0.43), residues: 132 loop : -2.26 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 750 TYR 0.018 0.001 TYR D 536 PHE 0.014 0.001 PHE D 513 TRP 0.016 0.001 TRP C 318 HIS 0.011 0.001 HIS D 759 Details of bonding type rmsd covalent geometry : bond 0.00276 (17082) covalent geometry : angle 0.58560 (23062) hydrogen bonds : bond 0.03399 ( 671) hydrogen bonds : angle 4.17795 ( 1974) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 314 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6368 (mt) REVERT: B 95 LEU cc_start: 0.8707 (mt) cc_final: 0.8362 (mt) REVERT: B 129 ASN cc_start: 0.8053 (m-40) cc_final: 0.7497 (t0) REVERT: B 135 TYR cc_start: 0.7457 (t80) cc_final: 0.7068 (t80) REVERT: B 288 MET cc_start: 0.8717 (tpp) cc_final: 0.8340 (mtp) REVERT: B 355 ASN cc_start: 0.7656 (p0) cc_final: 0.7436 (p0) REVERT: B 404 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8223 (p) REVERT: A 89 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: A 228 ASP cc_start: 0.7395 (m-30) cc_final: 0.6609 (m-30) REVERT: A 367 LYS cc_start: 0.8238 (tppt) cc_final: 0.7915 (tptp) REVERT: C 192 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7801 (tm-30) REVERT: C 212 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7379 (tm-30) REVERT: C 266 LEU cc_start: 0.6697 (mm) cc_final: 0.6433 (mm) REVERT: C 591 ASN cc_start: 0.8112 (p0) cc_final: 0.7805 (p0) REVERT: C 844 LEU cc_start: 0.8149 (mt) cc_final: 0.7870 (mt) REVERT: C 852 GLU cc_start: 0.7705 (pp20) cc_final: 0.7409 (pp20) REVERT: D 424 GLN cc_start: 0.8062 (tp40) cc_final: 0.7420 (tt0) REVERT: D 452 ASP cc_start: 0.6238 (t0) cc_final: 0.5949 (t0) REVERT: D 536 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7247 (t80) REVERT: D 706 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7566 (tp) outliers start: 70 outliers final: 50 residues processed: 354 average time/residue: 0.1136 time to fit residues: 63.5724 Evaluate side-chains 350 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 868 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 722 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 166 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 57 optimal weight: 0.0980 chunk 149 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN B 163 GLN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN A 16 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN D 238 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.156382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127485 restraints weight = 26794.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130000 restraints weight = 18777.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.130694 restraints weight = 14945.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.131648 restraints weight = 12942.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131733 restraints weight = 12150.638| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17082 Z= 0.119 Angle : 0.592 9.913 23062 Z= 0.300 Chirality : 0.041 0.211 2599 Planarity : 0.003 0.048 2919 Dihedral : 4.433 37.084 2188 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.46 % Allowed : 21.47 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.06 (0.19), residues: 1989 helix: 0.31 (0.16), residues: 1117 sheet: -1.20 (0.43), residues: 134 loop : -2.18 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 750 TYR 0.035 0.001 TYR C 782 PHE 0.020 0.001 PHE D 705 TRP 0.020 0.001 TRP C 318 HIS 0.011 0.001 HIS D 759 Details of bonding type rmsd covalent geometry : bond 0.00274 (17082) covalent geometry : angle 0.59181 (23062) hydrogen bonds : bond 0.03316 ( 671) hydrogen bonds : angle 4.13757 ( 1974) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 303 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6215 (pt) REVERT: B 95 LEU cc_start: 0.8703 (mt) cc_final: 0.8369 (mt) REVERT: B 129 ASN cc_start: 0.8078 (m-40) cc_final: 0.7527 (t0) REVERT: B 135 TYR cc_start: 0.7358 (t80) cc_final: 0.6950 (t80) REVERT: B 288 MET cc_start: 0.8697 (tpp) cc_final: 0.8237 (mtp) REVERT: A 89 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7379 (m-10) REVERT: A 186 ASP cc_start: 0.6535 (p0) cc_final: 0.6226 (p0) REVERT: A 367 LYS cc_start: 0.8256 (tppt) cc_final: 0.7974 (tptp) REVERT: C 192 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7935 (tm-30) REVERT: C 212 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 266 LEU cc_start: 0.6776 (mm) cc_final: 0.6568 (mm) REVERT: C 591 ASN cc_start: 0.8080 (p0) cc_final: 0.7796 (p0) REVERT: C 844 LEU cc_start: 0.8073 (mt) cc_final: 0.7812 (mt) REVERT: D 424 GLN cc_start: 0.8062 (tp40) cc_final: 0.7472 (tt0) REVERT: D 445 MET cc_start: 0.8211 (mmm) cc_final: 0.7771 (mmm) REVERT: D 452 ASP cc_start: 0.5940 (t0) cc_final: 0.5611 (t0) REVERT: D 536 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7193 (t80) outliers start: 66 outliers final: 47 residues processed: 347 average time/residue: 0.1128 time to fit residues: 61.4723 Evaluate side-chains 339 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 868 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 722 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 154 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 182 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN A 16 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN C 619 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 ASN C 832 GLN D 238 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN D 758 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.154743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.125985 restraints weight = 26886.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.128077 restraints weight = 18073.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.129042 restraints weight = 14458.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.129673 restraints weight = 12916.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129960 restraints weight = 11604.244| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17082 Z= 0.142 Angle : 0.624 12.445 23062 Z= 0.315 Chirality : 0.042 0.220 2599 Planarity : 0.003 0.047 2919 Dihedral : 4.483 37.142 2188 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.61 % Allowed : 21.68 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.96 (0.19), residues: 1989 helix: 0.39 (0.16), residues: 1119 sheet: -1.02 (0.44), residues: 136 loop : -2.17 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 750 TYR 0.039 0.001 TYR C 782 PHE 0.022 0.001 PHE D 636 TRP 0.019 0.001 TRP C 318 HIS 0.011 0.001 HIS D 759 Details of bonding type rmsd covalent geometry : bond 0.00336 (17082) covalent geometry : angle 0.62389 (23062) hydrogen bonds : bond 0.03457 ( 671) hydrogen bonds : angle 4.16355 ( 1974) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 303 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6353 (mt) REVERT: B 95 LEU cc_start: 0.8710 (mt) cc_final: 0.8382 (mt) REVERT: B 129 ASN cc_start: 0.8047 (m-40) cc_final: 0.7541 (t0) REVERT: B 135 TYR cc_start: 0.7407 (t80) cc_final: 0.6989 (t80) REVERT: B 323 ASP cc_start: 0.6457 (p0) cc_final: 0.5936 (p0) REVERT: A 89 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7417 (m-10) REVERT: A 367 LYS cc_start: 0.8298 (tppt) cc_final: 0.7977 (tptp) REVERT: C 186 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8178 (tp-100) REVERT: C 192 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7880 (tm-30) REVERT: C 212 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 591 ASN cc_start: 0.8026 (p0) cc_final: 0.7788 (p0) REVERT: C 737 ILE cc_start: 0.6985 (pt) cc_final: 0.6764 (pt) REVERT: C 844 LEU cc_start: 0.8100 (mt) cc_final: 0.7815 (mt) REVERT: D 424 GLN cc_start: 0.8153 (tp40) cc_final: 0.7532 (tt0) REVERT: D 445 MET cc_start: 0.8193 (mmm) cc_final: 0.7693 (mmm) REVERT: D 452 ASP cc_start: 0.6250 (t0) cc_final: 0.5994 (t0) REVERT: D 536 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7400 (t80) outliers start: 69 outliers final: 50 residues processed: 345 average time/residue: 0.1127 time to fit residues: 61.9142 Evaluate side-chains 344 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 291 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 868 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 700 GLN Chi-restraints excluded: chain D residue 722 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 43 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 202 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN B 294 ASN A 16 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN D 385 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 598 ASN D 700 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.155913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.126774 restraints weight = 26778.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.129455 restraints weight = 18603.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.130320 restraints weight = 14797.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.130867 restraints weight = 12559.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.131260 restraints weight = 11640.598| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17082 Z= 0.131 Angle : 0.625 12.167 23062 Z= 0.315 Chirality : 0.042 0.225 2599 Planarity : 0.003 0.046 2919 Dihedral : 4.465 36.990 2188 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.14 % Allowed : 22.77 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.84 (0.19), residues: 1989 helix: 0.52 (0.16), residues: 1115 sheet: -0.92 (0.44), residues: 136 loop : -2.16 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 750 TYR 0.040 0.001 TYR C 782 PHE 0.017 0.001 PHE C 457 TRP 0.015 0.001 TRP C 318 HIS 0.011 0.001 HIS D 759 Details of bonding type rmsd covalent geometry : bond 0.00307 (17082) covalent geometry : angle 0.62513 (23062) hydrogen bonds : bond 0.03359 ( 671) hydrogen bonds : angle 4.14211 ( 1974) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 297 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 LEU cc_start: 0.8705 (mt) cc_final: 0.8373 (mt) REVERT: B 112 MET cc_start: 0.7996 (ptt) cc_final: 0.7740 (ptt) REVERT: B 129 ASN cc_start: 0.8018 (m-40) cc_final: 0.7579 (t0) REVERT: B 135 TYR cc_start: 0.7406 (t80) cc_final: 0.6976 (t80) REVERT: B 222 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7414 (mpp80) REVERT: B 323 ASP cc_start: 0.6476 (p0) cc_final: 0.5933 (p0) REVERT: A 89 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7441 (m-10) REVERT: A 367 LYS cc_start: 0.8278 (tppt) cc_final: 0.7951 (tptp) REVERT: C 186 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8194 (tp-100) REVERT: C 192 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7948 (tm-30) REVERT: C 212 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7441 (tm-30) REVERT: C 266 LEU cc_start: 0.6782 (mm) cc_final: 0.6503 (mm) REVERT: C 591 ASN cc_start: 0.8090 (p0) cc_final: 0.7837 (p0) REVERT: C 844 LEU cc_start: 0.8079 (mt) cc_final: 0.7801 (mt) REVERT: D 424 GLN cc_start: 0.8167 (tp40) cc_final: 0.7570 (tt0) REVERT: D 445 MET cc_start: 0.8134 (mmm) cc_final: 0.7664 (mmm) REVERT: D 490 PHE cc_start: 0.7017 (p90) cc_final: 0.6809 (p90) REVERT: D 536 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7372 (t80) outliers start: 60 outliers final: 48 residues processed: 332 average time/residue: 0.1169 time to fit residues: 60.9124 Evaluate side-chains 336 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 285 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 868 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 700 GLN Chi-restraints excluded: chain D residue 722 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 61 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 176 optimal weight: 0.4980 chunk 197 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN B 294 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 612 ASN D 700 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.153770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.125539 restraints weight = 26784.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126352 restraints weight = 19181.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.127046 restraints weight = 17411.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.128231 restraints weight = 14131.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128157 restraints weight = 13396.630| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17082 Z= 0.174 Angle : 0.662 11.177 23062 Z= 0.334 Chirality : 0.044 0.242 2599 Planarity : 0.003 0.046 2919 Dihedral : 4.623 37.421 2188 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.40 % Allowed : 22.83 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.91 (0.19), residues: 1989 helix: 0.45 (0.16), residues: 1117 sheet: -0.85 (0.45), residues: 131 loop : -2.20 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 750 TYR 0.041 0.002 TYR C 782 PHE 0.018 0.002 PHE C 798 TRP 0.036 0.002 TRP C 318 HIS 0.011 0.001 HIS D 759 Details of bonding type rmsd covalent geometry : bond 0.00423 (17082) covalent geometry : angle 0.66209 (23062) hydrogen bonds : bond 0.03699 ( 671) hydrogen bonds : angle 4.27397 ( 1974) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 288 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 LEU cc_start: 0.8713 (mt) cc_final: 0.8428 (mp) REVERT: B 129 ASN cc_start: 0.8010 (m-40) cc_final: 0.7614 (t0) REVERT: B 135 TYR cc_start: 0.7417 (t80) cc_final: 0.6985 (t80) REVERT: B 222 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7377 (mpp80) REVERT: B 323 ASP cc_start: 0.6543 (p0) cc_final: 0.6019 (p0) REVERT: B 385 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7861 (p) REVERT: A 89 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7472 (m-10) REVERT: A 182 GLU cc_start: 0.7488 (tp30) cc_final: 0.7225 (tp30) REVERT: A 367 LYS cc_start: 0.8326 (tppt) cc_final: 0.7974 (tptp) REVERT: C 186 GLN cc_start: 0.8549 (tp-100) cc_final: 0.8216 (tp-100) REVERT: C 192 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 212 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7498 (tm-30) REVERT: C 844 LEU cc_start: 0.8102 (mt) cc_final: 0.7814 (mt) REVERT: D 397 GLN cc_start: 0.8421 (pt0) cc_final: 0.8151 (pt0) REVERT: D 424 GLN cc_start: 0.8261 (tp40) cc_final: 0.7665 (tt0) REVERT: D 536 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7587 (t80) REVERT: D 591 PHE cc_start: 0.7978 (t80) cc_final: 0.7746 (t80) outliers start: 65 outliers final: 49 residues processed: 329 average time/residue: 0.1131 time to fit residues: 58.2433 Evaluate side-chains 337 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 868 CYS Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 700 GLN Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 722 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 61 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 112 optimal weight: 0.0770 chunk 117 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN B 50 GLN B 294 ASN A 16 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 700 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.156764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.127876 restraints weight = 26711.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130215 restraints weight = 19631.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131547 restraints weight = 14648.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.132172 restraints weight = 12889.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.132246 restraints weight = 11811.466| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17082 Z= 0.125 Angle : 0.624 10.897 23062 Z= 0.316 Chirality : 0.042 0.226 2599 Planarity : 0.003 0.046 2919 Dihedral : 4.492 37.804 2188 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.14 % Allowed : 23.30 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.78 (0.19), residues: 1989 helix: 0.59 (0.16), residues: 1116 sheet: -0.91 (0.46), residues: 129 loop : -2.18 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 750 TYR 0.041 0.001 TYR C 782 PHE 0.014 0.001 PHE C 798 TRP 0.033 0.002 TRP C 318 HIS 0.011 0.001 HIS D 759 Details of bonding type rmsd covalent geometry : bond 0.00289 (17082) covalent geometry : angle 0.62397 (23062) hydrogen bonds : bond 0.03271 ( 671) hydrogen bonds : angle 4.14873 ( 1974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.44 seconds wall clock time: 45 minutes 20.16 seconds (2720.16 seconds total)