Starting phenix.real_space_refine on Tue Aug 26 13:11:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i8m_52729/08_2025/9i8m_52729.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i8m_52729/08_2025/9i8m_52729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i8m_52729/08_2025/9i8m_52729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i8m_52729/08_2025/9i8m_52729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i8m_52729/08_2025/9i8m_52729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i8m_52729/08_2025/9i8m_52729.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 180 5.16 5 C 23871 2.51 5 N 6370 2.21 5 O 6937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 395 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37358 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2211 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain breaks: 1 Chain: "B" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2363 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 7, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2014 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain breaks: 2 Chain: "D" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2059 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain breaks: 2 Chain: "E" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2038 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain breaks: 2 Chain: "F" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1964 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain breaks: 2 Chain: "G" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2014 Classifications: {'peptide': 250} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 241} Chain breaks: 2 Chain: "H" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2135 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 5, 'TRANS': 257} Chain breaks: 2 Chain: "I" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2325 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 11, 'TRANS': 275} Chain breaks: 2 Chain: "J" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2909 Classifications: {'peptide': 352} Link IDs: {'CIS': 4, 'PTRANS': 11, 'TRANS': 336} Chain breaks: 4 Chain: "K" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2325 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 11, 'TRANS': 275} Chain breaks: 2 Chain: "L" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3794 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 461} Chain breaks: 7 Chain: "O" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 753 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "Q" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 878 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "R" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 794 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "S" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 878 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "T" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 753 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 634 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Chain: "V" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 634 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Chain: "W" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 634 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Chain: "X" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 634 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Chain: "o" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 403 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "p" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "q" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "r" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "s" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 451 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "t" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 446 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Time building chain proxies: 7.00, per 1000 atoms: 0.19 Number of scatterers: 37358 At special positions: 0 Unit cell: (190.117, 202.982, 188.687, 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 180 16.00 O 6937 8.00 N 6370 7.00 C 23871 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: 2.82 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8830 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 12 sheets defined 67.0% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.844A pdb=" N VAL A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 280 removed outlier: 4.136A pdb=" N LYS A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Proline residue: A 264 - end of helix removed outlier: 4.526A pdb=" N TYR A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 275 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 286 through 303 removed outlier: 4.131A pdb=" N ALA A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.560A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 327 through 335 removed outlier: 4.105A pdb=" N ARG A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.807A pdb=" N ALA A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.936A pdb=" N LEU A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 395 removed outlier: 4.098A pdb=" N GLN A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) Proline residue: A 385 - end of helix removed outlier: 3.809A pdb=" N ARG A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 removed outlier: 3.868A pdb=" N LYS A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 490 removed outlier: 4.033A pdb=" N ARG A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 removed outlier: 3.525A pdb=" N VAL A 497 " --> pdb=" O TYR A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 removed outlier: 3.522A pdb=" N LEU B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 311 removed outlier: 3.584A pdb=" N SER B 291 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 304 " --> pdb=" O HIS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 removed outlier: 3.567A pdb=" N GLN B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.536A pdb=" N TYR B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 338 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 370 removed outlier: 3.597A pdb=" N THR B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 386 removed outlier: 3.852A pdb=" N VAL B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.728A pdb=" N ALA B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.622A pdb=" N SER B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 413 " --> pdb=" O TYR B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 4.103A pdb=" N LEU B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.913A pdb=" N TRP B 432 " --> pdb=" O PHE B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'B' and resid 481 through 491 removed outlier: 3.624A pdb=" N ILE B 485 " --> pdb=" O LYS B 481 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 494 No H-bonds generated for 'chain 'B' and resid 492 through 494' Processing helix chain 'B' and resid 504 through 520 removed outlier: 3.861A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS B 510 " --> pdb=" O MET B 506 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Proline residue: B 515 - end of helix removed outlier: 3.533A pdb=" N ALA B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 520 " --> pdb=" O LYS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 547 removed outlier: 3.582A pdb=" N TYR B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER B 541 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 226 removed outlier: 3.555A pdb=" N LEU C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 218 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY C 226 " --> pdb=" O TYR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 261 through 280 removed outlier: 4.242A pdb=" N VAL C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR C 269 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 272 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 314 removed outlier: 3.952A pdb=" N LEU C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 312 " --> pdb=" O GLN C 308 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 348 Proline residue: C 329 - end of helix removed outlier: 3.729A pdb=" N ARG C 332 " --> pdb=" O GLN C 328 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 365 removed outlier: 4.166A pdb=" N LEU C 355 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.629A pdb=" N LEU C 374 " --> pdb=" O GLN C 370 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 395 removed outlier: 4.396A pdb=" N TYR C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 389 " --> pdb=" O PRO C 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 390 " --> pdb=" O TYR C 386 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 451 removed outlier: 3.816A pdb=" N LYS C 448 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 495 removed outlier: 3.549A pdb=" N GLU C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR C 493 " --> pdb=" O LYS C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 259 removed outlier: 3.811A pdb=" N TYR D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 296 through 309 removed outlier: 3.506A pdb=" N ASN D 301 " --> pdb=" O GLY D 297 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 335 removed outlier: 3.514A pdb=" N ALA D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR D 334 " --> pdb=" O GLU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 346 removed outlier: 3.614A pdb=" N VAL D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 344 " --> pdb=" O VAL D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.880A pdb=" N ILE D 375 " --> pdb=" O PHE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 385 removed outlier: 3.769A pdb=" N ASP D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 removed outlier: 4.003A pdb=" N HIS D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 435 removed outlier: 3.758A pdb=" N ILE D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 418 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 420 " --> pdb=" O HIS D 416 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D 423 " --> pdb=" O GLY D 419 " (cutoff:3.500A) Proline residue: D 424 - end of helix removed outlier: 3.623A pdb=" N ASN D 427 " --> pdb=" O TYR D 423 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG D 431 " --> pdb=" O ASN D 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 434 " --> pdb=" O TYR D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.597A pdb=" N VAL D 482 " --> pdb=" O GLN D 478 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 483 " --> pdb=" O SER D 479 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.581A pdb=" N LYS D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 533 " --> pdb=" O PHE D 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 528 through 533' Processing helix chain 'D' and resid 533 through 538 Processing helix chain 'E' and resid 214 through 226 removed outlier: 3.815A pdb=" N GLU E 218 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE E 223 " --> pdb=" O ASP E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.633A pdb=" N LEU E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN E 260 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 282 removed outlier: 4.157A pdb=" N ALA E 266 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN E 268 " --> pdb=" O PRO E 264 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL E 272 " --> pdb=" O ASN E 268 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU E 277 " --> pdb=" O THR E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 312 removed outlier: 4.043A pdb=" N LEU E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU E 301 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE E 304 " --> pdb=" O LYS E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 348 removed outlier: 3.769A pdb=" N ARG E 332 " --> pdb=" O GLN E 328 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR E 333 " --> pdb=" O PRO E 329 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 337 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER E 343 " --> pdb=" O SER E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 365 removed outlier: 3.638A pdb=" N LEU E 355 " --> pdb=" O GLY E 351 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE E 363 " --> pdb=" O HIS E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 396 removed outlier: 4.257A pdb=" N LEU E 374 " --> pdb=" O GLN E 370 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Proline residue: E 385 - end of helix removed outlier: 3.681A pdb=" N ASP E 388 " --> pdb=" O ALA E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 457 removed outlier: 3.972A pdb=" N ILE E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 453 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 498 removed outlier: 3.578A pdb=" N TYR E 493 " --> pdb=" O LYS E 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 253 removed outlier: 3.726A pdb=" N LEU F 253 " --> pdb=" O LEU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 259 removed outlier: 3.601A pdb=" N PHE F 257 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 309 removed outlier: 3.978A pdb=" N GLU F 295 " --> pdb=" O SER F 291 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU F 296 " --> pdb=" O LYS F 292 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY F 297 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN F 301 " --> pdb=" O GLY F 297 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS F 302 " --> pdb=" O TRP F 298 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR F 306 " --> pdb=" O LYS F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 344 removed outlier: 3.614A pdb=" N GLN F 329 " --> pdb=" O ALA F 325 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU F 333 " --> pdb=" O GLN F 329 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR F 334 " --> pdb=" O GLU F 330 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 336 " --> pdb=" O LYS F 332 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 370 through 386 removed outlier: 4.129A pdb=" N ARG F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 378 " --> pdb=" O LYS F 374 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR F 379 " --> pdb=" O ILE F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 410 through 422 removed outlier: 3.893A pdb=" N ILE F 417 " --> pdb=" O LEU F 413 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY F 419 " --> pdb=" O GLN F 415 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU F 420 " --> pdb=" O HIS F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 435 removed outlier: 3.697A pdb=" N LEU F 429 " --> pdb=" O ILE F 425 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG F 431 " --> pdb=" O ASN F 427 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP F 432 " --> pdb=" O PHE F 428 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 433 " --> pdb=" O LEU F 429 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 490 removed outlier: 3.876A pdb=" N LYS F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU F 483 " --> pdb=" O SER F 479 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 489 " --> pdb=" O ILE F 485 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN F 490 " --> pdb=" O GLY F 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 226 removed outlier: 3.613A pdb=" N THR G 214 " --> pdb=" O PRO G 210 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS G 215 " --> pdb=" O SER G 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU G 216 " --> pdb=" O GLN G 212 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY G 226 " --> pdb=" O TYR G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 260 removed outlier: 3.753A pdb=" N LYS G 256 " --> pdb=" O ASP G 252 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G 258 " --> pdb=" O SER G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 274 removed outlier: 4.240A pdb=" N ALA G 266 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL G 272 " --> pdb=" O ASN G 268 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 273 " --> pdb=" O TYR G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 283 removed outlier: 4.132A pdb=" N SER G 280 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 301 removed outlier: 3.814A pdb=" N ALA G 290 " --> pdb=" O GLN G 286 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY G 292 " --> pdb=" O ASN G 288 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 293 " --> pdb=" O HIS G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 313 removed outlier: 3.986A pdb=" N LEU G 305 " --> pdb=" O GLU G 301 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU G 309 " --> pdb=" O LEU G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 328 removed outlier: 3.951A pdb=" N TYR G 326 " --> pdb=" O LYS G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 345 removed outlier: 3.556A pdb=" N VAL G 336 " --> pdb=" O ARG G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 365 removed outlier: 3.551A pdb=" N THR G 354 " --> pdb=" O PHE G 350 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU G 355 " --> pdb=" O GLY G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 382 removed outlier: 4.022A pdb=" N GLU G 373 " --> pdb=" O SER G 369 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU G 374 " --> pdb=" O GLN G 370 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR G 377 " --> pdb=" O GLU G 373 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU G 378 " --> pdb=" O LEU G 374 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 380 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA G 381 " --> pdb=" O TYR G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 395 removed outlier: 4.088A pdb=" N TYR G 386 " --> pdb=" O ALA G 382 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP G 388 " --> pdb=" O ALA G 384 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE G 389 " --> pdb=" O PRO G 385 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP G 393 " --> pdb=" O ILE G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 442 through 458 removed outlier: 4.022A pdb=" N ALA G 446 " --> pdb=" O LEU G 442 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY G 453 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS G 454 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR G 455 " --> pdb=" O SER G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 489 removed outlier: 4.074A pdb=" N GLU G 488 " --> pdb=" O VAL G 484 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS G 489 " --> pdb=" O GLU G 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 484 through 489' Processing helix chain 'G' and resid 490 through 494 removed outlier: 3.913A pdb=" N TYR G 493 " --> pdb=" O ALA G 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 258 removed outlier: 4.168A pdb=" N LEU H 254 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR H 255 " --> pdb=" O ARG H 251 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 256 " --> pdb=" O ASP H 252 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE H 257 " --> pdb=" O LEU H 253 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 293 removed outlier: 3.598A pdb=" N LEU H 293 " --> pdb=" O ILE H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 307 removed outlier: 3.743A pdb=" N GLY H 297 " --> pdb=" O LEU H 293 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU H 299 " --> pdb=" O GLU H 295 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS H 302 " --> pdb=" O TRP H 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE H 303 " --> pdb=" O LEU H 299 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR H 306 " --> pdb=" O LYS H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 342 removed outlier: 3.762A pdb=" N GLU H 330 " --> pdb=" O ALA H 326 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 331 " --> pdb=" O LEU H 327 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG H 336 " --> pdb=" O LYS H 332 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU H 338 " --> pdb=" O TYR H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 343 through 347 removed outlier: 3.802A pdb=" N GLN H 346 " --> pdb=" O SER H 343 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL H 347 " --> pdb=" O GLN H 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 343 through 347' Processing helix chain 'H' and resid 370 through 384 removed outlier: 3.677A pdb=" N ARG H 376 " --> pdb=" O ASP H 372 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS H 378 " --> pdb=" O LYS H 374 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR H 379 " --> pdb=" O ILE H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 402 Processing helix chain 'H' and resid 407 through 422 removed outlier: 3.566A pdb=" N ARG H 411 " --> pdb=" O ASP H 407 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU H 413 " --> pdb=" O TYR H 409 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY H 419 " --> pdb=" O GLN H 415 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU H 420 " --> pdb=" O HIS H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 435 removed outlier: 3.505A pdb=" N TYR H 430 " --> pdb=" O LEU H 426 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG H 431 " --> pdb=" O ASN H 427 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP H 432 " --> pdb=" O PHE H 428 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR H 434 " --> pdb=" O TYR H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 489 removed outlier: 3.576A pdb=" N LEU H 484 " --> pdb=" O ARG H 480 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE H 489 " --> pdb=" O ILE H 485 " (cutoff:3.500A) Processing helix chain 'H' and resid 528 through 533 removed outlier: 4.057A pdb=" N LYS H 532 " --> pdb=" O ALA H 528 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE H 533 " --> pdb=" O PHE H 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 528 through 533' Processing helix chain 'H' and resid 533 through 545 removed outlier: 3.875A pdb=" N PHE H 538 " --> pdb=" O ASP H 534 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP H 539 " --> pdb=" O ALA H 535 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER H 541 " --> pdb=" O TYR H 537 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS H 542 " --> pdb=" O PHE H 538 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR H 543 " --> pdb=" O ASP H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 546 through 551 removed outlier: 3.662A pdb=" N LYS H 550 " --> pdb=" O ASP H 546 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN H 551 " --> pdb=" O VAL H 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 546 through 551' Processing helix chain 'I' and resid 2 through 9 Processing helix chain 'I' and resid 35 through 41 removed outlier: 3.975A pdb=" N SER I 40 " --> pdb=" O PRO I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 51 removed outlier: 4.176A pdb=" N LEU I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 62 removed outlier: 3.526A pdb=" N THR I 56 " --> pdb=" O TYR I 52 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU I 60 " --> pdb=" O THR I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 94 Processing helix chain 'I' and resid 97 through 114 removed outlier: 3.691A pdb=" N LEU I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU I 110 " --> pdb=" O ASP I 106 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE I 111 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP I 114 " --> pdb=" O GLU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 126 removed outlier: 3.806A pdb=" N ILE I 122 " --> pdb=" O SER I 118 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR I 124 " --> pdb=" O SER I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 147 removed outlier: 4.088A pdb=" N VAL I 139 " --> pdb=" O SER I 135 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN I 146 " --> pdb=" O GLN I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 151 No H-bonds generated for 'chain 'I' and resid 149 through 151' Processing helix chain 'I' and resid 152 through 161 Processing helix chain 'I' and resid 165 through 190 removed outlier: 3.981A pdb=" N GLU I 173 " --> pdb=" O ARG I 169 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL I 178 " --> pdb=" O LYS I 174 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS I 179 " --> pdb=" O THR I 175 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL I 182 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN I 186 " --> pdb=" O VAL I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 283 removed outlier: 3.639A pdb=" N ALA I 273 " --> pdb=" O PRO I 269 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU I 274 " --> pdb=" O VAL I 270 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 275 " --> pdb=" O ARG I 271 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE I 276 " --> pdb=" O VAL I 272 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL I 279 " --> pdb=" O LYS I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 290 removed outlier: 3.682A pdb=" N ASN I 288 " --> pdb=" O GLN I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 314 removed outlier: 3.565A pdb=" N THR I 306 " --> pdb=" O ASN I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 322 through 333 removed outlier: 3.802A pdb=" N VAL I 328 " --> pdb=" O ASP I 324 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU I 329 " --> pdb=" O PHE I 325 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP I 330 " --> pdb=" O GLU I 326 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG I 331 " --> pdb=" O SER I 327 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG I 333 " --> pdb=" O LEU I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 339 removed outlier: 3.840A pdb=" N GLU I 338 " --> pdb=" O THR I 335 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS I 339 " --> pdb=" O VAL I 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 335 through 339' Processing helix chain 'I' and resid 340 through 345 removed outlier: 3.548A pdb=" N VAL I 345 " --> pdb=" O TRP I 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 216 Processing helix chain 'J' and resid 237 through 250 removed outlier: 3.513A pdb=" N ILE J 241 " --> pdb=" O ASN J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 274 Processing helix chain 'J' and resid 302 through 317 removed outlier: 4.031A pdb=" N SER J 308 " --> pdb=" O ASN J 304 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL J 309 " --> pdb=" O CYS J 305 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU J 310 " --> pdb=" O LEU J 306 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 315 " --> pdb=" O GLU J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 326 removed outlier: 3.554A pdb=" N LYS J 325 " --> pdb=" O PHE J 321 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE J 326 " --> pdb=" O ARG J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 384 removed outlier: 3.708A pdb=" N TYR J 367 " --> pdb=" O ALA J 363 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU J 373 " --> pdb=" O ILE J 369 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU J 374 " --> pdb=" O SER J 370 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU J 375 " --> pdb=" O PHE J 371 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU J 377 " --> pdb=" O GLU J 373 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS J 380 " --> pdb=" O THR J 376 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE J 382 " --> pdb=" O ILE J 378 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE J 383 " --> pdb=" O GLU J 379 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 416 removed outlier: 3.701A pdb=" N LYS J 406 " --> pdb=" O LEU J 402 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU J 408 " --> pdb=" O GLN J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 426 through 445 removed outlier: 4.027A pdb=" N LEU J 441 " --> pdb=" O TYR J 437 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP J 442 " --> pdb=" O LYS J 438 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR J 443 " --> pdb=" O ALA J 439 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN J 445 " --> pdb=" O LEU J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 463 removed outlier: 3.678A pdb=" N LEU J 456 " --> pdb=" O GLN J 452 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE J 458 " --> pdb=" O VAL J 454 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU J 463 " --> pdb=" O CYS J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 465 through 478 removed outlier: 3.589A pdb=" N GLU J 470 " --> pdb=" O ARG J 466 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL J 472 " --> pdb=" O TYR J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 549 through 566 removed outlier: 4.024A pdb=" N LYS J 553 " --> pdb=" O LYS J 549 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN J 554 " --> pdb=" O PRO J 550 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE J 555 " --> pdb=" O VAL J 551 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE J 556 " --> pdb=" O LEU J 552 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER J 561 " --> pdb=" O MET J 557 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 564 " --> pdb=" O LYS J 560 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU J 565 " --> pdb=" O SER J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 601 removed outlier: 3.600A pdb=" N ARG J 598 " --> pdb=" O SER J 594 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS J 601 " --> pdb=" O SER J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 678 through 698 removed outlier: 4.027A pdb=" N LEU J 682 " --> pdb=" O PHE J 678 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU J 686 " --> pdb=" O LEU J 682 " (cutoff:3.500A) Proline residue: J 688 - end of helix removed outlier: 4.371A pdb=" N GLN J 693 " --> pdb=" O HIS J 689 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU J 696 " --> pdb=" O LYS J 692 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 61 removed outlier: 3.538A pdb=" N VAL K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG K 44 " --> pdb=" O SER K 40 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP K 51 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 94 removed outlier: 3.624A pdb=" N ARG K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 109 removed outlier: 4.217A pdb=" N TYR K 100 " --> pdb=" O ILE K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 114 removed outlier: 3.639A pdb=" N ASP K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 127 Processing helix chain 'K' and resid 132 through 146 removed outlier: 4.400A pdb=" N VAL K 139 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL K 140 " --> pdb=" O ILE K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 151 No H-bonds generated for 'chain 'K' and resid 149 through 151' Processing helix chain 'K' and resid 152 through 159 removed outlier: 3.516A pdb=" N TYR K 158 " --> pdb=" O LEU K 154 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 193 removed outlier: 3.998A pdb=" N GLU K 173 " --> pdb=" O ARG K 169 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL K 178 " --> pdb=" O LYS K 174 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS K 179 " --> pdb=" O THR K 175 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET K 191 " --> pdb=" O LEU K 187 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS K 193 " --> pdb=" O ALA K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 290 removed outlier: 3.747A pdb=" N GLU K 274 " --> pdb=" O VAL K 270 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS K 275 " --> pdb=" O ARG K 271 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE K 276 " --> pdb=" O VAL K 272 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL K 279 " --> pdb=" O LYS K 275 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL K 283 " --> pdb=" O VAL K 279 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE K 286 " --> pdb=" O SER K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 316 removed outlier: 3.512A pdb=" N THR K 306 " --> pdb=" O ASN K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 322 through 335 removed outlier: 3.551A pdb=" N SER K 327 " --> pdb=" O VAL K 323 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL K 328 " --> pdb=" O ASP K 324 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG K 331 " --> pdb=" O SER K 327 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG K 333 " --> pdb=" O LEU K 329 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR K 335 " --> pdb=" O ARG K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 345 removed outlier: 4.141A pdb=" N LEU K 340 " --> pdb=" O VAL K 336 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP K 341 " --> pdb=" O ALA K 337 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL K 345 " --> pdb=" O TRP K 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 15 removed outlier: 3.719A pdb=" N GLY L 9 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS L 15 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 53 removed outlier: 3.524A pdb=" N GLN L 37 " --> pdb=" O ASN L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 removed outlier: 3.501A pdb=" N ILE L 81 " --> pdb=" O PHE L 77 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 101 removed outlier: 3.647A pdb=" N GLU L 99 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER L 101 " --> pdb=" O TYR L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 119 Processing helix chain 'L' and resid 156 through 184 removed outlier: 3.549A pdb=" N SER L 174 " --> pdb=" O GLU L 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET L 184 " --> pdb=" O THR L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 215 removed outlier: 3.893A pdb=" N SER L 215 " --> pdb=" O GLU L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 318 removed outlier: 3.710A pdb=" N GLY L 318 " --> pdb=" O VAL L 314 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 338 removed outlier: 4.007A pdb=" N GLY L 332 " --> pdb=" O LEU L 328 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU L 333 " --> pdb=" O HIS L 329 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE L 335 " --> pdb=" O GLY L 331 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU L 336 " --> pdb=" O GLY L 332 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 337 " --> pdb=" O LEU L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 349 through 360 removed outlier: 3.713A pdb=" N LEU L 353 " --> pdb=" O GLU L 349 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL L 354 " --> pdb=" O GLU L 350 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS L 355 " --> pdb=" O THR L 351 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU L 358 " --> pdb=" O VAL L 354 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN L 359 " --> pdb=" O LYS L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 363 No H-bonds generated for 'chain 'L' and resid 361 through 363' Processing helix chain 'L' and resid 393 through 415 removed outlier: 4.162A pdb=" N THR L 399 " --> pdb=" O SER L 395 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN L 400 " --> pdb=" O SER L 396 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR L 407 " --> pdb=" O GLU L 403 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR L 408 " --> pdb=" O TYR L 404 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER L 415 " --> pdb=" O LEU L 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 427 through 449 removed outlier: 3.531A pdb=" N THR L 434 " --> pdb=" O PHE L 430 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS L 439 " --> pdb=" O SER L 435 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR L 440 " --> pdb=" O GLY L 436 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR L 443 " --> pdb=" O LYS L 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR L 444 " --> pdb=" O TYR L 440 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG L 445 " --> pdb=" O LEU L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 462 Processing helix chain 'L' and resid 463 through 476 removed outlier: 4.305A pdb=" N LEU L 467 " --> pdb=" O LEU L 463 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG L 469 " --> pdb=" O ARG L 465 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN L 470 " --> pdb=" O LYS L 466 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG L 472 " --> pdb=" O GLY L 468 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR L 473 " --> pdb=" O ARG L 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU L 476 " --> pdb=" O ARG L 472 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 510 removed outlier: 3.531A pdb=" N TYR L 506 " --> pdb=" O LEU L 502 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 529 removed outlier: 3.818A pdb=" N LEU L 521 " --> pdb=" O ASN L 517 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU L 524 " --> pdb=" O VAL L 520 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR L 527 " --> pdb=" O SER L 523 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS L 529 " --> pdb=" O LEU L 525 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 538 removed outlier: 3.658A pdb=" N ARG L 534 " --> pdb=" O GLU L 530 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE L 535 " --> pdb=" O PRO L 531 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR L 537 " --> pdb=" O THR L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 602 removed outlier: 3.802A pdb=" N ILE L 597 " --> pdb=" O ASN L 593 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR L 601 " --> pdb=" O ILE L 597 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE L 602 " --> pdb=" O CYS L 598 " (cutoff:3.500A) Processing helix chain 'L' and resid 1361 through 1378 removed outlier: 3.672A pdb=" N VAL L1367 " --> pdb=" O MET L1363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR L1368 " --> pdb=" O LYS L1364 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA L1369 " --> pdb=" O TYR L1365 " (cutoff:3.500A) Proline residue: L1370 - end of helix removed outlier: 3.524A pdb=" N SER L1373 " --> pdb=" O ALA L1369 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL L1375 " --> pdb=" O MET L1371 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 22 removed outlier: 3.576A pdb=" N CYS O 17 " --> pdb=" O LEU O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 41 removed outlier: 3.660A pdb=" N SER O 41 " --> pdb=" O ARG O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 65 removed outlier: 4.351A pdb=" N VAL O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 84 removed outlier: 3.672A pdb=" N SER O 75 " --> pdb=" O GLY O 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG O 79 " --> pdb=" O SER O 75 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN O 84 " --> pdb=" O LYS O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 100 removed outlier: 3.755A pdb=" N ILE O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 22 Processing helix chain 'Q' and resid 28 through 41 removed outlier: 3.665A pdb=" N PHE Q 32 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG Q 37 " --> pdb=" O GLN Q 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 65 removed outlier: 3.810A pdb=" N VAL Q 54 " --> pdb=" O ASP Q 50 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU Q 56 " --> pdb=" O PHE Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 85 removed outlier: 3.759A pdb=" N GLY Q 71 " --> pdb=" O ARG Q 67 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA Q 72 " --> pdb=" O GLU Q 68 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN Q 82 " --> pdb=" O HIS Q 78 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER Q 83 " --> pdb=" O ARG Q 79 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN Q 84 " --> pdb=" O LYS Q 80 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY Q 85 " --> pdb=" O LEU Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 101 removed outlier: 4.072A pdb=" N ILE Q 93 " --> pdb=" O ASN Q 89 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU Q 100 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 117 removed outlier: 3.547A pdb=" N ALA Q 116 " --> pdb=" O SER Q 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 22 Processing helix chain 'R' and resid 28 through 40 removed outlier: 3.884A pdb=" N TYR R 34 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 65 removed outlier: 3.973A pdb=" N VAL R 54 " --> pdb=" O ASP R 50 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 85 removed outlier: 3.581A pdb=" N GLY R 71 " --> pdb=" O ARG R 67 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA R 72 " --> pdb=" O GLU R 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS R 80 " --> pdb=" O GLU R 76 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 100 removed outlier: 3.855A pdb=" N ILE R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 22 Processing helix chain 'S' and resid 28 through 40 Processing helix chain 'S' and resid 50 through 65 removed outlier: 4.029A pdb=" N VAL S 54 " --> pdb=" O ASP S 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR S 55 " --> pdb=" O GLU S 51 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS S 57 " --> pdb=" O LEU S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 85 removed outlier: 3.669A pdb=" N SER S 75 " --> pdb=" O GLY S 71 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU S 76 " --> pdb=" O ALA S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 100 Processing helix chain 'T' and resid 10 through 22 removed outlier: 3.632A pdb=" N LEU T 21 " --> pdb=" O CYS T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 40 Processing helix chain 'T' and resid 50 through 66 removed outlier: 3.585A pdb=" N VAL T 54 " --> pdb=" O ASP T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 85 removed outlier: 3.548A pdb=" N GLY T 71 " --> pdb=" O ARG T 67 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER T 75 " --> pdb=" O GLY T 71 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU T 76 " --> pdb=" O ALA T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 89 through 100 removed outlier: 3.796A pdb=" N ILE T 93 " --> pdb=" O ASN T 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU T 100 " --> pdb=" O LEU T 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 598 through 649 removed outlier: 3.755A pdb=" N GLU U 609 " --> pdb=" O ASN U 605 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU U 649 " --> pdb=" O GLU U 645 " (cutoff:3.500A) Processing helix chain 'U' and resid 650 through 669 removed outlier: 3.595A pdb=" N VAL U 654 " --> pdb=" O ASN U 650 " (cutoff:3.500A) Processing helix chain 'V' and resid 598 through 648 removed outlier: 3.534A pdb=" N ILE V 603 " --> pdb=" O GLN V 599 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP V 613 " --> pdb=" O GLU V 609 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE V 614 " --> pdb=" O THR V 610 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE V 630 " --> pdb=" O GLN V 626 " (cutoff:3.500A) Processing helix chain 'V' and resid 650 through 668 removed outlier: 3.517A pdb=" N VAL V 654 " --> pdb=" O ASN V 650 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU V 656 " --> pdb=" O SER V 652 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE V 657 " --> pdb=" O LEU V 653 " (cutoff:3.500A) Processing helix chain 'W' and resid 598 through 649 removed outlier: 3.630A pdb=" N LEU W 625 " --> pdb=" O ASP W 621 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE W 630 " --> pdb=" O GLN W 626 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR W 647 " --> pdb=" O LEU W 643 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER W 648 " --> pdb=" O LEU W 644 " (cutoff:3.500A) Processing helix chain 'W' and resid 650 through 670 Processing helix chain 'X' and resid 598 through 649 removed outlier: 3.510A pdb=" N MET X 606 " --> pdb=" O PHE X 602 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR X 647 " --> pdb=" O LEU X 643 " (cutoff:3.500A) Processing helix chain 'X' and resid 650 through 671 removed outlier: 3.735A pdb=" N GLU X 656 " --> pdb=" O SER X 652 " (cutoff:3.500A) Processing helix chain 'o' and resid 9 through 25 Processing helix chain 'o' and resid 30 through 43 removed outlier: 3.607A pdb=" N GLN o 43 " --> pdb=" O ARG o 39 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 59 removed outlier: 3.581A pdb=" N GLU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) Processing helix chain 'p' and resid 14 through 25 Processing helix chain 'p' and resid 30 through 42 removed outlier: 3.604A pdb=" N ILE p 36 " --> pdb=" O GLU p 32 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 67 removed outlier: 3.558A pdb=" N SER p 67 " --> pdb=" O THR p 63 " (cutoff:3.500A) Processing helix chain 'q' and resid 11 through 26 removed outlier: 3.590A pdb=" N VAL q 17 " --> pdb=" O GLU q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 43 removed outlier: 3.856A pdb=" N LEU q 34 " --> pdb=" O ASP q 30 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER q 35 " --> pdb=" O MET q 31 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG q 39 " --> pdb=" O SER q 35 " (cutoff:3.500A) Processing helix chain 'q' and resid 46 through 65 removed outlier: 3.838A pdb=" N ILE q 54 " --> pdb=" O LEU q 50 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS q 65 " --> pdb=" O SER q 61 " (cutoff:3.500A) Processing helix chain 'r' and resid 8 through 26 Processing helix chain 'r' and resid 30 through 43 Processing helix chain 'r' and resid 46 through 65 removed outlier: 3.999A pdb=" N LEU r 50 " --> pdb=" O ASN r 46 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP r 62 " --> pdb=" O ARG r 58 " (cutoff:3.500A) Processing helix chain 's' and resid 9 through 26 Processing helix chain 's' and resid 30 through 43 removed outlier: 3.514A pdb=" N ILE s 36 " --> pdb=" O GLU s 32 " (cutoff:3.500A) Processing helix chain 's' and resid 46 through 66 removed outlier: 3.509A pdb=" N LYS s 65 " --> pdb=" O SER s 61 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA s 66 " --> pdb=" O ASP s 62 " (cutoff:3.500A) Processing helix chain 't' and resid 9 through 26 removed outlier: 3.577A pdb=" N VAL t 17 " --> pdb=" O GLU t 13 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU t 25 " --> pdb=" O ILE t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 30 through 44 removed outlier: 3.772A pdb=" N VAL t 38 " --> pdb=" O LEU t 34 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG t 39 " --> pdb=" O SER t 35 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA2, first strand: chain 'B' and resid 448 through 449 Processing sheet with id=AA3, first strand: chain 'C' and resid 233 through 236 Processing sheet with id=AA4, first strand: chain 'E' and resid 232 through 235 Processing sheet with id=AA5, first strand: chain 'G' and resid 232 through 236 removed outlier: 3.756A pdb=" N GLN G 235 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER G 244 " --> pdb=" O GLN G 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 408 through 410 Processing sheet with id=AA7, first strand: chain 'I' and resid 205 through 206 Processing sheet with id=AA8, first strand: chain 'J' and resid 259 through 260 removed outlier: 6.979A pdb=" N THR J 259 " --> pdb=" O ILE J 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'J' and resid 284 through 286 removed outlier: 3.677A pdb=" N ASN J 286 " --> pdb=" O LYS J 289 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS J 289 " --> pdb=" O ASN J 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 493 through 494 removed outlier: 3.903A pdb=" N ASN J 493 " --> pdb=" O PHE J 503 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE J 503 " --> pdb=" O ASN J 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 17 through 20 Processing sheet with id=AB3, first strand: chain 'L' and resid 370 through 372 removed outlier: 3.919A pdb=" N SER L 377 " --> pdb=" O ASN L 372 " (cutoff:3.500A) 1734 hydrogen bonds defined for protein. 5175 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: 5.25 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.48: 21981 1.48 - 1.82: 15901 1.82 - 2.16: 134 2.16 - 2.49: 0 2.49 - 2.83: 1 Bond restraints: 38017 Sorted by residual: bond pdb=" CG1 ILE I 16 " pdb=" CD1 ILE I 16 " ideal model delta sigma weight residual 1.513 2.831 -1.318 3.90e-02 6.57e+02 1.14e+03 bond pdb=" CD2 TRP J 242 " pdb=" CE3 TRP J 242 " ideal model delta sigma weight residual 1.398 1.931 -0.533 1.60e-02 3.91e+03 1.11e+03 bond pdb=" CZ2 TRP J 242 " pdb=" CH2 TRP J 242 " ideal model delta sigma weight residual 1.368 1.866 -0.498 1.90e-02 2.77e+03 6.86e+02 bond pdb=" CE2 TRP J 242 " pdb=" CZ2 TRP J 242 " ideal model delta sigma weight residual 1.394 1.916 -0.522 2.10e-02 2.27e+03 6.18e+02 bond pdb=" CD2 TRP J 242 " pdb=" CE2 TRP J 242 " ideal model delta sigma weight residual 1.409 1.790 -0.381 1.70e-02 3.46e+03 5.02e+02 ... (remaining 38012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 40276 4.24 - 8.48: 10112 8.48 - 12.72: 876 12.72 - 16.96: 45 16.96 - 21.20: 3 Bond angle restraints: 51312 Sorted by residual: angle pdb=" N VAL R 86 " pdb=" CA VAL R 86 " pdb=" C VAL R 86 " ideal model delta sigma weight residual 112.96 101.07 11.89 1.00e+00 1.00e+00 1.41e+02 angle pdb=" N LEU D 361 " pdb=" CA LEU D 361 " pdb=" C LEU D 361 " ideal model delta sigma weight residual 113.38 99.54 13.84 1.23e+00 6.61e-01 1.27e+02 angle pdb=" CA PHE J 228 " pdb=" CB PHE J 228 " pdb=" CG PHE J 228 " ideal model delta sigma weight residual 113.80 124.93 -11.13 1.00e+00 1.00e+00 1.24e+02 angle pdb=" CA PHE E 441 " pdb=" CB PHE E 441 " pdb=" CG PHE E 441 " ideal model delta sigma weight residual 113.80 102.77 11.03 1.00e+00 1.00e+00 1.22e+02 angle pdb=" N ILE A 327 " pdb=" CA ILE A 327 " pdb=" C ILE A 327 " ideal model delta sigma weight residual 111.91 102.54 9.37 8.90e-01 1.26e+00 1.11e+02 ... (remaining 51307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.83: 20824 18.83 - 37.66: 1552 37.66 - 56.49: 321 56.49 - 75.32: 224 75.32 - 94.15: 118 Dihedral angle restraints: 23039 sinusoidal: 9444 harmonic: 13595 Sorted by residual: dihedral pdb=" C THR J 262 " pdb=" N THR J 262 " pdb=" CA THR J 262 " pdb=" CB THR J 262 " ideal model delta harmonic sigma weight residual -122.00 -148.29 26.29 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" N THR J 262 " pdb=" C THR J 262 " pdb=" CA THR J 262 " pdb=" CB THR J 262 " ideal model delta harmonic sigma weight residual 123.40 148.82 -25.42 0 2.50e+00 1.60e-01 1.03e+02 dihedral pdb=" CA PRO L 585 " pdb=" C PRO L 585 " pdb=" N VAL L 586 " pdb=" CA VAL L 586 " ideal model delta harmonic sigma weight residual 180.00 -131.02 -48.98 0 5.00e+00 4.00e-02 9.60e+01 ... (remaining 23036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.263: 4570 0.263 - 0.526: 1205 0.526 - 0.789: 92 0.789 - 1.052: 5 1.052 - 1.315: 2 Chirality restraints: 5874 Sorted by residual: chirality pdb=" CB ILE I 16 " pdb=" CA ILE I 16 " pdb=" CG1 ILE I 16 " pdb=" CG2 ILE I 16 " both_signs ideal model delta sigma weight residual False 2.64 1.33 1.32 2.00e-01 2.50e+01 4.33e+01 chirality pdb=" CA THR J 262 " pdb=" N THR J 262 " pdb=" C THR J 262 " pdb=" CB THR J 262 " both_signs ideal model delta sigma weight residual False 2.53 1.42 1.10 2.00e-01 2.50e+01 3.04e+01 chirality pdb=" CA ARG G 240 " pdb=" N ARG G 240 " pdb=" C ARG G 240 " pdb=" CB ARG G 240 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.90e+01 ... (remaining 5871 not shown) Planarity restraints: 6470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 306 " -0.228 2.00e-02 2.50e+03 1.57e-01 4.93e+02 pdb=" CG TYR D 306 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR D 306 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR D 306 " 0.099 2.00e-02 2.50e+03 pdb=" CE1 TYR D 306 " 0.138 2.00e-02 2.50e+03 pdb=" CE2 TYR D 306 " 0.136 2.00e-02 2.50e+03 pdb=" CZ TYR D 306 " 0.071 2.00e-02 2.50e+03 pdb=" OH TYR D 306 " -0.297 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 395 " -0.223 2.00e-02 2.50e+03 1.33e-01 3.53e+02 pdb=" CG TYR A 395 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 395 " 0.175 2.00e-02 2.50e+03 pdb=" CD2 TYR A 395 " 0.113 2.00e-02 2.50e+03 pdb=" CE1 TYR A 395 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 395 " 0.062 2.00e-02 2.50e+03 pdb=" CZ TYR A 395 " 0.064 2.00e-02 2.50e+03 pdb=" OH TYR A 395 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 242 " -0.202 2.00e-02 2.50e+03 1.18e-01 3.45e+02 pdb=" CG TRP J 242 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP J 242 " -0.095 2.00e-02 2.50e+03 pdb=" CD2 TRP J 242 " 0.189 2.00e-02 2.50e+03 pdb=" NE1 TRP J 242 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP J 242 " 0.097 2.00e-02 2.50e+03 pdb=" CE3 TRP J 242 " 0.120 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 242 " -0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 242 " -0.055 2.00e-02 2.50e+03 pdb=" CH2 TRP J 242 " -0.127 2.00e-02 2.50e+03 ... (remaining 6467 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5558 2.80 - 3.32: 35612 3.32 - 3.85: 58256 3.85 - 4.37: 75164 4.37 - 4.90: 119383 Nonbonded interactions: 293973 Sorted by model distance: nonbonded pdb=" CG1 ILE I 16 " pdb=" CZ2 TRP J 242 " model vdw 2.273 3.740 nonbonded pdb=" CG1 ILE I 16 " pdb=" CE2 TRP J 242 " model vdw 2.286 3.660 nonbonded pdb=" CD1 ILE I 16 " pdb=" CE2 TRP J 242 " model vdw 2.302 3.680 nonbonded pdb=" CG1 ILE I 16 " pdb=" CD2 TRP J 242 " model vdw 2.305 3.660 nonbonded pdb=" CD1 ILE I 16 " pdb=" CD2 TRP J 242 " model vdw 2.328 3.680 ... (remaining 293968 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 209 through 458 or resid 481 through 495)) selection = chain 'C' selection = (chain 'E' and resid 209 through 495) selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 246 through 490 or resid 524 through 542)) selection = chain 'D' selection = (chain 'H' and resid 246 through 542) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'O' selection = (chain 'Q' and resid 9 through 101) selection = (chain 'R' and resid 9 through 101) selection = (chain 'S' and resid 9 through 101) selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = (chain 'o' and resid 13 through 59) selection = (chain 'p' and resid 13 through 59) selection = (chain 'q' and resid 13 through 59) selection = (chain 'r' and resid 13 through 59) selection = (chain 's' and resid 13 through 59) selection = (chain 't' and resid 13 through 59) } 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: 1.290 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 26.740 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 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 : 0.036 1.318 38017 Z= 2.250 Angle : 3.470 21.205 51312 Z= 2.333 Chirality : 0.217 1.315 5874 Planarity : 0.030 0.307 6470 Dihedral : 17.468 94.154 14209 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 2.44 % Allowed : 5.25 % Favored : 92.31 % Rotamer: Outliers : 4.58 % Allowed : 8.45 % Favored : 86.97 % Cbeta Deviations : 8.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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 aren not related in a simple way. whole: -3.49 (0.10), residues: 4515 helix: -1.85 (0.08), residues: 2968 sheet: -1.98 (0.73), residues: 40 loop : -3.04 (0.13), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.116 0.013 ARG J 424 TYR 0.297 0.050 TYR D 306 PHE 0.193 0.041 PHE J 354 TRP 0.202 0.050 TRP J 242 HIS 0.066 0.016 HIS H 328 Details of bonding type rmsd covalent geometry : bond 0.03639 (38017) covalent geometry : angle 3.47029 (51312) hydrogen bonds : bond 0.32909 ( 1734) hydrogen bonds : angle 9.51032 ( 5175) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1743 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 1552 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.8801 (mt) cc_final: 0.8325 (mm) REVERT: A 288 ASN cc_start: 0.6845 (OUTLIER) cc_final: 0.6195 (p0) REVERT: A 289 HIS cc_start: 0.8368 (t-90) cc_final: 0.8135 (t-170) REVERT: A 454 LYS cc_start: 0.8603 (mttp) cc_final: 0.8010 (mtpp) REVERT: A 478 LEU cc_start: 0.8090 (mt) cc_final: 0.7726 (mt) REVERT: B 267 MET cc_start: 0.0662 (ptt) cc_final: 0.0311 (ptt) REVERT: B 328 HIS cc_start: 0.6736 (m-70) cc_final: 0.6252 (t-170) REVERT: B 410 MET cc_start: 0.7109 (ppp) cc_final: 0.6248 (mmt) REVERT: B 411 ARG cc_start: 0.8292 (mtm180) cc_final: 0.7898 (ptp90) REVERT: B 425 ILE cc_start: 0.8887 (mt) cc_final: 0.8440 (tt) REVERT: B 430 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.5950 (p90) REVERT: B 441 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7106 (t) REVERT: B 463 TYR cc_start: 0.4622 (m-80) cc_final: 0.4299 (m-80) REVERT: C 369 SER cc_start: 0.6311 (m) cc_final: 0.5949 (p) REVERT: C 380 LYS cc_start: 0.5045 (mmtt) cc_final: 0.4822 (pttp) REVERT: D 261 ASP cc_start: 0.6560 (m-30) cc_final: 0.6160 (m-30) REVERT: D 299 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6275 (mt) REVERT: D 335 TYR cc_start: 0.8263 (m-80) cc_final: 0.7464 (m-80) REVERT: D 410 MET cc_start: 0.7087 (ptm) cc_final: 0.5503 (ppp) REVERT: E 240 ARG cc_start: 0.2375 (OUTLIER) cc_final: 0.0944 (mmp80) REVERT: E 256 LYS cc_start: 0.8275 (tptp) cc_final: 0.7260 (tptt) REVERT: E 258 LEU cc_start: 0.8027 (mt) cc_final: 0.7700 (mt) REVERT: E 296 ARG cc_start: 0.0899 (tmt170) cc_final: 0.0698 (ttp-170) REVERT: E 306 ILE cc_start: 0.6122 (mt) cc_final: 0.5337 (mt) REVERT: E 312 LEU cc_start: 0.7886 (mt) cc_final: 0.7022 (mt) REVERT: F 267 MET cc_start: 0.0998 (pmt) cc_final: 0.0590 (ppp) REVERT: F 299 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5364 (mt) REVERT: F 454 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8717 (tmtt) REVERT: F 457 ARG cc_start: 0.3812 (mmm160) cc_final: 0.2646 (mtt180) REVERT: G 274 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.6858 (mmp80) REVERT: G 317 LEU cc_start: 0.7785 (pt) cc_final: 0.7555 (mp) REVERT: G 324 TRP cc_start: 0.7611 (t-100) cc_final: 0.6934 (t-100) REVERT: G 483 TYR cc_start: 0.4970 (p90) cc_final: 0.3120 (m-10) REVERT: H 305 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5694 (mmtt) REVERT: H 371 PHE cc_start: 0.7701 (m-80) cc_final: 0.7201 (t80) REVERT: H 427 ASN cc_start: 0.6898 (m-40) cc_final: 0.6404 (m-40) REVERT: H 458 LEU cc_start: -0.1628 (OUTLIER) cc_final: -0.2134 (tt) REVERT: H 485 ILE cc_start: 0.6737 (mt) cc_final: 0.6377 (tt) REVERT: I 1 MET cc_start: 0.6241 (pmt) cc_final: 0.5685 (pmt) REVERT: I 27 VAL cc_start: 0.4469 (OUTLIER) cc_final: 0.4264 (m) REVERT: I 184 TYR cc_start: 0.6129 (m-80) cc_final: 0.5923 (m-80) REVERT: I 259 LEU cc_start: 0.7856 (tp) cc_final: 0.7447 (mp) REVERT: I 260 ARG cc_start: 0.7577 (mtm180) cc_final: 0.6999 (mtp180) REVERT: I 274 GLU cc_start: 0.8023 (pt0) cc_final: 0.7790 (tm-30) REVERT: I 314 LEU cc_start: 0.6613 (mt) cc_final: 0.5921 (mt) REVERT: J 258 LYS cc_start: 0.6853 (mttt) cc_final: 0.6634 (mttt) REVERT: J 316 TYR cc_start: 0.7025 (m-80) cc_final: 0.6454 (m-10) REVERT: J 325 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7070 (ttpp) REVERT: J 501 ARG cc_start: 0.1578 (OUTLIER) cc_final: -0.0326 (mmt90) REVERT: J 568 LEU cc_start: 0.7110 (tp) cc_final: 0.6860 (tp) REVERT: J 680 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.4825 (mp) REVERT: J 681 THR cc_start: 0.5766 (OUTLIER) cc_final: 0.5087 (m) REVERT: K 15 SER cc_start: 0.8771 (m) cc_final: 0.8254 (p) REVERT: K 109 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6847 (pp30) REVERT: K 187 LEU cc_start: 0.8571 (mt) cc_final: 0.7602 (tt) REVERT: K 266 SER cc_start: 0.8669 (m) cc_final: 0.8380 (p) REVERT: K 278 PHE cc_start: 0.8057 (m-10) cc_final: 0.7233 (m-80) REVERT: K 302 ASN cc_start: 0.8475 (p0) cc_final: 0.8083 (p0) REVERT: K 305 ASP cc_start: 0.7960 (m-30) cc_final: 0.7307 (m-30) REVERT: L 389 THR cc_start: 0.7708 (p) cc_final: 0.7290 (p) REVERT: L 471 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.5945 (tp) REVERT: L 518 TYR cc_start: 0.6957 (t80) cc_final: 0.6659 (t80) REVERT: O 50 ASP cc_start: 0.6528 (t0) cc_final: 0.6216 (t70) REVERT: O 53 LEU cc_start: 0.7879 (tp) cc_final: 0.7407 (tt) REVERT: O 57 LYS cc_start: 0.6986 (mtmp) cc_final: 0.6703 (ttpp) REVERT: O 75 SER cc_start: 0.7595 (m) cc_final: 0.7075 (p) REVERT: O 88 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6827 (mttp) REVERT: O 89 ASN cc_start: 0.8330 (t0) cc_final: 0.7811 (t0) REVERT: Q 53 LEU cc_start: 0.9556 (mt) cc_final: 0.9202 (pp) REVERT: Q 62 PHE cc_start: 0.9262 (m-80) cc_final: 0.8937 (m-80) REVERT: Q 70 ASP cc_start: 0.9100 (m-30) cc_final: 0.8798 (m-30) REVERT: R 95 TYR cc_start: 0.8459 (t80) cc_final: 0.8116 (t80) REVERT: R 96 LEU cc_start: 0.9394 (tp) cc_final: 0.9177 (mm) REVERT: S 41 SER cc_start: 0.8089 (m) cc_final: 0.7579 (t) REVERT: S 53 LEU cc_start: 0.8912 (mt) cc_final: 0.8650 (mt) REVERT: T 15 ASN cc_start: 0.7286 (m-40) cc_final: 0.6910 (m-40) REVERT: T 52 PHE cc_start: 0.9072 (m-80) cc_final: 0.8315 (p90) REVERT: U 620 ARG cc_start: 0.8272 (mtt180) cc_final: 0.7030 (tpt170) REVERT: U 650 ASN cc_start: 0.8377 (m110) cc_final: 0.8130 (t0) REVERT: U 660 LEU cc_start: 0.8289 (mt) cc_final: 0.7738 (mt) REVERT: V 614 PHE cc_start: 0.8908 (t80) cc_final: 0.8650 (t80) REVERT: V 656 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8229 (tt0) REVERT: W 634 HIS cc_start: 0.8038 (t70) cc_final: 0.7265 (t70) REVERT: W 635 ILE cc_start: 0.8495 (mm) cc_final: 0.8173 (tt) REVERT: W 640 ILE cc_start: 0.9546 (mm) cc_final: 0.9294 (mm) REVERT: W 659 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8263 (mmtp) REVERT: X 598 ILE cc_start: 0.8757 (mt) cc_final: 0.8503 (mm) REVERT: X 613 ASP cc_start: 0.9220 (t70) cc_final: 0.8832 (m-30) REVERT: X 631 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8678 (ttpt) REVERT: o 12 ARG cc_start: 0.6631 (mtt180) cc_final: 0.4766 (tpp80) REVERT: o 33 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7836 (m) REVERT: o 34 LEU cc_start: 0.7593 (tp) cc_final: 0.6948 (mt) REVERT: p 30 ASP cc_start: 0.6679 (p0) cc_final: 0.5920 (p0) REVERT: p 35 SER cc_start: 0.9604 (t) cc_final: 0.9371 (p) REVERT: p 36 ILE cc_start: 0.8603 (mt) cc_final: 0.8079 (mt) REVERT: q 59 ARG cc_start: 0.7811 (tpt170) cc_final: 0.7412 (tpt170) REVERT: r 20 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8510 (tp30) REVERT: r 38 VAL cc_start: 0.8924 (t) cc_final: 0.8712 (t) REVERT: s 14 THR cc_start: 0.8224 (p) cc_final: 0.7981 (p) REVERT: s 16 ASP cc_start: 0.8106 (t0) cc_final: 0.7608 (p0) outliers start: 191 outliers final: 33 residues processed: 1685 average time/residue: 0.2309 time to fit residues: 607.0504 Evaluate side-chains 947 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 896 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 279 ASN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 HIS A 321 GLN A 359 HIS B 301 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN C 435 GLN D 258 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 427 ASN D 443 HIS E 268 ASN E 286 GLN E 311 HIS E 481 GLN F 300 HIS F 342 HIS F 530 GLN G 260 ASN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 ASN ** G 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 GLN H 321 GLN H 342 HIS ** H 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 HIS H 530 GLN I 123 ASN I 130 HIS ** I 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 288 ASN J 218 HIS J 219 GLN J 245 HIS J 284 GLN J 294 ASN ** J 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 431 HIS J 445 ASN J 480 ASN J 500 HIS K 3 HIS K 180 HIS ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 GLN L 70 ASN L 100 GLN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 178 GLN L 344 GLN L 359 ASN L 515 ASN L 557 ASN L 571 HIS Q 65 GLN Q 84 GLN R 82 GLN S 14 GLN S 84 GLN T 78 HIS T 84 GLN U 632 GLN U 636 GLN V 599 GLN V 632 GLN V 670 ASN X 605 ASN X 624 ASN X 626 GLN X 670 ASN q 26 ASN q 43 GLN t 43 GLN t 46 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.207360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.179408 restraints weight = 59039.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.183128 restraints weight = 69559.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.182809 restraints weight = 50421.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.183101 restraints weight = 42775.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.183827 restraints weight = 35465.246| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 2.473 38017 Z= 0.399 Angle : 0.843 15.360 51312 Z= 0.446 Chirality : 0.046 0.339 5874 Planarity : 0.006 0.099 6470 Dihedral : 6.361 85.727 5032 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.65 % Favored : 95.02 % Rotamer: Outliers : 0.22 % Allowed : 4.70 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -2.15 (0.11), residues: 4515 helix: -0.88 (0.09), residues: 2998 sheet: -2.02 (0.60), residues: 58 loop : -2.35 (0.14), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 67 TYR 0.030 0.003 TYR E 395 PHE 0.043 0.003 PHE K 307 TRP 0.027 0.004 TRP F 432 HIS 0.016 0.002 HIS J 245 Details of bonding type rmsd covalent geometry : bond 0.01363 (38017) covalent geometry : angle 0.84315 (51312) hydrogen bonds : bond 0.07203 ( 1734) hydrogen bonds : angle 5.16333 ( 5175) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1115 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8495 (mt) cc_final: 0.8108 (pp) REVERT: A 288 ASN cc_start: 0.8091 (p0) cc_final: 0.7183 (p0) REVERT: A 337 LEU cc_start: 0.7407 (mt) cc_final: 0.7102 (pp) REVERT: A 442 LEU cc_start: 0.7822 (tp) cc_final: 0.7452 (tt) REVERT: A 444 LYS cc_start: 0.7416 (pttm) cc_final: 0.7126 (pttm) REVERT: A 454 LYS cc_start: 0.8437 (mttp) cc_final: 0.7754 (mttp) REVERT: B 410 MET cc_start: 0.7489 (ppp) cc_final: 0.6682 (mmt) REVERT: B 411 ARG cc_start: 0.8339 (mtm180) cc_final: 0.7468 (ptp-110) REVERT: B 470 ILE cc_start: 0.6693 (mm) cc_final: 0.6374 (tp) REVERT: B 533 ILE cc_start: 0.8198 (pt) cc_final: 0.7902 (pt) REVERT: C 267 THR cc_start: 0.7227 (p) cc_final: 0.6915 (p) REVERT: C 300 LYS cc_start: 0.7404 (tttp) cc_final: 0.6786 (tptt) REVERT: C 322 LYS cc_start: 0.7000 (mmmt) cc_final: 0.6786 (mmmt) REVERT: C 370 GLN cc_start: 0.7513 (pp30) cc_final: 0.6646 (pm20) REVERT: C 380 LYS cc_start: 0.5958 (mmtt) cc_final: 0.5613 (pttp) REVERT: D 538 PHE cc_start: 0.6348 (m-10) cc_final: 0.6133 (m-10) REVERT: E 256 LYS cc_start: 0.7250 (tptp) cc_final: 0.6865 (tptt) REVERT: E 322 LYS cc_start: 0.7946 (tptm) cc_final: 0.7608 (tttp) REVERT: F 295 GLU cc_start: 0.6599 (pp20) cc_final: 0.6294 (pp20) REVERT: F 410 MET cc_start: 0.5827 (tmm) cc_final: 0.4953 (mmp) REVERT: F 457 ARG cc_start: 0.4298 (mmm160) cc_final: 0.2434 (mtt180) REVERT: G 219 ASP cc_start: 0.6915 (m-30) cc_final: 0.6631 (m-30) REVERT: G 317 LEU cc_start: 0.7703 (pt) cc_final: 0.7462 (mt) REVERT: G 483 TYR cc_start: 0.5104 (p90) cc_final: 0.3172 (m-10) REVERT: H 316 PHE cc_start: 0.4314 (m-80) cc_final: 0.3906 (m-10) REVERT: H 441 THR cc_start: 0.7190 (m) cc_final: 0.6881 (m) REVERT: I 1 MET cc_start: 0.7187 (pmm) cc_final: 0.5473 (mmt) REVERT: I 19 TRP cc_start: 0.6842 (t-100) cc_final: 0.5619 (t-100) REVERT: I 183 MET cc_start: 0.7309 (ttp) cc_final: 0.7060 (ttp) REVERT: I 184 TYR cc_start: 0.7129 (m-80) cc_final: 0.6687 (m-80) REVERT: I 259 LEU cc_start: 0.8246 (tp) cc_final: 0.7992 (mp) REVERT: J 442 ASP cc_start: 0.7427 (m-30) cc_final: 0.6674 (m-30) REVERT: J 557 MET cc_start: 0.7676 (tmm) cc_final: 0.7110 (tmm) REVERT: J 560 LYS cc_start: 0.7512 (mttm) cc_final: 0.7166 (tttp) REVERT: J 568 LEU cc_start: 0.7196 (tp) cc_final: 0.6985 (tp) REVERT: J 689 HIS cc_start: 0.6894 (m90) cc_final: 0.6558 (m90) REVERT: K 15 SER cc_start: 0.8554 (m) cc_final: 0.7988 (p) REVERT: K 35 HIS cc_start: 0.7481 (t-90) cc_final: 0.6709 (t-90) REVERT: K 47 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7725 (mmtp) REVERT: K 167 PRO cc_start: 0.7962 (Cg_exo) cc_final: 0.7744 (Cg_endo) REVERT: L 84 MET cc_start: 0.7617 (mpp) cc_final: 0.6968 (mpp) REVERT: L 250 VAL cc_start: 0.7920 (t) cc_final: 0.7644 (p) REVERT: L 348 LEU cc_start: 0.6747 (tp) cc_final: 0.6508 (mt) REVERT: L 352 ASP cc_start: 0.7760 (m-30) cc_final: 0.7536 (m-30) REVERT: O 31 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7678 (mp10) REVERT: O 34 TYR cc_start: 0.6897 (t80) cc_final: 0.6439 (t80) REVERT: O 65 GLN cc_start: 0.5476 (mm110) cc_final: 0.5168 (tp40) REVERT: Q 43 PHE cc_start: 0.8093 (p90) cc_final: 0.7872 (p90) REVERT: V 637 SER cc_start: 0.9236 (m) cc_final: 0.8972 (t) REVERT: V 653 LEU cc_start: 0.8215 (mm) cc_final: 0.7959 (mm) REVERT: W 614 PHE cc_start: 0.6699 (t80) cc_final: 0.6149 (t80) REVERT: W 634 HIS cc_start: 0.7655 (t70) cc_final: 0.7401 (t70) REVERT: o 12 ARG cc_start: 0.6173 (mtt180) cc_final: 0.4888 (tpt-90) REVERT: o 48 GLU cc_start: 0.7431 (mp0) cc_final: 0.6865 (mp0) REVERT: p 38 VAL cc_start: 0.8972 (t) cc_final: 0.8561 (p) REVERT: p 55 LYS cc_start: 0.9151 (mttt) cc_final: 0.8694 (mtmm) REVERT: q 59 ARG cc_start: 0.6354 (tpt170) cc_final: 0.6111 (tpt170) REVERT: s 11 VAL cc_start: 0.8502 (t) cc_final: 0.8190 (p) outliers start: 9 outliers final: 2 residues processed: 1121 average time/residue: 0.2203 time to fit residues: 392.4987 Evaluate side-chains 791 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 789 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 373 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 411 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 311 HIS B 258 GLN B 328 HIS B 344 GLN B 386 HIS B 493 HIS B 497 HIS ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN D 300 HIS D 443 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 GLN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 400 ASN H 344 GLN I 82 HIS I 130 HIS I 193 HIS J 294 ASN ** J 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 HIS K 160 HIS K 180 HIS K 339 HIS L 70 ASN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN L 571 HIS O 84 GLN ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 GLN S 84 GLN V 632 GLN X 632 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.202922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.170590 restraints weight = 62447.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.174095 restraints weight = 95792.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.175141 restraints weight = 64036.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.175968 restraints weight = 47181.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.176651 restraints weight = 39917.251| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5790 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 2.474 38017 Z= 0.399 Angle : 0.784 16.413 51312 Z= 0.411 Chirality : 0.045 0.375 5874 Planarity : 0.005 0.070 6470 Dihedral : 5.788 80.290 5032 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.96 % Favored : 94.80 % Rotamer: Outliers : 0.10 % Allowed : 4.42 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.73 (0.12), residues: 4515 helix: -0.55 (0.09), residues: 3014 sheet: -2.18 (0.55), residues: 67 loop : -2.21 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.001 ARG T 19 TYR 0.039 0.002 TYR G 395 PHE 0.051 0.003 PHE K 307 TRP 0.019 0.002 TRP K 190 HIS 0.015 0.002 HIS L1374 Details of bonding type rmsd covalent geometry : bond 0.01370 (38017) covalent geometry : angle 0.78371 (51312) hydrogen bonds : bond 0.05905 ( 1734) hydrogen bonds : angle 4.80765 ( 5175) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1017 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 HIS cc_start: 0.8794 (t-170) cc_final: 0.8237 (t-170) REVERT: A 454 LYS cc_start: 0.8481 (mttp) cc_final: 0.8089 (mtpp) REVERT: A 478 LEU cc_start: 0.7119 (mp) cc_final: 0.6797 (mp) REVERT: B 251 ARG cc_start: 0.7546 (ptm160) cc_final: 0.7163 (ptp-170) REVERT: B 344 GLN cc_start: 0.7523 (pt0) cc_final: 0.7178 (pt0) REVERT: B 410 MET cc_start: 0.7627 (ppp) cc_final: 0.7096 (mmt) REVERT: B 411 ARG cc_start: 0.8426 (mtm180) cc_final: 0.7680 (ttm110) REVERT: B 418 LEU cc_start: 0.7243 (tp) cc_final: 0.6965 (tp) REVERT: C 221 LEU cc_start: 0.8567 (mt) cc_final: 0.8294 (mt) REVERT: C 300 LYS cc_start: 0.7291 (tttp) cc_final: 0.6876 (tptt) REVERT: C 380 LYS cc_start: 0.6232 (mmtt) cc_final: 0.5792 (pttp) REVERT: C 443 GLN cc_start: 0.6103 (mm-40) cc_final: 0.5893 (mp10) REVERT: D 410 MET cc_start: 0.6363 (ppp) cc_final: 0.5842 (ppp) REVERT: D 538 PHE cc_start: 0.6776 (m-10) cc_final: 0.6563 (m-10) REVERT: E 256 LYS cc_start: 0.7434 (tptp) cc_final: 0.7036 (tptt) REVERT: E 300 LYS cc_start: 0.6027 (mmmt) cc_final: 0.4290 (mmtt) REVERT: F 333 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6831 (pp20) REVERT: F 457 ARG cc_start: 0.3734 (mmm160) cc_final: 0.2102 (mtt180) REVERT: G 394 ILE cc_start: 0.7481 (pt) cc_final: 0.7149 (mt) REVERT: G 447 ASP cc_start: 0.8612 (m-30) cc_final: 0.8320 (m-30) REVERT: G 483 TYR cc_start: 0.5469 (p90) cc_final: 0.3486 (m-10) REVERT: I 61 GLN cc_start: 0.7170 (tp-100) cc_final: 0.6573 (tm-30) REVERT: I 259 LEU cc_start: 0.8418 (tp) cc_final: 0.8173 (mp) REVERT: I 342 LYS cc_start: 0.4047 (mmtt) cc_final: 0.3541 (mmtm) REVERT: J 278 LYS cc_start: 0.7192 (mttt) cc_final: 0.6714 (mppt) REVERT: J 296 ILE cc_start: 0.8582 (mm) cc_final: 0.8322 (mt) REVERT: J 379 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7262 (tt0) REVERT: J 469 LEU cc_start: 0.8170 (tp) cc_final: 0.7940 (tp) REVERT: J 557 MET cc_start: 0.7737 (tmm) cc_final: 0.7071 (tmm) REVERT: J 568 LEU cc_start: 0.7325 (tp) cc_final: 0.7064 (tp) REVERT: K 15 SER cc_start: 0.8195 (m) cc_final: 0.7747 (p) REVERT: K 35 HIS cc_start: 0.8119 (t-90) cc_final: 0.6897 (t-90) REVERT: K 44 ARG cc_start: 0.6945 (mmm-85) cc_final: 0.6583 (mmm-85) REVERT: K 47 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7757 (mmtp) REVERT: K 48 LEU cc_start: 0.9288 (tp) cc_final: 0.8962 (tp) REVERT: K 97 LEU cc_start: 0.7729 (mt) cc_final: 0.7505 (mt) REVERT: L 7 LEU cc_start: 0.9046 (mt) cc_final: 0.8843 (mp) REVERT: L 84 MET cc_start: 0.7917 (mpp) cc_final: 0.7589 (mpp) REVERT: L 502 LEU cc_start: 0.8296 (tt) cc_final: 0.8084 (pp) REVERT: O 31 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7621 (mp10) REVERT: O 33 GLN cc_start: 0.7489 (tp-100) cc_final: 0.7179 (mm-40) REVERT: O 57 LYS cc_start: 0.6769 (mtmm) cc_final: 0.6044 (mtpt) REVERT: O 65 GLN cc_start: 0.5771 (mm110) cc_final: 0.5136 (tp40) REVERT: T 53 LEU cc_start: 0.8758 (mt) cc_final: 0.8536 (mm) REVERT: U 620 ARG cc_start: 0.8796 (mtt180) cc_final: 0.7614 (mmt180) REVERT: U 642 MET cc_start: 0.8869 (ttp) cc_final: 0.8521 (ttp) REVERT: V 637 SER cc_start: 0.9213 (m) cc_final: 0.8807 (t) REVERT: V 650 ASN cc_start: 0.6344 (p0) cc_final: 0.6089 (p0) REVERT: W 634 HIS cc_start: 0.7866 (t70) cc_final: 0.7535 (t70) REVERT: X 624 ASN cc_start: 0.7712 (t0) cc_final: 0.7161 (t0) REVERT: X 628 GLU cc_start: 0.7837 (pt0) cc_final: 0.7623 (pt0) REVERT: o 12 ARG cc_start: 0.6371 (mtt180) cc_final: 0.4867 (tpt-90) REVERT: o 48 GLU cc_start: 0.8008 (mp0) cc_final: 0.7498 (mp0) REVERT: p 38 VAL cc_start: 0.8995 (t) cc_final: 0.8367 (t) REVERT: p 39 ARG cc_start: 0.8481 (ptt90) cc_final: 0.8137 (ptt-90) REVERT: q 59 ARG cc_start: 0.6444 (tpt170) cc_final: 0.6047 (tpm170) REVERT: r 38 VAL cc_start: 0.9261 (t) cc_final: 0.8958 (t) REVERT: s 11 VAL cc_start: 0.8656 (t) cc_final: 0.8193 (p) REVERT: s 31 MET cc_start: 0.7572 (ppp) cc_final: 0.7340 (ppp) outliers start: 4 outliers final: 2 residues processed: 1020 average time/residue: 0.2261 time to fit residues: 365.4564 Evaluate side-chains 753 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 751 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 242 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 229 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 339 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 286 GLN A 308 GLN A 311 HIS B 328 HIS ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 HIS D 400 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS ** I 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS J 237 ASN ** J 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 HIS L 70 ASN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 342 GLN L 590 HIS ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 GLN ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 632 GLN V 634 HIS W 624 ASN X 624 ASN X 632 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.207768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.182085 restraints weight = 65685.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.183554 restraints weight = 97277.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.185053 restraints weight = 78352.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.185474 restraints weight = 54317.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.186215 restraints weight = 48646.847| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 2.475 38017 Z= 0.375 Angle : 0.692 16.269 51312 Z= 0.361 Chirality : 0.043 0.445 5874 Planarity : 0.005 0.067 6470 Dihedral : 5.441 76.807 5032 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.67 % Favored : 95.13 % Rotamer: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.38 (0.12), residues: 4515 helix: -0.25 (0.09), residues: 3013 sheet: -2.02 (0.58), residues: 67 loop : -2.14 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 392 TYR 0.028 0.002 TYR L1376 PHE 0.036 0.002 PHE X 614 TRP 0.028 0.002 TRP L 539 HIS 0.009 0.001 HIS L1374 Details of bonding type rmsd covalent geometry : bond 0.01334 (38017) covalent geometry : angle 0.69226 (51312) hydrogen bonds : bond 0.05264 ( 1734) hydrogen bonds : angle 4.54148 ( 5175) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 971 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 HIS cc_start: 0.8632 (t-170) cc_final: 0.7930 (t-170) REVERT: A 454 LYS cc_start: 0.8389 (mttp) cc_final: 0.7920 (mtpp) REVERT: B 399 VAL cc_start: 0.5847 (m) cc_final: 0.5609 (m) REVERT: B 410 MET cc_start: 0.7469 (ppp) cc_final: 0.7254 (mmt) REVERT: B 411 ARG cc_start: 0.8365 (mtm180) cc_final: 0.7918 (ttm110) REVERT: D 299 LEU cc_start: 0.7543 (mm) cc_final: 0.7303 (mt) REVERT: D 410 MET cc_start: 0.6555 (ppp) cc_final: 0.6022 (ppp) REVERT: D 473 PHE cc_start: 0.5788 (p90) cc_final: 0.5578 (p90) REVERT: E 256 LYS cc_start: 0.7145 (tptp) cc_final: 0.6888 (tptt) REVERT: E 300 LYS cc_start: 0.5902 (mmmt) cc_final: 0.4422 (mmtt) REVERT: E 334 MET cc_start: 0.4468 (ptt) cc_final: 0.3607 (ppp) REVERT: F 333 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7103 (pp20) REVERT: G 394 ILE cc_start: 0.7498 (pt) cc_final: 0.7099 (mt) REVERT: G 447 ASP cc_start: 0.8146 (m-30) cc_final: 0.7942 (m-30) REVERT: G 483 TYR cc_start: 0.5774 (p90) cc_final: 0.3350 (m-10) REVERT: H 341 LEU cc_start: 0.7947 (mp) cc_final: 0.7653 (tt) REVERT: H 362 THR cc_start: 0.7577 (m) cc_final: 0.7351 (m) REVERT: H 441 THR cc_start: 0.7033 (m) cc_final: 0.6586 (m) REVERT: I 1 MET cc_start: 0.7779 (pmm) cc_final: 0.7290 (ppp) REVERT: I 311 LEU cc_start: 0.7967 (tp) cc_final: 0.7653 (tp) REVERT: I 342 LYS cc_start: 0.3700 (mmtt) cc_final: 0.3227 (mmtm) REVERT: J 228 PHE cc_start: 0.6220 (p90) cc_final: 0.5865 (t80) REVERT: J 278 LYS cc_start: 0.6930 (mttt) cc_final: 0.6562 (mppt) REVERT: J 296 ILE cc_start: 0.8455 (mm) cc_final: 0.8180 (mt) REVERT: J 557 MET cc_start: 0.7369 (tmm) cc_final: 0.6930 (tmm) REVERT: J 568 LEU cc_start: 0.7316 (tp) cc_final: 0.7074 (tp) REVERT: K 35 HIS cc_start: 0.7790 (t-90) cc_final: 0.6646 (t-90) REVERT: K 47 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7720 (mmtp) REVERT: K 48 LEU cc_start: 0.9120 (tp) cc_final: 0.8686 (tp) REVERT: K 125 SER cc_start: 0.8419 (m) cc_final: 0.8190 (t) REVERT: L 7 LEU cc_start: 0.8992 (mt) cc_final: 0.8743 (mp) REVERT: L 84 MET cc_start: 0.8318 (mpp) cc_final: 0.7842 (mpp) REVERT: L 213 ARG cc_start: 0.7078 (ttm-80) cc_final: 0.6701 (ptp-170) REVERT: L 228 MET cc_start: 0.2487 (mmp) cc_final: 0.2112 (mmm) REVERT: L 518 TYR cc_start: 0.6884 (t80) cc_final: 0.6400 (t80) REVERT: L 553 MET cc_start: 0.2863 (ttt) cc_final: 0.2608 (ttt) REVERT: O 31 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7594 (mp10) REVERT: O 57 LYS cc_start: 0.7186 (mtmm) cc_final: 0.6816 (mtpt) REVERT: O 65 GLN cc_start: 0.5619 (mm110) cc_final: 0.5100 (tp40) REVERT: R 16 LEU cc_start: 0.8909 (tp) cc_final: 0.8529 (tp) REVERT: T 96 LEU cc_start: 0.7282 (tt) cc_final: 0.6726 (mm) REVERT: U 615 ARG cc_start: 0.7551 (mmm160) cc_final: 0.7269 (mmm-85) REVERT: U 620 ARG cc_start: 0.8690 (mtt180) cc_final: 0.7551 (mmt180) REVERT: U 642 MET cc_start: 0.8784 (ttp) cc_final: 0.8473 (ttp) REVERT: V 605 ASN cc_start: 0.8908 (p0) cc_final: 0.8332 (p0) REVERT: V 637 SER cc_start: 0.9049 (m) cc_final: 0.8641 (t) REVERT: V 642 MET cc_start: 0.9155 (ppp) cc_final: 0.8954 (ppp) REVERT: W 614 PHE cc_start: 0.6132 (t80) cc_final: 0.5885 (t80) REVERT: X 631 LYS cc_start: 0.8754 (tttt) cc_final: 0.8262 (tppt) REVERT: o 12 ARG cc_start: 0.6313 (mtt180) cc_final: 0.5101 (tpt-90) REVERT: o 32 GLU cc_start: 0.7067 (pp20) cc_final: 0.6832 (pp20) REVERT: o 48 GLU cc_start: 0.8069 (mp0) cc_final: 0.7493 (mp0) REVERT: p 38 VAL cc_start: 0.8927 (t) cc_final: 0.8364 (t) REVERT: p 39 ARG cc_start: 0.8352 (ptt90) cc_final: 0.8011 (ptt-90) REVERT: p 55 LYS cc_start: 0.9061 (mttt) cc_final: 0.8847 (mttp) REVERT: q 15 MET cc_start: 0.3380 (ttt) cc_final: 0.2703 (tpt) REVERT: q 59 ARG cc_start: 0.6202 (tpt170) cc_final: 0.5842 (tpm170) REVERT: r 38 VAL cc_start: 0.9168 (t) cc_final: 0.8931 (t) REVERT: s 11 VAL cc_start: 0.8598 (t) cc_final: 0.8100 (p) REVERT: s 31 MET cc_start: 0.7510 (ppp) cc_final: 0.7299 (ppp) outliers start: 5 outliers final: 1 residues processed: 974 average time/residue: 0.2059 time to fit residues: 323.2020 Evaluate side-chains 739 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 738 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 311 optimal weight: 2.9990 chunk 383 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 399 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 78 optimal weight: 0.9980 chunk 411 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 311 HIS B 328 HIS B 344 GLN B 386 HIS ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN D 460 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 HIS ** H 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 HIS I 130 HIS J 303 GLN ** J 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS K 180 HIS ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 14 GLN O 89 ASN ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 GLN ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 624 ASN X 632 GLN t 26 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.189799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.161351 restraints weight = 57083.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.166205 restraints weight = 100580.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.165172 restraints weight = 51420.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.166090 restraints weight = 41785.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.166531 restraints weight = 32589.970| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.7500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 2.481 38017 Z= 0.429 Angle : 0.826 16.990 51312 Z= 0.430 Chirality : 0.048 0.383 5874 Planarity : 0.006 0.094 6470 Dihedral : 5.608 72.183 5032 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.25 % Favored : 94.57 % Rotamer: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.12), residues: 4515 helix: -0.41 (0.09), residues: 3026 sheet: -2.68 (0.60), residues: 57 loop : -2.27 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 364 TYR 0.036 0.003 TYR F 306 PHE 0.055 0.003 PHE S 62 TRP 0.033 0.002 TRP D 369 HIS 0.016 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.01424 (38017) covalent geometry : angle 0.82643 (51312) hydrogen bonds : bond 0.05521 ( 1734) hydrogen bonds : angle 4.91724 ( 5175) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 940 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 HIS cc_start: 0.8737 (t-170) cc_final: 0.8208 (t-170) REVERT: A 334 MET cc_start: 0.6410 (ptp) cc_final: 0.5906 (ptp) REVERT: A 454 LYS cc_start: 0.8455 (mttp) cc_final: 0.8023 (mtpp) REVERT: A 478 LEU cc_start: 0.7224 (mp) cc_final: 0.6945 (mp) REVERT: B 251 ARG cc_start: 0.7138 (ptm160) cc_final: 0.6802 (ptp-170) REVERT: B 410 MET cc_start: 0.7751 (ppp) cc_final: 0.7531 (mmt) REVERT: B 411 ARG cc_start: 0.8562 (mtm180) cc_final: 0.8087 (ttm110) REVERT: B 418 LEU cc_start: 0.7971 (tp) cc_final: 0.7591 (tp) REVERT: D 299 LEU cc_start: 0.7692 (mm) cc_final: 0.7408 (mt) REVERT: D 410 MET cc_start: 0.6495 (ppp) cc_final: 0.6114 (ppp) REVERT: D 473 PHE cc_start: 0.5592 (p90) cc_final: 0.5302 (p90) REVERT: E 300 LYS cc_start: 0.6125 (mmmt) cc_final: 0.4545 (mmtt) REVERT: E 334 MET cc_start: 0.4554 (ptt) cc_final: 0.3721 (ppp) REVERT: F 251 ARG cc_start: 0.7961 (ptt-90) cc_final: 0.7702 (ptm-80) REVERT: F 267 MET cc_start: 0.0631 (ppp) cc_final: 0.0102 (ppp) REVERT: F 333 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6900 (pp20) REVERT: G 377 TYR cc_start: 0.6921 (t80) cc_final: 0.6690 (t80) REVERT: G 394 ILE cc_start: 0.7578 (pt) cc_final: 0.7257 (mt) REVERT: G 483 TYR cc_start: 0.6523 (p90) cc_final: 0.4465 (m-80) REVERT: I 1 MET cc_start: 0.7786 (pmm) cc_final: 0.7345 (ppp) REVERT: I 173 GLU cc_start: 0.6606 (mm-30) cc_final: 0.6386 (tm-30) REVERT: J 228 PHE cc_start: 0.6443 (p90) cc_final: 0.5990 (t80) REVERT: J 278 LYS cc_start: 0.7546 (mttt) cc_final: 0.6994 (mppt) REVERT: J 316 TYR cc_start: 0.6964 (m-10) cc_final: 0.6727 (m-10) REVERT: J 327 ILE cc_start: 0.7061 (mm) cc_final: 0.6595 (mm) REVERT: J 557 MET cc_start: 0.7518 (tmm) cc_final: 0.6967 (tmm) REVERT: J 568 LEU cc_start: 0.7049 (tp) cc_final: 0.6776 (tp) REVERT: K 47 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8022 (mmtp) REVERT: K 141 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6711 (tp30) REVERT: K 316 GLN cc_start: 0.5853 (mm110) cc_final: 0.5623 (tp-100) REVERT: K 322 LEU cc_start: 0.7963 (mp) cc_final: 0.7668 (mp) REVERT: L 41 LYS cc_start: 0.7264 (tptt) cc_final: 0.7037 (mmtt) REVERT: L 213 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.6772 (ptp-170) REVERT: L 228 MET cc_start: 0.3632 (mmp) cc_final: 0.3030 (mmm) REVERT: L 397 LEU cc_start: 0.8603 (tp) cc_final: 0.8382 (tp) REVERT: L 553 MET cc_start: 0.3528 (ttt) cc_final: 0.3096 (ttt) REVERT: L 593 ASN cc_start: 0.7630 (m-40) cc_final: 0.6750 (p0) REVERT: O 56 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7428 (mm-30) REVERT: O 65 GLN cc_start: 0.6432 (mm110) cc_final: 0.5578 (tp40) REVERT: Q 43 PHE cc_start: 0.7511 (p90) cc_final: 0.7154 (p90) REVERT: Q 51 GLU cc_start: 0.4372 (mp0) cc_final: 0.4140 (mp0) REVERT: R 16 LEU cc_start: 0.8753 (tp) cc_final: 0.8502 (tp) REVERT: R 37 ARG cc_start: 0.8847 (mtp85) cc_final: 0.8421 (mtp85) REVERT: T 32 PHE cc_start: 0.5921 (t80) cc_final: 0.5703 (t80) REVERT: T 50 ASP cc_start: 0.5785 (p0) cc_final: 0.5517 (p0) REVERT: U 620 ARG cc_start: 0.8762 (mtt180) cc_final: 0.7674 (mmt180) REVERT: U 642 MET cc_start: 0.9052 (ttp) cc_final: 0.8665 (ttp) REVERT: V 605 ASN cc_start: 0.8467 (p0) cc_final: 0.8199 (p0) REVERT: V 620 ARG cc_start: 0.7635 (ptm160) cc_final: 0.7421 (ptm160) REVERT: V 637 SER cc_start: 0.9213 (m) cc_final: 0.8807 (t) REVERT: W 634 HIS cc_start: 0.7570 (t70) cc_final: 0.7311 (t70) REVERT: X 604 LYS cc_start: 0.4736 (mmtt) cc_final: 0.4499 (mmtt) REVERT: X 629 MET cc_start: 0.8870 (tpp) cc_final: 0.8568 (tpp) REVERT: o 12 ARG cc_start: 0.6205 (mtt180) cc_final: 0.4304 (tpt-90) REVERT: o 48 GLU cc_start: 0.8404 (mp0) cc_final: 0.7971 (mp0) REVERT: q 59 ARG cc_start: 0.6174 (tpt170) cc_final: 0.5866 (tpm170) REVERT: s 11 VAL cc_start: 0.8814 (t) cc_final: 0.8205 (p) REVERT: s 42 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6682 (pp20) outliers start: 3 outliers final: 1 residues processed: 941 average time/residue: 0.2121 time to fit residues: 318.9281 Evaluate side-chains 714 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 713 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 437 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 256 optimal weight: 0.5980 chunk 426 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 446 optimal weight: 7.9990 chunk 431 optimal weight: 8.9990 chunk 319 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 152 optimal weight: 20.0000 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 311 HIS ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 HIS E 370 GLN G 289 HIS G 311 HIS G 429 GLN H 258 GLN ** I 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS ** J 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 339 HIS L 70 ASN Q 42 ASN R 82 GLN ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 624 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.189969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.156674 restraints weight = 57039.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.160324 restraints weight = 85851.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.161372 restraints weight = 59502.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.162337 restraints weight = 43748.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.163133 restraints weight = 36349.583| |-----------------------------------------------------------------------------| r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.7695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 2.475 38017 Z= 0.374 Angle : 0.704 16.733 51312 Z= 0.363 Chirality : 0.042 0.333 5874 Planarity : 0.005 0.082 6470 Dihedral : 5.320 68.343 5032 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.02 % Rotamer: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.28 (0.12), residues: 4515 helix: -0.14 (0.09), residues: 3023 sheet: -2.32 (0.56), residues: 69 loop : -2.19 (0.15), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 332 TYR 0.030 0.002 TYR L1376 PHE 0.035 0.002 PHE Q 74 TRP 0.027 0.002 TRP J 475 HIS 0.010 0.001 HIS L1374 Details of bonding type rmsd covalent geometry : bond 0.01335 (38017) covalent geometry : angle 0.70444 (51312) hydrogen bonds : bond 0.04892 ( 1734) hydrogen bonds : angle 4.57692 ( 5175) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 922 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8213 (mp) cc_final: 0.7366 (tt) REVERT: A 289 HIS cc_start: 0.8969 (t-170) cc_final: 0.8303 (t-170) REVERT: A 334 MET cc_start: 0.6422 (ptp) cc_final: 0.6162 (ptp) REVERT: A 390 LEU cc_start: 0.8617 (tp) cc_final: 0.8413 (tp) REVERT: A 454 LYS cc_start: 0.8512 (mttp) cc_final: 0.8085 (mtpp) REVERT: A 478 LEU cc_start: 0.7190 (mp) cc_final: 0.6762 (mp) REVERT: B 410 MET cc_start: 0.7945 (ppp) cc_final: 0.7355 (mmt) REVERT: B 411 ARG cc_start: 0.8429 (mtm180) cc_final: 0.7999 (ttm110) REVERT: B 418 LEU cc_start: 0.7737 (tp) cc_final: 0.7300 (tp) REVERT: C 271 THR cc_start: 0.8538 (p) cc_final: 0.8313 (p) REVERT: C 377 TYR cc_start: 0.7561 (t80) cc_final: 0.7074 (t80) REVERT: D 299 LEU cc_start: 0.7784 (mm) cc_final: 0.7520 (mt) REVERT: D 473 PHE cc_start: 0.5899 (p90) cc_final: 0.5622 (p90) REVERT: E 256 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7600 (mmpt) REVERT: E 295 MET cc_start: 0.5337 (ttt) cc_final: 0.4673 (tpp) REVERT: E 300 LYS cc_start: 0.6006 (mmmt) cc_final: 0.4515 (mmtt) REVERT: E 334 MET cc_start: 0.4354 (ptt) cc_final: 0.3548 (ppp) REVERT: F 251 ARG cc_start: 0.8104 (ptt-90) cc_final: 0.7714 (ptm-80) REVERT: F 267 MET cc_start: 0.0733 (ppp) cc_final: 0.0270 (ppp) REVERT: F 333 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6582 (pp20) REVERT: G 377 TYR cc_start: 0.6815 (t80) cc_final: 0.6559 (t80) REVERT: G 394 ILE cc_start: 0.7541 (pt) cc_final: 0.7244 (mt) REVERT: G 447 ASP cc_start: 0.8594 (m-30) cc_final: 0.8321 (m-30) REVERT: G 483 TYR cc_start: 0.5856 (p90) cc_final: 0.4497 (m-80) REVERT: H 285 SER cc_start: 0.6559 (p) cc_final: 0.6000 (p) REVERT: H 441 THR cc_start: 0.7244 (m) cc_final: 0.7024 (m) REVERT: I 1 MET cc_start: 0.7541 (pmm) cc_final: 0.7253 (ppp) REVERT: I 82 HIS cc_start: 0.7526 (t-90) cc_final: 0.7204 (m90) REVERT: I 110 GLU cc_start: 0.7067 (tt0) cc_final: 0.6390 (mm-30) REVERT: J 228 PHE cc_start: 0.6544 (p90) cc_final: 0.5881 (t80) REVERT: J 278 LYS cc_start: 0.7317 (mttt) cc_final: 0.6846 (mppt) REVERT: J 327 ILE cc_start: 0.6700 (mm) cc_final: 0.6323 (mm) REVERT: J 418 GLU cc_start: 0.6884 (mt-10) cc_final: 0.5384 (mm-30) REVERT: J 557 MET cc_start: 0.7737 (tmm) cc_final: 0.7214 (tmm) REVERT: J 568 LEU cc_start: 0.7131 (tp) cc_final: 0.6913 (tp) REVERT: J 680 LEU cc_start: 0.6820 (pp) cc_final: 0.6572 (pp) REVERT: K 44 ARG cc_start: 0.7233 (mtp85) cc_final: 0.6949 (ttt-90) REVERT: K 47 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7800 (mmtp) REVERT: K 141 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6613 (tp30) REVERT: K 316 GLN cc_start: 0.6461 (mm110) cc_final: 0.6044 (tp-100) REVERT: L 14 SER cc_start: 0.8945 (t) cc_final: 0.8169 (t) REVERT: L 41 LYS cc_start: 0.6263 (tptt) cc_final: 0.6009 (mmtt) REVERT: L 74 MET cc_start: 0.6937 (tpp) cc_final: 0.6649 (mmm) REVERT: L 213 ARG cc_start: 0.7348 (ttm-80) cc_final: 0.6843 (ptp-170) REVERT: L 228 MET cc_start: 0.3331 (mmp) cc_final: 0.2429 (mmm) REVERT: L 397 LEU cc_start: 0.8628 (tp) cc_final: 0.8350 (tp) REVERT: L 553 MET cc_start: 0.3633 (ttt) cc_final: 0.3105 (ttt) REVERT: O 65 GLN cc_start: 0.6070 (mm110) cc_final: 0.5507 (tp40) REVERT: Q 51 GLU cc_start: 0.4785 (mp0) cc_final: 0.4552 (mp0) REVERT: R 37 ARG cc_start: 0.9086 (mtp85) cc_final: 0.8785 (mtp85) REVERT: T 32 PHE cc_start: 0.6239 (t80) cc_final: 0.6031 (t80) REVERT: U 620 ARG cc_start: 0.8841 (mtt180) cc_final: 0.7535 (mmt180) REVERT: U 642 MET cc_start: 0.9069 (ttp) cc_final: 0.8610 (ttp) REVERT: V 605 ASN cc_start: 0.8703 (p0) cc_final: 0.8459 (p0) REVERT: V 629 MET cc_start: 0.8405 (ppp) cc_final: 0.7763 (ppp) REVERT: W 634 HIS cc_start: 0.7819 (t70) cc_final: 0.7329 (t70) REVERT: X 606 MET cc_start: 0.8034 (tmm) cc_final: 0.7714 (tmm) REVERT: X 624 ASN cc_start: 0.7999 (t160) cc_final: 0.7670 (t0) REVERT: X 629 MET cc_start: 0.9094 (tpp) cc_final: 0.8776 (tpt) REVERT: o 12 ARG cc_start: 0.5786 (mtt180) cc_final: 0.4133 (tpt-90) REVERT: o 48 GLU cc_start: 0.8505 (mp0) cc_final: 0.8124 (mp0) REVERT: q 59 ARG cc_start: 0.6453 (tpt170) cc_final: 0.6002 (tpm170) REVERT: s 42 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7280 (pp20) outliers start: 4 outliers final: 2 residues processed: 925 average time/residue: 0.2099 time to fit residues: 312.5734 Evaluate side-chains 709 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 707 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 402 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 423 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 409 optimal weight: 9.9990 chunk 297 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 286 GLN A 308 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 HIS ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 GLN G 289 HIS G 321 GLN ** I 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS ** J 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN O 33 GLN O 89 ASN ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 GLN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 624 ASN ** V 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 624 ASN X 632 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.191597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.167103 restraints weight = 56506.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.170967 restraints weight = 93950.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.168781 restraints weight = 49757.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.168883 restraints weight = 56840.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.169259 restraints weight = 40156.209| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.8033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 2.466 38017 Z= 0.384 Angle : 0.738 16.701 51312 Z= 0.381 Chirality : 0.044 0.335 5874 Planarity : 0.005 0.074 6470 Dihedral : 5.281 62.933 5032 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.20 % Favored : 94.64 % Rotamer: Outliers : 0.05 % Allowed : 2.16 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -1.32 (0.12), residues: 4515 helix: -0.18 (0.09), residues: 3008 sheet: -2.05 (0.59), residues: 67 loop : -2.17 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG s 39 TYR 0.028 0.002 TYR L1376 PHE 0.042 0.002 PHE X 602 TRP 0.050 0.002 TRP J 242 HIS 0.013 0.001 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.01350 (38017) covalent geometry : angle 0.73845 (51312) hydrogen bonds : bond 0.04871 ( 1734) hydrogen bonds : angle 4.65350 ( 5175) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 918 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8129 (tp) cc_final: 0.7910 (tp) REVERT: A 454 LYS cc_start: 0.8277 (mttp) cc_final: 0.7936 (mtpp) REVERT: A 478 LEU cc_start: 0.6990 (mp) cc_final: 0.6708 (mp) REVERT: B 411 ARG cc_start: 0.8360 (mtm180) cc_final: 0.7992 (ttm110) REVERT: B 418 LEU cc_start: 0.7859 (tp) cc_final: 0.7465 (tp) REVERT: B 445 PHE cc_start: 0.7100 (t80) cc_final: 0.6357 (t80) REVERT: C 267 THR cc_start: 0.8022 (p) cc_final: 0.7801 (p) REVERT: C 271 THR cc_start: 0.8357 (p) cc_final: 0.8095 (p) REVERT: C 377 TYR cc_start: 0.7242 (t80) cc_final: 0.6764 (t80) REVERT: E 256 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7318 (mmmm) REVERT: E 300 LYS cc_start: 0.5835 (mmmt) cc_final: 0.4359 (mmtt) REVERT: F 267 MET cc_start: 0.0633 (ppp) cc_final: 0.0194 (ppp) REVERT: F 333 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6815 (pp20) REVERT: G 258 LEU cc_start: 0.7643 (pp) cc_final: 0.7318 (pp) REVERT: G 394 ILE cc_start: 0.7765 (pt) cc_final: 0.7319 (mt) REVERT: G 483 TYR cc_start: 0.5959 (p90) cc_final: 0.4469 (m-80) REVERT: I 82 HIS cc_start: 0.7515 (t-90) cc_final: 0.7149 (m90) REVERT: I 206 ARG cc_start: 0.5792 (tpp80) cc_final: 0.5589 (tpp80) REVERT: I 263 MET cc_start: 0.7078 (mmt) cc_final: 0.6865 (tpp) REVERT: I 312 HIS cc_start: 0.6529 (m170) cc_final: 0.6273 (m170) REVERT: J 228 PHE cc_start: 0.6300 (p90) cc_final: 0.5898 (t80) REVERT: J 258 LYS cc_start: 0.8176 (tmmt) cc_final: 0.7943 (tttp) REVERT: J 278 LYS cc_start: 0.7238 (mttt) cc_final: 0.6755 (mppt) REVERT: J 327 ILE cc_start: 0.6833 (mm) cc_final: 0.6388 (mm) REVERT: J 418 GLU cc_start: 0.6954 (mt-10) cc_final: 0.5432 (mm-30) REVERT: J 504 TRP cc_start: 0.5775 (t60) cc_final: 0.5211 (t-100) REVERT: J 557 MET cc_start: 0.7419 (tmm) cc_final: 0.6955 (tmm) REVERT: K 47 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8102 (mmtp) REVERT: K 141 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6868 (tp30) REVERT: K 315 LYS cc_start: 0.8025 (tttp) cc_final: 0.7618 (tptt) REVERT: K 316 GLN cc_start: 0.6342 (mm110) cc_final: 0.6009 (tp-100) REVERT: L 14 SER cc_start: 0.8738 (t) cc_final: 0.7929 (t) REVERT: L 39 LEU cc_start: 0.8835 (mm) cc_final: 0.8567 (mt) REVERT: L 41 LYS cc_start: 0.6425 (tptt) cc_final: 0.6119 (mmtt) REVERT: L 74 MET cc_start: 0.6610 (tpp) cc_final: 0.6286 (mmm) REVERT: L 213 ARG cc_start: 0.7197 (ttm-80) cc_final: 0.6827 (ptp-170) REVERT: L 228 MET cc_start: 0.3974 (mmp) cc_final: 0.3654 (mmm) REVERT: L 397 LEU cc_start: 0.8617 (tp) cc_final: 0.8363 (tp) REVERT: L 459 THR cc_start: 0.6424 (p) cc_final: 0.6152 (t) REVERT: L 553 MET cc_start: 0.2774 (ttt) cc_final: 0.2480 (ttt) REVERT: L 593 ASN cc_start: 0.7703 (m-40) cc_final: 0.7055 (p0) REVERT: O 65 GLN cc_start: 0.6485 (mm110) cc_final: 0.5579 (tp40) REVERT: Q 58 ILE cc_start: 0.8693 (pt) cc_final: 0.8420 (pt) REVERT: R 37 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8464 (mtp85) REVERT: R 78 HIS cc_start: 0.7398 (t-90) cc_final: 0.6964 (t-90) REVERT: U 620 ARG cc_start: 0.8709 (mtt180) cc_final: 0.7581 (mmt180) REVERT: U 632 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7895 (tm-30) REVERT: U 642 MET cc_start: 0.8784 (ttp) cc_final: 0.8509 (ttm) REVERT: V 605 ASN cc_start: 0.8410 (p0) cc_final: 0.8186 (p0) REVERT: V 629 MET cc_start: 0.7787 (ppp) cc_final: 0.6111 (ppp) REVERT: W 634 HIS cc_start: 0.7648 (t70) cc_final: 0.7393 (t70) REVERT: X 606 MET cc_start: 0.7581 (tmm) cc_final: 0.7033 (tmm) REVERT: o 12 ARG cc_start: 0.6039 (mtt180) cc_final: 0.4313 (tpt-90) REVERT: o 48 GLU cc_start: 0.8359 (mp0) cc_final: 0.7884 (mp0) REVERT: s 36 ILE cc_start: 0.7529 (mm) cc_final: 0.7283 (mm) REVERT: s 42 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7186 (pp20) REVERT: t 54 ILE cc_start: 0.8764 (pt) cc_final: 0.8530 (pt) outliers start: 2 outliers final: 0 residues processed: 920 average time/residue: 0.2135 time to fit residues: 314.3744 Evaluate side-chains 709 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 709 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 137 optimal weight: 0.9980 chunk 359 optimal weight: 8.9990 chunk 181 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 314 optimal weight: 0.7980 chunk 232 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 286 GLN A 308 GLN A 359 HIS ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN E 370 GLN G 289 HIS ** I 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS J 324 GLN J 404 GLN ** J 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN O 89 ASN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 624 ASN ** X 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.188026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.154826 restraints weight = 57231.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.159122 restraints weight = 90500.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.159968 restraints weight = 57998.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.160660 restraints weight = 43283.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.161877 restraints weight = 34832.192| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.8219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 2.478 38017 Z= 0.375 Angle : 0.716 17.023 51312 Z= 0.367 Chirality : 0.043 0.328 5874 Planarity : 0.005 0.112 6470 Dihedral : 5.182 58.898 5032 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.02 % Rotamer: Outliers : 0.02 % Allowed : 1.32 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -1.19 (0.12), residues: 4515 helix: -0.09 (0.09), residues: 3012 sheet: -1.66 (0.65), residues: 58 loop : -2.12 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG W 615 TYR 0.036 0.002 TYR J 588 PHE 0.036 0.002 PHE Q 74 TRP 0.025 0.002 TRP J 242 HIS 0.009 0.001 HIS L1374 Details of bonding type rmsd covalent geometry : bond 0.01338 (38017) covalent geometry : angle 0.71589 (51312) hydrogen bonds : bond 0.04594 ( 1734) hydrogen bonds : angle 4.57762 ( 5175) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 913 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8445 (mp) cc_final: 0.7746 (tt) REVERT: A 390 LEU cc_start: 0.8548 (tp) cc_final: 0.8330 (tp) REVERT: A 454 LYS cc_start: 0.8495 (mttp) cc_final: 0.8128 (mtpp) REVERT: A 478 LEU cc_start: 0.7149 (mp) cc_final: 0.6751 (mp) REVERT: B 411 ARG cc_start: 0.8332 (mtm180) cc_final: 0.8054 (ttm110) REVERT: B 418 LEU cc_start: 0.7565 (tp) cc_final: 0.7188 (tp) REVERT: B 445 PHE cc_start: 0.7035 (t80) cc_final: 0.6398 (t80) REVERT: B 477 ASP cc_start: 0.7321 (m-30) cc_final: 0.6149 (m-30) REVERT: C 215 CYS cc_start: 0.8248 (m) cc_final: 0.7936 (m) REVERT: C 269 TYR cc_start: 0.5936 (p90) cc_final: 0.5573 (p90) REVERT: C 271 THR cc_start: 0.8529 (p) cc_final: 0.8303 (p) REVERT: C 377 TYR cc_start: 0.7385 (t80) cc_final: 0.6942 (t80) REVERT: F 267 MET cc_start: 0.0926 (ppp) cc_final: 0.0463 (ppp) REVERT: F 365 ARG cc_start: 0.7537 (ptm-80) cc_final: 0.6586 (ptm-80) REVERT: F 444 GLU cc_start: 0.6307 (mp0) cc_final: 0.6066 (mp0) REVERT: F 469 MET cc_start: 0.3223 (mtt) cc_final: 0.1805 (ptt) REVERT: G 261 ARG cc_start: 0.5183 (ptt-90) cc_final: 0.4929 (ptt90) REVERT: G 447 ASP cc_start: 0.8528 (m-30) cc_final: 0.8233 (m-30) REVERT: G 483 TYR cc_start: 0.6467 (p90) cc_final: 0.4513 (m-80) REVERT: H 341 LEU cc_start: 0.8148 (mp) cc_final: 0.7714 (tt) REVERT: I 82 HIS cc_start: 0.7449 (t-90) cc_final: 0.6974 (m90) REVERT: I 110 GLU cc_start: 0.7033 (tt0) cc_final: 0.6364 (mm-30) REVERT: I 137 MET cc_start: 0.7499 (tpp) cc_final: 0.7230 (ttt) REVERT: I 183 MET cc_start: 0.7030 (tmm) cc_final: 0.6824 (tmm) REVERT: I 195 LEU cc_start: 0.7462 (tp) cc_final: 0.7198 (tt) REVERT: J 228 PHE cc_start: 0.6315 (p90) cc_final: 0.5688 (t80) REVERT: J 327 ILE cc_start: 0.6783 (mm) cc_final: 0.6451 (mm) REVERT: J 418 GLU cc_start: 0.6938 (mt-10) cc_final: 0.5346 (mm-30) REVERT: J 480 ASN cc_start: 0.7120 (t0) cc_final: 0.6226 (t0) REVERT: J 557 MET cc_start: 0.7772 (tmm) cc_final: 0.7219 (tmm) REVERT: K 44 ARG cc_start: 0.6890 (mtp85) cc_final: 0.6688 (ttt-90) REVERT: K 47 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7874 (mmtp) REVERT: K 141 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6987 (tp30) REVERT: K 315 LYS cc_start: 0.8210 (tttp) cc_final: 0.7660 (tptp) REVERT: K 316 GLN cc_start: 0.6924 (mm110) cc_final: 0.6394 (tp-100) REVERT: L 14 SER cc_start: 0.8962 (t) cc_final: 0.7952 (t) REVERT: L 39 LEU cc_start: 0.8592 (mm) cc_final: 0.8373 (mt) REVERT: L 41 LYS cc_start: 0.6284 (tptt) cc_final: 0.5999 (mmtt) REVERT: L 213 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.6897 (ptp-170) REVERT: L 397 LEU cc_start: 0.8347 (tp) cc_final: 0.8039 (tp) REVERT: L 459 THR cc_start: 0.6471 (p) cc_final: 0.6210 (t) REVERT: L 518 TYR cc_start: 0.7119 (t80) cc_final: 0.6668 (t80) REVERT: L 553 MET cc_start: 0.2414 (ttt) cc_final: 0.2141 (ttt) REVERT: L 593 ASN cc_start: 0.8232 (m-40) cc_final: 0.7381 (p0) REVERT: O 65 GLN cc_start: 0.6366 (mm110) cc_final: 0.5403 (tp40) REVERT: Q 58 ILE cc_start: 0.8698 (pt) cc_final: 0.8233 (pt) REVERT: R 10 ASN cc_start: 0.8412 (m-40) cc_final: 0.7866 (t0) REVERT: R 14 GLN cc_start: 0.8670 (pm20) cc_final: 0.8245 (pm20) REVERT: R 16 LEU cc_start: 0.8960 (tp) cc_final: 0.8729 (tp) REVERT: R 37 ARG cc_start: 0.9102 (mtp85) cc_final: 0.8734 (mtp85) REVERT: R 78 HIS cc_start: 0.8056 (t-90) cc_final: 0.7632 (t-90) REVERT: T 32 PHE cc_start: 0.6273 (t80) cc_final: 0.6059 (t80) REVERT: U 620 ARG cc_start: 0.8754 (mtt180) cc_final: 0.7506 (mmt180) REVERT: U 642 MET cc_start: 0.8997 (ttp) cc_final: 0.8682 (ttm) REVERT: V 605 ASN cc_start: 0.8690 (p0) cc_final: 0.8398 (p0) REVERT: V 620 ARG cc_start: 0.7873 (ptm160) cc_final: 0.7535 (tmm-80) REVERT: V 642 MET cc_start: 0.8887 (ppp) cc_final: 0.8415 (tmm) REVERT: W 634 HIS cc_start: 0.8001 (t70) cc_final: 0.7337 (t-170) REVERT: W 642 MET cc_start: 0.8688 (ppp) cc_final: 0.8397 (ppp) REVERT: X 606 MET cc_start: 0.8228 (tmm) cc_final: 0.7978 (tmm) REVERT: X 626 GLN cc_start: 0.8316 (tp40) cc_final: 0.8091 (tp-100) REVERT: o 12 ARG cc_start: 0.5765 (mtt180) cc_final: 0.4137 (tpt-90) REVERT: o 48 GLU cc_start: 0.8583 (mp0) cc_final: 0.8144 (mp0) REVERT: p 55 LYS cc_start: 0.8932 (mtmm) cc_final: 0.8609 (mttp) REVERT: r 12 ARG cc_start: 0.8514 (ttm110) cc_final: 0.8137 (mmt90) REVERT: s 37 CYS cc_start: 0.6179 (m) cc_final: 0.5973 (m) REVERT: s 42 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7532 (pp20) outliers start: 1 outliers final: 0 residues processed: 914 average time/residue: 0.2102 time to fit residues: 310.9564 Evaluate side-chains 710 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 710 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 18 optimal weight: 5.9990 chunk 406 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 363 optimal weight: 1.9990 chunk 418 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 chunk 426 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 286 GLN A 308 GLN B 386 HIS ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN E 370 GLN E 437 GLN G 289 HIS G 328 GLN H 328 HIS I 186 GLN ** I 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS ** J 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS L 70 ASN L 376 GLN L 413 HIS O 14 GLN O 89 ASN Q 42 ASN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 624 ASN X 624 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.188475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.162858 restraints weight = 56495.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.166156 restraints weight = 99009.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.165317 restraints weight = 54259.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.165892 restraints weight = 44345.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.166144 restraints weight = 35901.577| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.8570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 2.481 38017 Z= 0.402 Angle : 0.784 16.959 51312 Z= 0.406 Chirality : 0.046 0.342 5874 Planarity : 0.005 0.085 6470 Dihedral : 5.310 46.888 5032 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.58 % Favored : 94.29 % Rotamer: Outliers : 0.10 % Allowed : 0.94 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.45 (0.12), residues: 4515 helix: -0.30 (0.09), residues: 3038 sheet: -1.63 (0.68), residues: 58 loop : -2.22 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 430 TYR 0.044 0.002 TYR F 306 PHE 0.044 0.003 PHE O 74 TRP 0.038 0.002 TRP A 427 HIS 0.013 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.01382 (38017) covalent geometry : angle 0.78354 (51312) hydrogen bonds : bond 0.04894 ( 1734) hydrogen bonds : angle 4.85045 ( 5175) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 898 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 PHE cc_start: 0.5999 (m-80) cc_final: 0.5569 (m-10) REVERT: A 295 MET cc_start: 0.6464 (ppp) cc_final: 0.5983 (ppp) REVERT: A 334 MET cc_start: 0.6433 (ptp) cc_final: 0.5927 (ptp) REVERT: A 454 LYS cc_start: 0.8268 (mttp) cc_final: 0.7918 (mtpp) REVERT: A 478 LEU cc_start: 0.7294 (mp) cc_final: 0.6846 (mp) REVERT: B 251 ARG cc_start: 0.6465 (ptp-170) cc_final: 0.6195 (ptm160) REVERT: B 411 ARG cc_start: 0.8181 (mtm180) cc_final: 0.7759 (ttm-80) REVERT: B 445 PHE cc_start: 0.7008 (t80) cc_final: 0.6476 (t80) REVERT: B 477 ASP cc_start: 0.6171 (m-30) cc_final: 0.5418 (m-30) REVERT: C 269 TYR cc_start: 0.5659 (p90) cc_final: 0.5443 (p90) REVERT: C 271 THR cc_start: 0.8201 (p) cc_final: 0.7964 (p) REVERT: C 322 LYS cc_start: 0.7294 (mmmt) cc_final: 0.7066 (mmmt) REVERT: C 377 TYR cc_start: 0.7042 (t80) cc_final: 0.6647 (t80) REVERT: F 365 ARG cc_start: 0.7648 (ptm-80) cc_final: 0.6644 (ptm-80) REVERT: F 469 MET cc_start: 0.3850 (mtt) cc_final: 0.1916 (ptt) REVERT: G 261 ARG cc_start: 0.5466 (ptt-90) cc_final: 0.5122 (ptt-90) REVERT: G 447 ASP cc_start: 0.8081 (m-30) cc_final: 0.7873 (m-30) REVERT: G 483 TYR cc_start: 0.6050 (p90) cc_final: 0.4608 (m-80) REVERT: I 82 HIS cc_start: 0.7645 (t-90) cc_final: 0.7056 (m90) REVERT: J 218 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.7205 (p-80) REVERT: J 228 PHE cc_start: 0.6363 (p90) cc_final: 0.6005 (t80) REVERT: J 327 ILE cc_start: 0.6895 (mm) cc_final: 0.6566 (mm) REVERT: J 418 GLU cc_start: 0.7111 (mt-10) cc_final: 0.5602 (mm-30) REVERT: J 480 ASN cc_start: 0.7566 (t0) cc_final: 0.6579 (t0) REVERT: J 504 TRP cc_start: 0.5745 (t60) cc_final: 0.5314 (t-100) REVERT: J 557 MET cc_start: 0.7626 (tmm) cc_final: 0.7175 (tmm) REVERT: J 560 LYS cc_start: 0.7789 (mttm) cc_final: 0.6749 (tttp) REVERT: K 47 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8112 (mmtp) REVERT: K 122 ILE cc_start: 0.8135 (mt) cc_final: 0.7840 (mt) REVERT: K 141 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6950 (tp30) REVERT: K 315 LYS cc_start: 0.8271 (tttp) cc_final: 0.7834 (tptt) REVERT: K 316 GLN cc_start: 0.6680 (mm110) cc_final: 0.6439 (tp-100) REVERT: L 14 SER cc_start: 0.8394 (t) cc_final: 0.7195 (t) REVERT: L 39 LEU cc_start: 0.8893 (mm) cc_final: 0.8668 (mt) REVERT: L 73 ILE cc_start: 0.8440 (mt) cc_final: 0.7975 (mm) REVERT: L 213 ARG cc_start: 0.7104 (ttm-80) cc_final: 0.6814 (ptp-170) REVERT: L 228 MET cc_start: 0.5457 (mmt) cc_final: 0.4780 (mmm) REVERT: L 397 LEU cc_start: 0.8533 (tp) cc_final: 0.8099 (tp) REVERT: L 445 ARG cc_start: 0.6774 (mmt180) cc_final: 0.6367 (mmm160) REVERT: L 553 MET cc_start: 0.2427 (ttt) cc_final: 0.2204 (ttt) REVERT: O 49 ARG cc_start: 0.6321 (mtp85) cc_final: 0.5210 (ptt-90) REVERT: O 56 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7255 (mm-30) REVERT: O 57 LYS cc_start: 0.7466 (mtmm) cc_final: 0.6754 (mtpt) REVERT: O 65 GLN cc_start: 0.6489 (mm110) cc_final: 0.5453 (tp40) REVERT: Q 42 ASN cc_start: 0.6953 (OUTLIER) cc_final: 0.6416 (p0) REVERT: Q 43 PHE cc_start: 0.7183 (p90) cc_final: 0.6729 (p90) REVERT: R 10 ASN cc_start: 0.7451 (m-40) cc_final: 0.7231 (t0) REVERT: R 16 LEU cc_start: 0.8590 (tp) cc_final: 0.8265 (tp) REVERT: R 37 ARG cc_start: 0.8841 (mtp85) cc_final: 0.8461 (mtp85) REVERT: R 78 HIS cc_start: 0.6949 (t-90) cc_final: 0.6449 (t-90) REVERT: U 620 ARG cc_start: 0.8690 (mtt180) cc_final: 0.7685 (mmt180) REVERT: V 620 ARG cc_start: 0.7303 (ptm160) cc_final: 0.6820 (tmm-80) REVERT: V 642 MET cc_start: 0.9011 (ppp) cc_final: 0.8168 (tmm) REVERT: W 628 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7359 (mm-30) REVERT: W 634 HIS cc_start: 0.7676 (t70) cc_final: 0.7151 (t70) REVERT: W 642 MET cc_start: 0.8381 (ppp) cc_final: 0.8147 (ppp) REVERT: X 606 MET cc_start: 0.7528 (tmm) cc_final: 0.7155 (tmm) REVERT: o 12 ARG cc_start: 0.6366 (mtt180) cc_final: 0.4618 (tpt-90) REVERT: o 48 GLU cc_start: 0.8336 (mp0) cc_final: 0.7908 (mp0) REVERT: p 55 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8376 (mttp) REVERT: t 54 ILE cc_start: 0.8741 (pt) cc_final: 0.8508 (pt) outliers start: 4 outliers final: 0 residues processed: 901 average time/residue: 0.2138 time to fit residues: 309.4752 Evaluate side-chains 696 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 694 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 138 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 413 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 375 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 440 optimal weight: 6.9990 chunk 446 optimal weight: 9.9990 chunk 335 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 HIS ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 GLN G 289 HIS ** I 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN L 413 HIS ** L1374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN Q 14 GLN Q 42 ASN ** T 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 624 ASN ** X 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.192605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.169252 restraints weight = 55958.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.171993 restraints weight = 87085.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.168858 restraints weight = 50728.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.169153 restraints weight = 52576.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.169224 restraints weight = 37701.443| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.8679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 38017 Z= 0.149 Angle : 0.733 14.572 51312 Z= 0.374 Chirality : 0.043 0.223 5874 Planarity : 0.005 0.092 6470 Dihedral : 5.118 43.804 5032 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.17 % Rotamer: Outliers : 0.02 % Allowed : 0.34 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -1.28 (0.12), residues: 4515 helix: -0.18 (0.09), residues: 3024 sheet: -1.45 (0.72), residues: 58 loop : -2.13 (0.16), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG r 58 TYR 0.028 0.002 TYR L1376 PHE 0.034 0.002 PHE K 307 TRP 0.046 0.002 TRP J 242 HIS 0.010 0.001 HIS L1374 Details of bonding type rmsd covalent geometry : bond 0.00335 (38017) covalent geometry : angle 0.73332 (51312) hydrogen bonds : bond 0.04563 ( 1734) hydrogen bonds : angle 4.62937 ( 5175) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 899 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 PHE cc_start: 0.6367 (m-80) cc_final: 0.6027 (m-10) REVERT: A 295 MET cc_start: 0.6848 (ppp) cc_final: 0.6427 (ppp) REVERT: A 334 MET cc_start: 0.6743 (ptp) cc_final: 0.5957 (ptp) REVERT: A 390 LEU cc_start: 0.8431 (tp) cc_final: 0.8152 (tp) REVERT: A 454 LYS cc_start: 0.8401 (mttp) cc_final: 0.7971 (mtpp) REVERT: A 478 LEU cc_start: 0.7321 (mp) cc_final: 0.6803 (mp) REVERT: B 379 THR cc_start: 0.8923 (m) cc_final: 0.8676 (m) REVERT: B 402 TYR cc_start: 0.7033 (t80) cc_final: 0.6428 (t80) REVERT: B 411 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7892 (ttm-80) REVERT: B 445 PHE cc_start: 0.7214 (t80) cc_final: 0.6598 (t80) REVERT: C 269 TYR cc_start: 0.5718 (p90) cc_final: 0.5222 (p90) REVERT: C 322 LYS cc_start: 0.7448 (mmmt) cc_final: 0.6981 (mmmt) REVERT: C 377 TYR cc_start: 0.7350 (t80) cc_final: 0.6962 (t80) REVERT: F 365 ARG cc_start: 0.7530 (ptm-80) cc_final: 0.6642 (ptm-80) REVERT: F 410 MET cc_start: 0.6294 (tmm) cc_final: 0.4228 (mmp) REVERT: F 469 MET cc_start: 0.3527 (mtt) cc_final: 0.1639 (ptt) REVERT: G 261 ARG cc_start: 0.5153 (ptt-90) cc_final: 0.4907 (ptt90) REVERT: G 447 ASP cc_start: 0.8349 (m-30) cc_final: 0.8086 (m-30) REVERT: G 483 TYR cc_start: 0.6138 (p90) cc_final: 0.4565 (m-80) REVERT: H 341 LEU cc_start: 0.8199 (mp) cc_final: 0.7750 (tt) REVERT: I 1 MET cc_start: 0.7598 (ppp) cc_final: 0.6739 (tpt) REVERT: I 82 HIS cc_start: 0.7667 (t-90) cc_final: 0.7171 (m90) REVERT: J 228 PHE cc_start: 0.6193 (p90) cc_final: 0.5631 (t80) REVERT: J 327 ILE cc_start: 0.6740 (mm) cc_final: 0.6375 (mm) REVERT: J 470 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7091 (mt-10) REVERT: J 480 ASN cc_start: 0.7195 (t0) cc_final: 0.6636 (t0) REVERT: J 557 MET cc_start: 0.7727 (tmm) cc_final: 0.7104 (tmm) REVERT: J 560 LYS cc_start: 0.7456 (mttm) cc_final: 0.6516 (tttp) REVERT: K 47 LYS cc_start: 0.8547 (mtmt) cc_final: 0.7944 (mmtp) REVERT: K 48 LEU cc_start: 0.9081 (tp) cc_final: 0.8722 (tp) REVERT: K 141 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7058 (tp30) REVERT: K 315 LYS cc_start: 0.8384 (tttp) cc_final: 0.7983 (tptt) REVERT: L 213 ARG cc_start: 0.7314 (ttm-80) cc_final: 0.7044 (ptp-170) REVERT: L 228 MET cc_start: 0.5537 (mmt) cc_final: 0.5052 (mmm) REVERT: L 397 LEU cc_start: 0.8409 (tp) cc_final: 0.7959 (tp) REVERT: L 445 ARG cc_start: 0.7134 (mmt180) cc_final: 0.6707 (mmm160) REVERT: L 593 ASN cc_start: 0.8057 (m-40) cc_final: 0.7839 (m-40) REVERT: O 49 ARG cc_start: 0.6112 (mtp85) cc_final: 0.4958 (ptt-90) REVERT: O 57 LYS cc_start: 0.7463 (mtmm) cc_final: 0.6764 (mtpt) REVERT: O 65 GLN cc_start: 0.6636 (mm110) cc_final: 0.5581 (tp40) REVERT: Q 42 ASN cc_start: 0.6519 (OUTLIER) cc_final: 0.6301 (p0) REVERT: Q 43 PHE cc_start: 0.7538 (p90) cc_final: 0.7198 (p90) REVERT: R 16 LEU cc_start: 0.9151 (tp) cc_final: 0.8858 (tp) REVERT: R 78 HIS cc_start: 0.7634 (t-90) cc_final: 0.7216 (t-90) REVERT: V 605 ASN cc_start: 0.8152 (p0) cc_final: 0.7793 (p0) REVERT: V 620 ARG cc_start: 0.7507 (ptm160) cc_final: 0.6812 (tmm-80) REVERT: V 621 ASP cc_start: 0.7446 (m-30) cc_final: 0.7237 (m-30) REVERT: V 631 LYS cc_start: 0.8923 (pttp) cc_final: 0.8527 (pptt) REVERT: V 642 MET cc_start: 0.9063 (ppp) cc_final: 0.8466 (tmm) REVERT: W 634 HIS cc_start: 0.7747 (t70) cc_final: 0.7261 (t-170) REVERT: W 642 MET cc_start: 0.8630 (ppp) cc_final: 0.8334 (ppp) REVERT: X 606 MET cc_start: 0.8052 (tmm) cc_final: 0.7748 (tmm) REVERT: o 12 ARG cc_start: 0.5870 (mtt180) cc_final: 0.4210 (tpt-90) REVERT: o 48 GLU cc_start: 0.8466 (mp0) cc_final: 0.8118 (mp0) REVERT: p 55 LYS cc_start: 0.8891 (mtmm) cc_final: 0.8530 (mttp) REVERT: s 30 ASP cc_start: 0.6348 (t0) cc_final: 0.5822 (t0) REVERT: s 36 ILE cc_start: 0.7584 (mm) cc_final: 0.7171 (mm) outliers start: 1 outliers final: 0 residues processed: 900 average time/residue: 0.2059 time to fit residues: 300.7627 Evaluate side-chains 703 residues out of total 4166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 702 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 114 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 370 optimal weight: 9.9990 chunk 385 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 chunk 221 optimal weight: 0.4980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN B 386 HIS ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN E 286 GLN E 370 GLN G 289 HIS ** H 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 HIS ** I 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS ** J 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN ** L1374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN Q 42 ASN ** T 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 624 ASN ** V 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 670 ASN W 624 ASN X 624 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.184958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.160132 restraints weight = 57383.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.163142 restraints weight = 108043.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.161328 restraints weight = 56788.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.161577 restraints weight = 56364.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.161830 restraints weight = 40104.700| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.9058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 38017 Z= 0.256 Angle : 0.855 14.371 51312 Z= 0.443 Chirality : 0.048 0.250 5874 Planarity : 0.006 0.081 6470 Dihedral : 5.483 47.844 5032 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 0.05 % Allowed : 0.62 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -1.63 (0.12), residues: 4515 helix: -0.46 (0.09), residues: 3017 sheet: -1.69 (0.63), residues: 68 loop : -2.23 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG p 39 TYR 0.037 0.002 TYR K 184 PHE 0.048 0.003 PHE O 74 TRP 0.050 0.003 TRP J 242 HIS 0.010 0.002 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00590 (38017) covalent geometry : angle 0.85546 (51312) hydrogen bonds : bond 0.05158 ( 1734) hydrogen bonds : angle 5.06316 ( 5175) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6831.57 seconds wall clock time: 118 minutes 36.58 seconds (7116.58 seconds total)