Starting phenix.real_space_refine on Fri Dec 27 15:00:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bou_30134/12_2024/7bou_30134.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bou_30134/12_2024/7bou_30134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bou_30134/12_2024/7bou_30134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bou_30134/12_2024/7bou_30134.map" model { file = "/net/cci-nas-00/data/ceres_data/7bou_30134/12_2024/7bou_30134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bou_30134/12_2024/7bou_30134.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.038 sd= 0.736 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 276 5.16 5 C 30516 2.51 5 N 8256 2.21 5 O 9660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48708 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4059 Classifications: {'peptide': 525} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 494} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 10.08, per 1000 atoms: 0.21 Number of scatterers: 48708 At special positions: 0 Unit cell: (189.23, 189.23, 157.48, 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 276 16.00 O 9660 8.00 N 8256 7.00 C 30516 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: 8.43 Conformation dependent library (CDL) restraints added in 4.9 seconds 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11736 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 48 sheets defined 52.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.651A pdb=" N GLU A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 39 removed outlier: 3.700A pdb=" N ARG A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) Proline residue: A 26 - end of helix removed outlier: 3.530A pdb=" N ASN A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 38 " --> pdb=" O CYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 78 removed outlier: 3.984A pdb=" N ASN A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.595A pdb=" N LEU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 122 removed outlier: 3.908A pdb=" N ALA A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 removed outlier: 3.660A pdb=" N THR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.541A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 271 Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.637A pdb=" N ASN A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.067A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.912A pdb=" N THR A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.053A pdb=" N ARG A 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.564A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.589A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 removed outlier: 3.622A pdb=" N LEU A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.696A pdb=" N ARG A 456 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.513A pdb=" N LYS A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 517 removed outlier: 3.504A pdb=" N GLN A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 496 " --> pdb=" O MET A 492 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.675A pdb=" N SER A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.649A pdb=" N GLU B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 removed outlier: 3.700A pdb=" N ARG B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Proline residue: B 26 - end of helix removed outlier: 3.529A pdb=" N ASN B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 38 " --> pdb=" O CYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 78 removed outlier: 3.983A pdb=" N ASN B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.594A pdb=" N LEU B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 122 removed outlier: 3.909A pdb=" N ALA B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 removed outlier: 3.659A pdb=" N THR B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.542A pdb=" N LYS B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.637A pdb=" N ASN B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 287 " --> pdb=" O GLN B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 removed outlier: 4.067A pdb=" N LYS B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 353 removed outlier: 3.910A pdb=" N THR B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.054A pdb=" N ARG B 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 removed outlier: 3.563A pdb=" N VAL B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 398 through 411 removed outlier: 3.590A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 3.623A pdb=" N LEU B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.695A pdb=" N ARG B 456 " --> pdb=" O ALA B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 474 removed outlier: 3.514A pdb=" N LYS B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 517 removed outlier: 3.505A pdb=" N GLN B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 496 " --> pdb=" O MET B 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 531 removed outlier: 3.674A pdb=" N SER B 529 " --> pdb=" O ALA B 525 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 3.650A pdb=" N GLU C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 39 removed outlier: 3.699A pdb=" N ARG C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) Proline residue: C 26 - end of helix removed outlier: 3.529A pdb=" N ASN C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 37 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR C 38 " --> pdb=" O CYS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 78 removed outlier: 3.985A pdb=" N ASN C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.594A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 122 removed outlier: 3.909A pdb=" N ALA C 104 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 115 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 removed outlier: 3.658A pdb=" N THR C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 202 removed outlier: 3.541A pdb=" N LYS C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 271 Processing helix chain 'C' and resid 272 through 295 removed outlier: 3.637A pdb=" N ASN C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 287 " --> pdb=" O GLN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 314 removed outlier: 4.067A pdb=" N LYS C 313 " --> pdb=" O ARG C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 353 removed outlier: 3.911A pdb=" N THR C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.053A pdb=" N ARG C 375 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.563A pdb=" N VAL C 388 " --> pdb=" O THR C 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 398 through 411 removed outlier: 3.590A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 451 removed outlier: 3.621A pdb=" N LEU C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR C 447 " --> pdb=" O GLU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 456 removed outlier: 3.696A pdb=" N ARG C 456 " --> pdb=" O ALA C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 474 removed outlier: 3.514A pdb=" N LYS C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 517 removed outlier: 3.506A pdb=" N GLN C 495 " --> pdb=" O LYS C 491 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 496 " --> pdb=" O MET C 492 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 509 " --> pdb=" O ALA C 505 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 531 removed outlier: 3.675A pdb=" N SER C 529 " --> pdb=" O ALA C 525 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 530 " --> pdb=" O ALA C 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.649A pdb=" N GLU D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 39 removed outlier: 3.700A pdb=" N ARG D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 25 " --> pdb=" O LYS D 21 " (cutoff:3.500A) Proline residue: D 26 - end of helix removed outlier: 3.528A pdb=" N ASN D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR D 38 " --> pdb=" O CYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 78 removed outlier: 3.983A pdb=" N ASN D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS D 72 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 96 removed outlier: 3.595A pdb=" N LEU D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 122 removed outlier: 3.908A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 removed outlier: 3.660A pdb=" N THR D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 202 removed outlier: 3.543A pdb=" N LYS D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 271 Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.637A pdb=" N ASN D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 285 " --> pdb=" O ASN D 281 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 287 " --> pdb=" O GLN D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 removed outlier: 4.067A pdb=" N LYS D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 353 removed outlier: 3.911A pdb=" N THR D 339 " --> pdb=" O GLN D 335 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.054A pdb=" N ARG D 375 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 389 removed outlier: 3.564A pdb=" N VAL D 388 " --> pdb=" O THR D 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 398 through 411 removed outlier: 3.591A pdb=" N LEU D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 451 removed outlier: 3.622A pdb=" N LEU D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR D 447 " --> pdb=" O GLU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 456 removed outlier: 3.698A pdb=" N ARG D 456 " --> pdb=" O ALA D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 474 removed outlier: 3.514A pdb=" N LYS D 467 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 517 removed outlier: 3.504A pdb=" N GLN D 495 " --> pdb=" O LYS D 491 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D 496 " --> pdb=" O MET D 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 509 " --> pdb=" O ALA D 505 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR D 517 " --> pdb=" O ALA D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 531 removed outlier: 3.673A pdb=" N SER D 529 " --> pdb=" O ALA D 525 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.650A pdb=" N GLU E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 39 removed outlier: 3.700A pdb=" N ARG E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 25 " --> pdb=" O LYS E 21 " (cutoff:3.500A) Proline residue: E 26 - end of helix removed outlier: 3.529A pdb=" N ASN E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR E 38 " --> pdb=" O CYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.985A pdb=" N ASN E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS E 72 " --> pdb=" O ASN E 68 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 96 removed outlier: 3.594A pdb=" N LEU E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 122 removed outlier: 3.909A pdb=" N ALA E 104 " --> pdb=" O PRO E 100 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 140 removed outlier: 3.659A pdb=" N THR E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 202 removed outlier: 3.541A pdb=" N LYS E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 271 Processing helix chain 'E' and resid 272 through 295 removed outlier: 3.637A pdb=" N ASN E 281 " --> pdb=" O ARG E 277 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA E 285 " --> pdb=" O ASN E 281 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 287 " --> pdb=" O GLN E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 314 removed outlier: 4.068A pdb=" N LYS E 313 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.912A pdb=" N THR E 339 " --> pdb=" O GLN E 335 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 377 removed outlier: 4.054A pdb=" N ARG E 375 " --> pdb=" O GLU E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.564A pdb=" N VAL E 388 " --> pdb=" O THR E 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR E 389 " --> pdb=" O LEU E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 396 Processing helix chain 'E' and resid 398 through 411 removed outlier: 3.590A pdb=" N LEU E 404 " --> pdb=" O LEU E 400 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS E 406 " --> pdb=" O ARG E 402 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 451 removed outlier: 3.622A pdb=" N LEU E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR E 447 " --> pdb=" O GLU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 456 removed outlier: 3.697A pdb=" N ARG E 456 " --> pdb=" O ALA E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 474 removed outlier: 3.514A pdb=" N LYS E 467 " --> pdb=" O LEU E 463 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU E 468 " --> pdb=" O ALA E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 517 removed outlier: 3.505A pdb=" N GLN E 495 " --> pdb=" O LYS E 491 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER E 496 " --> pdb=" O MET E 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E 509 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 513 " --> pdb=" O ALA E 509 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN E 515 " --> pdb=" O GLY E 511 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR E 517 " --> pdb=" O ALA E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 531 removed outlier: 3.675A pdb=" N SER E 529 " --> pdb=" O ALA E 525 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL E 530 " --> pdb=" O ALA E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.649A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 39 removed outlier: 3.700A pdb=" N ARG F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) Proline residue: F 26 - end of helix removed outlier: 3.529A pdb=" N ASN F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR F 37 " --> pdb=" O ASN F 33 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR F 38 " --> pdb=" O CYS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 78 removed outlier: 3.985A pdb=" N ASN F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 76 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 96 removed outlier: 3.594A pdb=" N LEU F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 122 removed outlier: 3.908A pdb=" N ALA F 104 " --> pdb=" O PRO F 100 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 140 removed outlier: 3.660A pdb=" N THR F 129 " --> pdb=" O SER F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.542A pdb=" N LYS F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 271 Processing helix chain 'F' and resid 272 through 295 removed outlier: 3.636A pdb=" N ASN F 281 " --> pdb=" O ARG F 277 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA F 285 " --> pdb=" O ASN F 281 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 314 removed outlier: 4.068A pdb=" N LYS F 313 " --> pdb=" O ARG F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 353 removed outlier: 3.912A pdb=" N THR F 339 " --> pdb=" O GLN F 335 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 377 removed outlier: 4.054A pdb=" N ARG F 375 " --> pdb=" O GLU F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 389 removed outlier: 3.564A pdb=" N VAL F 388 " --> pdb=" O THR F 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR F 389 " --> pdb=" O LEU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 396 Processing helix chain 'F' and resid 398 through 411 removed outlier: 3.590A pdb=" N LEU F 404 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS F 406 " --> pdb=" O ARG F 402 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 451 removed outlier: 3.621A pdb=" N LEU F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F 447 " --> pdb=" O GLU F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 456 removed outlier: 3.697A pdb=" N ARG F 456 " --> pdb=" O ALA F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 474 removed outlier: 3.515A pdb=" N LYS F 467 " --> pdb=" O LEU F 463 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 517 removed outlier: 3.505A pdb=" N GLN F 495 " --> pdb=" O LYS F 491 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER F 496 " --> pdb=" O MET F 492 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA F 509 " --> pdb=" O ALA F 505 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA F 513 " --> pdb=" O ALA F 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN F 515 " --> pdb=" O GLY F 511 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR F 517 " --> pdb=" O ALA F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 531 removed outlier: 3.675A pdb=" N SER F 529 " --> pdb=" O ALA F 525 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL F 530 " --> pdb=" O ALA F 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 20 removed outlier: 3.650A pdb=" N GLU G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 39 removed outlier: 3.700A pdb=" N ARG G 24 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) Proline residue: G 26 - end of helix removed outlier: 3.528A pdb=" N ASN G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR G 38 " --> pdb=" O CYS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 78 removed outlier: 3.985A pdb=" N ASN G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 removed outlier: 3.594A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 122 removed outlier: 3.907A pdb=" N ALA G 104 " --> pdb=" O PRO G 100 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG G 115 " --> pdb=" O SER G 111 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET G 118 " --> pdb=" O GLU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 140 removed outlier: 3.660A pdb=" N THR G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 202 removed outlier: 3.542A pdb=" N LYS G 196 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 271 Processing helix chain 'G' and resid 272 through 295 removed outlier: 3.637A pdb=" N ASN G 281 " --> pdb=" O ARG G 277 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA G 285 " --> pdb=" O ASN G 281 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL G 287 " --> pdb=" O GLN G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 314 removed outlier: 4.068A pdb=" N LYS G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 353 removed outlier: 3.910A pdb=" N THR G 339 " --> pdb=" O GLN G 335 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 377 removed outlier: 4.054A pdb=" N ARG G 375 " --> pdb=" O GLU G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 389 removed outlier: 3.562A pdb=" N VAL G 388 " --> pdb=" O THR G 384 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR G 389 " --> pdb=" O LEU G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 396 Processing helix chain 'G' and resid 398 through 411 removed outlier: 3.589A pdb=" N LEU G 404 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 406 " --> pdb=" O ARG G 402 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN G 409 " --> pdb=" O LEU G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 451 removed outlier: 3.622A pdb=" N LEU G 442 " --> pdb=" O ASP G 438 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR G 447 " --> pdb=" O GLU G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 456 removed outlier: 3.697A pdb=" N ARG G 456 " --> pdb=" O ALA G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 474 removed outlier: 3.515A pdb=" N LYS G 467 " --> pdb=" O LEU G 463 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU G 468 " --> pdb=" O ALA G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 517 removed outlier: 3.503A pdb=" N GLN G 495 " --> pdb=" O LYS G 491 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER G 496 " --> pdb=" O MET G 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA G 509 " --> pdb=" O ALA G 505 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 513 " --> pdb=" O ALA G 509 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR G 517 " --> pdb=" O ALA G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 520 through 531 removed outlier: 3.675A pdb=" N SER G 529 " --> pdb=" O ALA G 525 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL G 530 " --> pdb=" O ALA G 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.651A pdb=" N GLU H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 39 removed outlier: 3.700A pdb=" N ARG H 24 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA H 25 " --> pdb=" O LYS H 21 " (cutoff:3.500A) Proline residue: H 26 - end of helix removed outlier: 3.529A pdb=" N ASN H 33 " --> pdb=" O THR H 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR H 37 " --> pdb=" O ASN H 33 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR H 38 " --> pdb=" O CYS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 78 removed outlier: 3.984A pdb=" N ASN H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 96 removed outlier: 3.595A pdb=" N LEU H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 122 removed outlier: 3.907A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG H 115 " --> pdb=" O SER H 111 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET H 118 " --> pdb=" O GLU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 140 removed outlier: 3.660A pdb=" N THR H 129 " --> pdb=" O SER H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 202 removed outlier: 3.542A pdb=" N LYS H 196 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 271 Processing helix chain 'H' and resid 272 through 295 removed outlier: 3.637A pdb=" N ASN H 281 " --> pdb=" O ARG H 277 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA H 285 " --> pdb=" O ASN H 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL H 287 " --> pdb=" O GLN H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 314 removed outlier: 4.067A pdb=" N LYS H 313 " --> pdb=" O ARG H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 353 removed outlier: 3.910A pdb=" N THR H 339 " --> pdb=" O GLN H 335 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL H 340 " --> pdb=" O ALA H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 377 removed outlier: 4.053A pdb=" N ARG H 375 " --> pdb=" O GLU H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 389 removed outlier: 3.563A pdb=" N VAL H 388 " --> pdb=" O THR H 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR H 389 " --> pdb=" O LEU H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 396 Processing helix chain 'H' and resid 398 through 411 removed outlier: 3.589A pdb=" N LEU H 404 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS H 406 " --> pdb=" O ARG H 402 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN H 409 " --> pdb=" O LEU H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 451 removed outlier: 3.622A pdb=" N LEU H 442 " --> pdb=" O ASP H 438 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR H 447 " --> pdb=" O GLU H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 456 removed outlier: 3.697A pdb=" N ARG H 456 " --> pdb=" O ALA H 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 474 removed outlier: 3.514A pdb=" N LYS H 467 " --> pdb=" O LEU H 463 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU H 468 " --> pdb=" O ALA H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 517 removed outlier: 3.504A pdb=" N GLN H 495 " --> pdb=" O LYS H 491 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 496 " --> pdb=" O MET H 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA H 509 " --> pdb=" O ALA H 505 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 513 " --> pdb=" O ALA H 509 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN H 515 " --> pdb=" O GLY H 511 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR H 517 " --> pdb=" O ALA H 513 " (cutoff:3.500A) Processing helix chain 'H' and resid 520 through 531 removed outlier: 3.675A pdb=" N SER H 529 " --> pdb=" O ALA H 525 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL H 530 " --> pdb=" O ALA H 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 20 removed outlier: 3.650A pdb=" N GLU I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 39 removed outlier: 3.700A pdb=" N ARG I 24 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) Proline residue: I 26 - end of helix removed outlier: 3.529A pdb=" N ASN I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR I 38 " --> pdb=" O CYS I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.984A pdb=" N ASN I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS I 72 " --> pdb=" O ASN I 68 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 76 " --> pdb=" O LYS I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 96 removed outlier: 3.595A pdb=" N LEU I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 122 removed outlier: 3.909A pdb=" N ALA I 104 " --> pdb=" O PRO I 100 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG I 115 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 140 removed outlier: 3.660A pdb=" N THR I 129 " --> pdb=" O SER I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 202 removed outlier: 3.542A pdb=" N LYS I 196 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA I 197 " --> pdb=" O ASP I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 271 Processing helix chain 'I' and resid 272 through 295 removed outlier: 3.637A pdb=" N ASN I 281 " --> pdb=" O ARG I 277 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA I 285 " --> pdb=" O ASN I 281 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL I 287 " --> pdb=" O GLN I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 314 removed outlier: 4.068A pdb=" N LYS I 313 " --> pdb=" O ARG I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 353 removed outlier: 3.911A pdb=" N THR I 339 " --> pdb=" O GLN I 335 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 377 removed outlier: 4.053A pdb=" N ARG I 375 " --> pdb=" O GLU I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.564A pdb=" N VAL I 388 " --> pdb=" O THR I 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR I 389 " --> pdb=" O LEU I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 396 Processing helix chain 'I' and resid 398 through 411 removed outlier: 3.590A pdb=" N LEU I 404 " --> pdb=" O LEU I 400 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS I 406 " --> pdb=" O ARG I 402 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN I 409 " --> pdb=" O LEU I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 451 removed outlier: 3.622A pdb=" N LEU I 442 " --> pdb=" O ASP I 438 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS I 445 " --> pdb=" O LYS I 441 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR I 447 " --> pdb=" O GLU I 443 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 456 removed outlier: 3.697A pdb=" N ARG I 456 " --> pdb=" O ALA I 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 474 removed outlier: 3.515A pdb=" N LYS I 467 " --> pdb=" O LEU I 463 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU I 468 " --> pdb=" O ALA I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 517 removed outlier: 3.505A pdb=" N GLN I 495 " --> pdb=" O LYS I 491 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER I 496 " --> pdb=" O MET I 492 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA I 509 " --> pdb=" O ALA I 505 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA I 513 " --> pdb=" O ALA I 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN I 515 " --> pdb=" O GLY I 511 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR I 517 " --> pdb=" O ALA I 513 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 531 removed outlier: 3.675A pdb=" N SER I 529 " --> pdb=" O ALA I 525 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL I 530 " --> pdb=" O ALA I 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 20 removed outlier: 3.649A pdb=" N GLU J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 39 removed outlier: 3.700A pdb=" N ARG J 24 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) Proline residue: J 26 - end of helix removed outlier: 3.529A pdb=" N ASN J 33 " --> pdb=" O THR J 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR J 37 " --> pdb=" O ASN J 33 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR J 38 " --> pdb=" O CYS J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 78 removed outlier: 3.984A pdb=" N ASN J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS J 72 " --> pdb=" O ASN J 68 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA J 76 " --> pdb=" O LYS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.594A pdb=" N LEU J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 122 removed outlier: 3.909A pdb=" N ALA J 104 " --> pdb=" O PRO J 100 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG J 115 " --> pdb=" O SER J 111 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET J 118 " --> pdb=" O GLU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 140 removed outlier: 3.659A pdb=" N THR J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 202 removed outlier: 3.542A pdb=" N LYS J 196 " --> pdb=" O GLU J 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 271 Processing helix chain 'J' and resid 272 through 295 removed outlier: 3.636A pdb=" N ASN J 281 " --> pdb=" O ARG J 277 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA J 285 " --> pdb=" O ASN J 281 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL J 287 " --> pdb=" O GLN J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 314 removed outlier: 4.068A pdb=" N LYS J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 353 removed outlier: 3.911A pdb=" N THR J 339 " --> pdb=" O GLN J 335 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 377 removed outlier: 4.053A pdb=" N ARG J 375 " --> pdb=" O GLU J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 389 removed outlier: 3.565A pdb=" N VAL J 388 " --> pdb=" O THR J 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR J 389 " --> pdb=" O LEU J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 396 Processing helix chain 'J' and resid 398 through 411 removed outlier: 3.589A pdb=" N LEU J 404 " --> pdb=" O LEU J 400 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS J 406 " --> pdb=" O ARG J 402 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN J 409 " --> pdb=" O LEU J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 436 through 451 removed outlier: 3.622A pdb=" N LEU J 442 " --> pdb=" O ASP J 438 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS J 445 " --> pdb=" O LYS J 441 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR J 447 " --> pdb=" O GLU J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 456 removed outlier: 3.697A pdb=" N ARG J 456 " --> pdb=" O ALA J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 474 removed outlier: 3.514A pdb=" N LYS J 467 " --> pdb=" O LEU J 463 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU J 468 " --> pdb=" O ALA J 464 " (cutoff:3.500A) Processing helix chain 'J' and resid 488 through 517 removed outlier: 3.506A pdb=" N GLN J 495 " --> pdb=" O LYS J 491 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER J 496 " --> pdb=" O MET J 492 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA J 509 " --> pdb=" O ALA J 505 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA J 513 " --> pdb=" O ALA J 509 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN J 515 " --> pdb=" O GLY J 511 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR J 517 " --> pdb=" O ALA J 513 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 531 removed outlier: 3.674A pdb=" N SER J 529 " --> pdb=" O ALA J 525 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL J 530 " --> pdb=" O ALA J 526 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 20 removed outlier: 3.650A pdb=" N GLU K 18 " --> pdb=" O LYS K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 39 removed outlier: 3.701A pdb=" N ARG K 24 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA K 25 " --> pdb=" O LYS K 21 " (cutoff:3.500A) Proline residue: K 26 - end of helix removed outlier: 3.529A pdb=" N ASN K 33 " --> pdb=" O THR K 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR K 37 " --> pdb=" O ASN K 33 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR K 38 " --> pdb=" O CYS K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 78 removed outlier: 3.984A pdb=" N ASN K 67 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU K 69 " --> pdb=" O GLY K 65 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS K 72 " --> pdb=" O ASN K 68 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA K 76 " --> pdb=" O LYS K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 96 removed outlier: 3.594A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 122 removed outlier: 3.907A pdb=" N ALA K 104 " --> pdb=" O PRO K 100 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG K 115 " --> pdb=" O SER K 111 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET K 118 " --> pdb=" O GLU K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 140 removed outlier: 3.660A pdb=" N THR K 129 " --> pdb=" O SER K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 202 removed outlier: 3.541A pdb=" N LYS K 196 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA K 197 " --> pdb=" O ASP K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 271 Processing helix chain 'K' and resid 272 through 295 removed outlier: 3.637A pdb=" N ASN K 281 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA K 285 " --> pdb=" O ASN K 281 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL K 287 " --> pdb=" O GLN K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 314 removed outlier: 4.067A pdb=" N LYS K 313 " --> pdb=" O ARG K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 353 removed outlier: 3.910A pdb=" N THR K 339 " --> pdb=" O GLN K 335 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL K 340 " --> pdb=" O ALA K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 377 removed outlier: 4.054A pdb=" N ARG K 375 " --> pdb=" O GLU K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 389 removed outlier: 3.563A pdb=" N VAL K 388 " --> pdb=" O THR K 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR K 389 " --> pdb=" O LEU K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 391 through 396 Processing helix chain 'K' and resid 398 through 411 removed outlier: 3.588A pdb=" N LEU K 404 " --> pdb=" O LEU K 400 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS K 406 " --> pdb=" O ARG K 402 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN K 409 " --> pdb=" O LEU K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 451 removed outlier: 3.621A pdb=" N LEU K 442 " --> pdb=" O ASP K 438 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS K 445 " --> pdb=" O LYS K 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR K 447 " --> pdb=" O GLU K 443 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 456 removed outlier: 3.696A pdb=" N ARG K 456 " --> pdb=" O ALA K 453 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 474 removed outlier: 3.514A pdb=" N LYS K 467 " --> pdb=" O LEU K 463 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU K 468 " --> pdb=" O ALA K 464 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 517 removed outlier: 3.505A pdb=" N GLN K 495 " --> pdb=" O LYS K 491 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER K 496 " --> pdb=" O MET K 492 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA K 509 " --> pdb=" O ALA K 505 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA K 513 " --> pdb=" O ALA K 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN K 515 " --> pdb=" O GLY K 511 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR K 517 " --> pdb=" O ALA K 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 520 through 531 removed outlier: 3.675A pdb=" N SER K 529 " --> pdb=" O ALA K 525 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL K 530 " --> pdb=" O ALA K 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 20 removed outlier: 3.650A pdb=" N GLU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 39 removed outlier: 3.699A pdb=" N ARG L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA L 25 " --> pdb=" O LYS L 21 " (cutoff:3.500A) Proline residue: L 26 - end of helix removed outlier: 3.528A pdb=" N ASN L 33 " --> pdb=" O THR L 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR L 37 " --> pdb=" O ASN L 33 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR L 38 " --> pdb=" O CYS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 78 removed outlier: 3.984A pdb=" N ASN L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU L 69 " --> pdb=" O GLY L 65 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS L 72 " --> pdb=" O ASN L 68 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA L 76 " --> pdb=" O LYS L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 96 removed outlier: 3.594A pdb=" N LEU L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 122 removed outlier: 3.907A pdb=" N ALA L 104 " --> pdb=" O PRO L 100 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG L 115 " --> pdb=" O SER L 111 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 140 removed outlier: 3.659A pdb=" N THR L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 202 removed outlier: 3.542A pdb=" N LYS L 196 " --> pdb=" O GLU L 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA L 197 " --> pdb=" O ASP L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 271 Processing helix chain 'L' and resid 272 through 295 removed outlier: 3.637A pdb=" N ASN L 281 " --> pdb=" O ARG L 277 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA L 285 " --> pdb=" O ASN L 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL L 287 " --> pdb=" O GLN L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 314 removed outlier: 4.068A pdb=" N LYS L 313 " --> pdb=" O ARG L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 353 removed outlier: 3.911A pdb=" N THR L 339 " --> pdb=" O GLN L 335 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL L 340 " --> pdb=" O ALA L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 377 removed outlier: 4.053A pdb=" N ARG L 375 " --> pdb=" O GLU L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 389 removed outlier: 3.563A pdb=" N VAL L 388 " --> pdb=" O THR L 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR L 389 " --> pdb=" O LEU L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 391 through 396 Processing helix chain 'L' and resid 398 through 411 removed outlier: 3.588A pdb=" N LEU L 404 " --> pdb=" O LEU L 400 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS L 406 " --> pdb=" O ARG L 402 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN L 409 " --> pdb=" O LEU L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 436 through 451 removed outlier: 3.620A pdb=" N LEU L 442 " --> pdb=" O ASP L 438 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS L 445 " --> pdb=" O LYS L 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR L 447 " --> pdb=" O GLU L 443 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 456 removed outlier: 3.697A pdb=" N ARG L 456 " --> pdb=" O ALA L 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 474 removed outlier: 3.515A pdb=" N LYS L 467 " --> pdb=" O LEU L 463 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU L 468 " --> pdb=" O ALA L 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 517 removed outlier: 3.505A pdb=" N GLN L 495 " --> pdb=" O LYS L 491 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER L 496 " --> pdb=" O MET L 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA L 509 " --> pdb=" O ALA L 505 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA L 513 " --> pdb=" O ALA L 509 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN L 515 " --> pdb=" O GLY L 511 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR L 517 " --> pdb=" O ALA L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 520 through 531 removed outlier: 3.675A pdb=" N SER L 529 " --> pdb=" O ALA L 525 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL L 530 " --> pdb=" O ALA L 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.592A pdb=" N LEU A 144 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 145 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 252 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.650A pdb=" N THR A 181 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 330 removed outlier: 4.552A pdb=" N ILE A 297 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.489A pdb=" N VAL A 320 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE B 297 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 removed outlier: 3.591A pdb=" N LEU B 144 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 145 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 252 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.651A pdb=" N THR B 181 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.316A pdb=" N VAL B 320 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE C 297 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AB2, first strand: chain 'C' and resid 159 through 161 removed outlier: 3.592A pdb=" N LEU C 144 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 145 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 252 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.651A pdb=" N THR C 181 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 319 through 321 removed outlier: 6.472A pdb=" N VAL C 320 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 297 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.592A pdb=" N LEU D 144 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 145 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 252 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.651A pdb=" N THR D 181 " --> pdb=" O THR D 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 319 through 321 removed outlier: 6.015A pdb=" N VAL D 320 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE E 297 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AC1, first strand: chain 'E' and resid 159 through 161 removed outlier: 3.592A pdb=" N LEU E 144 " --> pdb=" O TYR E 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 145 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE E 252 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.651A pdb=" N THR E 181 " --> pdb=" O THR E 215 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 319 through 321 removed outlier: 6.186A pdb=" N VAL E 320 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE F 297 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AC5, first strand: chain 'F' and resid 159 through 161 removed outlier: 3.592A pdb=" N LEU F 144 " --> pdb=" O TYR F 161 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 145 " --> pdb=" O ILE F 252 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE F 252 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 166 through 170 removed outlier: 3.651A pdb=" N THR F 181 " --> pdb=" O THR F 215 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 319 through 321 removed outlier: 6.497A pdb=" N VAL F 320 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE G 297 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AC9, first strand: chain 'G' and resid 159 through 161 removed outlier: 3.592A pdb=" N LEU G 144 " --> pdb=" O TYR G 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 145 " --> pdb=" O ILE G 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE G 252 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 166 through 170 removed outlier: 3.652A pdb=" N THR G 181 " --> pdb=" O THR G 215 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 319 through 321 removed outlier: 6.085A pdb=" N VAL G 320 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE H 297 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 87 through 88 Processing sheet with id=AD4, first strand: chain 'H' and resid 159 through 161 removed outlier: 3.592A pdb=" N LEU H 144 " --> pdb=" O TYR H 161 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU H 145 " --> pdb=" O ILE H 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE H 252 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 166 through 170 removed outlier: 3.651A pdb=" N THR H 181 " --> pdb=" O THR H 215 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 319 through 321 removed outlier: 6.197A pdb=" N VAL H 320 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE I 297 " --> pdb=" O LEU I 330 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 87 through 88 Processing sheet with id=AD8, first strand: chain 'I' and resid 159 through 161 removed outlier: 3.592A pdb=" N LEU I 144 " --> pdb=" O TYR I 161 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 145 " --> pdb=" O ILE I 252 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE I 252 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 166 through 170 removed outlier: 3.651A pdb=" N THR I 181 " --> pdb=" O THR I 215 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 319 through 321 removed outlier: 6.183A pdb=" N VAL I 320 " --> pdb=" O VAL J 300 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE J 297 " --> pdb=" O LEU J 330 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AE3, first strand: chain 'J' and resid 159 through 161 removed outlier: 3.593A pdb=" N LEU J 144 " --> pdb=" O TYR J 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU J 145 " --> pdb=" O ILE J 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE J 252 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.651A pdb=" N THR J 181 " --> pdb=" O THR J 215 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 319 through 321 removed outlier: 6.398A pdb=" N VAL J 320 " --> pdb=" O VAL K 300 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE K 297 " --> pdb=" O LEU K 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'K' and resid 159 through 161 removed outlier: 3.592A pdb=" N LEU K 144 " --> pdb=" O TYR K 161 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU K 145 " --> pdb=" O ILE K 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE K 252 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 166 through 170 removed outlier: 3.650A pdb=" N THR K 181 " --> pdb=" O THR K 215 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 319 through 321 removed outlier: 6.027A pdb=" N VAL K 320 " --> pdb=" O VAL L 300 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE L 297 " --> pdb=" O LEU L 330 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 87 through 88 Processing sheet with id=AF2, first strand: chain 'L' and resid 159 through 161 removed outlier: 3.593A pdb=" N LEU L 144 " --> pdb=" O TYR L 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU L 145 " --> pdb=" O ILE L 252 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE L 252 " --> pdb=" O LEU L 145 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 166 through 170 removed outlier: 3.650A pdb=" N THR L 181 " --> pdb=" O THR L 215 " (cutoff:3.500A) 2102 hydrogen bonds defined for protein. 6018 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: 14.05 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15795 1.34 - 1.45: 6413 1.45 - 1.57: 26704 1.57 - 1.69: 12 1.69 - 1.81: 516 Bond restraints: 49440 Sorted by residual: bond pdb=" N PRO D 534 " pdb=" CD PRO D 534 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" N PRO G 534 " pdb=" CD PRO G 534 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" N PRO C 534 " pdb=" CD PRO C 534 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" N PRO A 534 " pdb=" CD PRO A 534 " ideal model delta sigma weight residual 1.473 1.518 -0.045 1.40e-02 5.10e+03 1.06e+01 bond pdb=" N PRO K 534 " pdb=" CD PRO K 534 " ideal model delta sigma weight residual 1.473 1.518 -0.045 1.40e-02 5.10e+03 1.04e+01 ... (remaining 49435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 65818 3.93 - 7.86: 876 7.86 - 11.79: 170 11.79 - 15.71: 24 15.71 - 19.64: 24 Bond angle restraints: 66912 Sorted by residual: angle pdb=" N VAL E 369 " pdb=" CA VAL E 369 " pdb=" C VAL E 369 " ideal model delta sigma weight residual 109.34 128.98 -19.64 2.08e+00 2.31e-01 8.92e+01 angle pdb=" N VAL A 369 " pdb=" CA VAL A 369 " pdb=" C VAL A 369 " ideal model delta sigma weight residual 109.34 128.95 -19.61 2.08e+00 2.31e-01 8.88e+01 angle pdb=" N VAL G 369 " pdb=" CA VAL G 369 " pdb=" C VAL G 369 " ideal model delta sigma weight residual 109.34 128.94 -19.60 2.08e+00 2.31e-01 8.88e+01 angle pdb=" N VAL F 369 " pdb=" CA VAL F 369 " pdb=" C VAL F 369 " ideal model delta sigma weight residual 109.34 128.94 -19.60 2.08e+00 2.31e-01 8.88e+01 angle pdb=" N VAL C 369 " pdb=" CA VAL C 369 " pdb=" C VAL C 369 " ideal model delta sigma weight residual 109.34 128.94 -19.60 2.08e+00 2.31e-01 8.88e+01 ... (remaining 66907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.42: 28930 19.42 - 38.85: 1418 38.85 - 58.27: 180 58.27 - 77.70: 36 77.70 - 97.12: 12 Dihedral angle restraints: 30576 sinusoidal: 12300 harmonic: 18276 Sorted by residual: dihedral pdb=" CA ARG D 368 " pdb=" C ARG D 368 " pdb=" N VAL D 369 " pdb=" CA VAL D 369 " ideal model delta harmonic sigma weight residual 180.00 82.88 97.12 0 5.00e+00 4.00e-02 3.77e+02 dihedral pdb=" CA ARG B 368 " pdb=" C ARG B 368 " pdb=" N VAL B 369 " pdb=" CA VAL B 369 " ideal model delta harmonic sigma weight residual 180.00 82.95 97.05 0 5.00e+00 4.00e-02 3.77e+02 dihedral pdb=" CA ARG J 368 " pdb=" C ARG J 368 " pdb=" N VAL J 369 " pdb=" CA VAL J 369 " ideal model delta harmonic sigma weight residual 180.00 82.96 97.04 0 5.00e+00 4.00e-02 3.77e+02 ... (remaining 30573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5741 0.064 - 0.128: 1510 0.128 - 0.192: 208 0.192 - 0.256: 66 0.256 - 0.320: 47 Chirality restraints: 7572 Sorted by residual: chirality pdb=" CA VAL B 369 " pdb=" N VAL B 369 " pdb=" C VAL B 369 " pdb=" CB VAL B 369 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA VAL J 369 " pdb=" N VAL J 369 " pdb=" C VAL J 369 " pdb=" CB VAL J 369 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL G 369 " pdb=" N VAL G 369 " pdb=" C VAL G 369 " pdb=" CB VAL G 369 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 7569 not shown) Planarity restraints: 8832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 533 " 0.081 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO D 534 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO D 534 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 534 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 533 " 0.081 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO C 534 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 534 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 534 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 533 " 0.081 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO B 534 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 534 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 534 " 0.059 5.00e-02 4.00e+02 ... (remaining 8829 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 15536 2.83 - 3.35: 45585 3.35 - 3.86: 78725 3.86 - 4.38: 93400 4.38 - 4.90: 151150 Nonbonded interactions: 384396 Sorted by model distance: nonbonded pdb=" OG1 THR H 181 " pdb=" OG1 THR H 215 " model vdw 2.311 3.040 nonbonded pdb=" OG1 THR L 181 " pdb=" OG1 THR L 215 " model vdw 2.311 3.040 nonbonded pdb=" OG1 THR B 181 " pdb=" OG1 THR B 215 " model vdw 2.311 3.040 nonbonded pdb=" OG1 THR K 181 " pdb=" OG1 THR K 215 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR G 181 " pdb=" OG1 THR G 215 " model vdw 2.312 3.040 ... (remaining 384391 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.10 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: 2.040 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: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 66.040 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 49440 Z= 0.468 Angle : 1.275 19.642 66912 Z= 0.681 Chirality : 0.064 0.320 7572 Planarity : 0.009 0.112 8832 Dihedral : 12.074 97.123 18840 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 1.34 % Allowed : 7.10 % Favored : 91.55 % Rotamer: Outliers : 0.92 % Allowed : 7.14 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.00 % Twisted Proline : 4.17 % Twisted General : 1.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.82 (0.07), residues: 6252 helix: -4.37 (0.04), residues: 2904 sheet: -2.85 (0.16), residues: 708 loop : -3.34 (0.09), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 449 HIS 0.003 0.002 HIS C 216 PHE 0.031 0.005 PHE K 78 TYR 0.022 0.003 TYR A 54 ARG 0.010 0.002 ARG H 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1862 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1814 time to evaluate : 4.151 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: A 75 LEU cc_start: 0.9066 (tt) cc_final: 0.8724 (mm) REVERT: A 120 TYR cc_start: 0.9147 (t80) cc_final: 0.8664 (t80) REVERT: A 237 VAL cc_start: 0.8583 (p) cc_final: 0.8050 (m) REVERT: A 240 SER cc_start: 0.8306 (m) cc_final: 0.7969 (p) REVERT: A 268 TYR cc_start: 0.8926 (t80) cc_final: 0.8702 (t80) REVERT: A 279 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9118 (tp) REVERT: A 461 ILE cc_start: 0.8783 (mt) cc_final: 0.8420 (mt) REVERT: A 474 ILE cc_start: 0.8847 (mm) cc_final: 0.8562 (mm) REVERT: A 477 ASP cc_start: 0.8037 (p0) cc_final: 0.7651 (p0) REVERT: A 494 GLN cc_start: 0.8540 (mm110) cc_final: 0.7765 (tm-30) REVERT: B 23 ASP cc_start: 0.7949 (t70) cc_final: 0.7520 (t0) REVERT: B 118 MET cc_start: 0.8775 (mmm) cc_final: 0.8558 (mmm) REVERT: B 474 ILE cc_start: 0.9158 (mm) cc_final: 0.8952 (mp) REVERT: B 477 ASP cc_start: 0.7748 (p0) cc_final: 0.7543 (p0) REVERT: B 489 GLN cc_start: 0.7673 (mt0) cc_final: 0.7405 (tp40) REVERT: B 494 GLN cc_start: 0.8637 (mm110) cc_final: 0.8211 (tm-30) REVERT: B 501 MET cc_start: 0.8404 (mtt) cc_final: 0.8021 (mtp) REVERT: B 503 ASN cc_start: 0.8943 (t0) cc_final: 0.8614 (m-40) REVERT: C 75 LEU cc_start: 0.9053 (tt) cc_final: 0.8797 (tp) REVERT: C 84 MET cc_start: 0.8251 (pmm) cc_final: 0.7989 (pmm) REVERT: C 156 ASN cc_start: 0.8460 (t0) cc_final: 0.8111 (t0) REVERT: C 164 SER cc_start: 0.8905 (m) cc_final: 0.8649 (t) REVERT: C 478 THR cc_start: 0.7371 (p) cc_final: 0.6850 (p) REVERT: C 498 GLN cc_start: 0.8759 (tp40) cc_final: 0.8435 (tp40) REVERT: C 501 MET cc_start: 0.7416 (mtt) cc_final: 0.6917 (mtp) REVERT: D 118 MET cc_start: 0.8158 (mmm) cc_final: 0.7597 (mmm) REVERT: D 405 LEU cc_start: 0.8659 (mt) cc_final: 0.8300 (mt) REVERT: D 439 LEU cc_start: 0.8775 (tm) cc_final: 0.8487 (tp) REVERT: D 490 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7803 (tm-30) REVERT: D 494 GLN cc_start: 0.8497 (mm110) cc_final: 0.8287 (mm-40) REVERT: E 94 LYS cc_start: 0.8702 (mmtt) cc_final: 0.7798 (tptt) REVERT: E 105 LYS cc_start: 0.8471 (tptt) cc_final: 0.7951 (ttpp) REVERT: E 120 TYR cc_start: 0.8848 (t80) cc_final: 0.8637 (t80) REVERT: E 171 ASP cc_start: 0.7257 (t0) cc_final: 0.6971 (t70) REVERT: E 237 VAL cc_start: 0.8306 (p) cc_final: 0.7711 (m) REVERT: E 240 SER cc_start: 0.8305 (m) cc_final: 0.7974 (p) REVERT: E 252 ILE cc_start: 0.8261 (pp) cc_final: 0.7542 (tp) REVERT: E 258 ARG cc_start: 0.7942 (ttm110) cc_final: 0.7567 (mtm-85) REVERT: E 338 PHE cc_start: 0.8263 (t80) cc_final: 0.7974 (t80) REVERT: E 472 ASN cc_start: 0.8399 (t0) cc_final: 0.7952 (m-40) REVERT: E 477 ASP cc_start: 0.7393 (p0) cc_final: 0.7178 (p0) REVERT: E 489 GLN cc_start: 0.8227 (mt0) cc_final: 0.8003 (tp-100) REVERT: E 494 GLN cc_start: 0.8585 (mm110) cc_final: 0.8003 (tm-30) REVERT: F 11 ASP cc_start: 0.7863 (p0) cc_final: 0.7563 (p0) REVERT: F 23 ASP cc_start: 0.8038 (t70) cc_final: 0.7815 (t0) REVERT: F 118 MET cc_start: 0.8771 (mmm) cc_final: 0.8359 (mmm) REVERT: F 127 ARG cc_start: 0.8234 (mmt90) cc_final: 0.7958 (mmm-85) REVERT: F 198 VAL cc_start: 0.8766 (t) cc_final: 0.8528 (m) REVERT: F 227 LEU cc_start: 0.8080 (mt) cc_final: 0.7530 (mm) REVERT: F 235 MET cc_start: 0.7039 (ttm) cc_final: 0.6665 (ttm) REVERT: F 328 SER cc_start: 0.8609 (t) cc_final: 0.8374 (p) REVERT: F 489 GLN cc_start: 0.7403 (mt0) cc_final: 0.7149 (tp40) REVERT: F 494 GLN cc_start: 0.8716 (mm110) cc_final: 0.8372 (tm-30) REVERT: F 501 MET cc_start: 0.8637 (mtt) cc_final: 0.8296 (mtp) REVERT: F 503 ASN cc_start: 0.8975 (t0) cc_final: 0.8570 (m-40) REVERT: G 84 MET cc_start: 0.8364 (pmm) cc_final: 0.8021 (pmm) REVERT: G 105 LYS cc_start: 0.8591 (tptt) cc_final: 0.7768 (ttpp) REVERT: G 120 TYR cc_start: 0.9004 (t80) cc_final: 0.8636 (t80) REVERT: G 235 MET cc_start: 0.6282 (ttm) cc_final: 0.5978 (ttm) REVERT: G 240 SER cc_start: 0.7997 (m) cc_final: 0.7433 (p) REVERT: G 268 TYR cc_start: 0.8802 (t80) cc_final: 0.8480 (t80) REVERT: G 326 ASP cc_start: 0.7847 (m-30) cc_final: 0.7381 (m-30) REVERT: G 423 GLU cc_start: 0.8454 (pm20) cc_final: 0.8112 (pm20) REVERT: G 461 ILE cc_start: 0.8809 (mt) cc_final: 0.8553 (mt) REVERT: H 84 MET cc_start: 0.8189 (pmm) cc_final: 0.7953 (pmm) REVERT: H 105 LYS cc_start: 0.7794 (tptt) cc_final: 0.7582 (tttp) REVERT: H 118 MET cc_start: 0.8778 (mmm) cc_final: 0.8355 (mpp) REVERT: H 227 LEU cc_start: 0.8436 (mt) cc_final: 0.8226 (mt) REVERT: H 489 GLN cc_start: 0.7756 (mt0) cc_final: 0.7067 (tp40) REVERT: H 501 MET cc_start: 0.8412 (mtt) cc_final: 0.8174 (mtp) REVERT: H 503 ASN cc_start: 0.8459 (t0) cc_final: 0.8200 (m110) REVERT: I 105 LYS cc_start: 0.8459 (tptt) cc_final: 0.7873 (ttpp) REVERT: I 164 SER cc_start: 0.9153 (m) cc_final: 0.8715 (t) REVERT: I 268 TYR cc_start: 0.8631 (t80) cc_final: 0.8303 (t80) REVERT: I 279 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9301 (tt) REVERT: I 326 ASP cc_start: 0.7851 (m-30) cc_final: 0.7639 (m-30) REVERT: I 474 ILE cc_start: 0.8497 (mm) cc_final: 0.8235 (mt) REVERT: I 494 GLN cc_start: 0.8417 (mm110) cc_final: 0.8093 (tm-30) REVERT: I 498 GLN cc_start: 0.8846 (tp40) cc_final: 0.8602 (tp-100) REVERT: I 501 MET cc_start: 0.7876 (mtt) cc_final: 0.7397 (mtp) REVERT: J 23 ASP cc_start: 0.8041 (t70) cc_final: 0.7681 (t70) REVERT: J 91 TYR cc_start: 0.8539 (t80) cc_final: 0.7911 (t80) REVERT: J 118 MET cc_start: 0.8669 (mmm) cc_final: 0.8345 (mmm) REVERT: J 220 ASP cc_start: 0.6794 (t0) cc_final: 0.6165 (t0) REVERT: J 227 LEU cc_start: 0.8345 (mt) cc_final: 0.8023 (mm) REVERT: J 256 MET cc_start: 0.7856 (tpt) cc_final: 0.7638 (tpt) REVERT: K 156 ASN cc_start: 0.8101 (t0) cc_final: 0.7889 (t0) REVERT: K 187 PHE cc_start: 0.8781 (t80) cc_final: 0.8509 (t80) REVERT: K 235 MET cc_start: 0.6090 (ttm) cc_final: 0.5588 (ttm) REVERT: K 474 ILE cc_start: 0.9127 (mm) cc_final: 0.8872 (mm) REVERT: K 501 MET cc_start: 0.7613 (mtt) cc_final: 0.7312 (mtp) REVERT: L 23 ASP cc_start: 0.8014 (t70) cc_final: 0.7735 (t0) REVERT: L 91 TYR cc_start: 0.8481 (t80) cc_final: 0.8004 (t80) REVERT: L 118 MET cc_start: 0.8870 (mmm) cc_final: 0.8621 (mmm) REVERT: L 228 ARG cc_start: 0.8232 (tmt170) cc_final: 0.7928 (tmm160) REVERT: L 256 MET cc_start: 0.7692 (tpt) cc_final: 0.7446 (tpt) REVERT: L 426 ILE cc_start: 0.7273 (mt) cc_final: 0.6976 (mm) REVERT: L 501 MET cc_start: 0.8568 (mtt) cc_final: 0.8249 (mtm) outliers start: 48 outliers final: 0 residues processed: 1847 average time/residue: 0.4963 time to fit residues: 1502.7656 Evaluate side-chains 1089 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1087 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain I residue 279 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 0.6980 chunk 472 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 319 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 489 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 297 optimal weight: 0.7980 chunk 364 optimal weight: 0.0470 chunk 566 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN A 184 GLN A 472 ASN A 498 GLN A 503 ASN B 119 ASN B 184 GLN B 472 ASN B 487 GLN B 503 ASN C 33 ASN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN C 397 GLN C 472 ASN C 503 ASN D 184 GLN D 281 ASN D 472 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 184 GLN E 472 ASN E 503 ASN F 68 ASN F 119 ASN F 184 GLN F 487 GLN F 495 GLN G 184 GLN ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN G 397 GLN G 409 GLN G 472 ASN ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 503 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 472 ASN H 487 GLN H 503 ASN I 184 GLN I 397 GLN I 409 GLN I 472 ASN J 397 GLN J 472 ASN K 33 ASN K 315 GLN K 397 GLN K 472 ASN L 68 ASN L 184 GLN L 472 ASN L 487 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 49440 Z= 0.227 Angle : 0.848 12.225 66912 Z= 0.425 Chirality : 0.048 0.432 7572 Planarity : 0.006 0.064 8832 Dihedral : 7.256 43.914 6880 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.15 % Favored : 92.18 % Rotamer: Outliers : 3.17 % Allowed : 14.17 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.09), residues: 6252 helix: -2.37 (0.07), residues: 3060 sheet: -2.24 (0.17), residues: 696 loop : -2.79 (0.11), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 83 HIS 0.003 0.001 HIS C 216 PHE 0.018 0.002 PHE L 78 TYR 0.022 0.002 TYR D 389 ARG 0.006 0.001 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 1259 time to evaluate : 4.119 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: A 75 LEU cc_start: 0.8987 (tt) cc_final: 0.8719 (mm) REVERT: A 80 MET cc_start: 0.7554 (mmm) cc_final: 0.7044 (mmt) REVERT: A 84 MET cc_start: 0.7781 (pmm) cc_final: 0.7327 (pmm) REVERT: A 94 LYS cc_start: 0.8740 (mmtt) cc_final: 0.7704 (tptt) REVERT: A 105 LYS cc_start: 0.8680 (tptt) cc_final: 0.7926 (ttpp) REVERT: A 120 TYR cc_start: 0.9260 (t80) cc_final: 0.9025 (t80) REVERT: A 164 SER cc_start: 0.9317 (m) cc_final: 0.9065 (t) REVERT: A 279 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9135 (tp) REVERT: A 333 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6432 (tt0) REVERT: A 423 GLU cc_start: 0.8043 (pm20) cc_final: 0.7826 (pm20) REVERT: A 461 ILE cc_start: 0.8696 (mt) cc_final: 0.8409 (mt) REVERT: A 472 ASN cc_start: 0.9044 (t0) cc_final: 0.8504 (t0) REVERT: A 477 ASP cc_start: 0.7954 (p0) cc_final: 0.7529 (p0) REVERT: A 494 GLN cc_start: 0.8668 (mm110) cc_final: 0.7908 (tm-30) REVERT: B 23 ASP cc_start: 0.8082 (t70) cc_final: 0.7747 (t0) REVERT: B 118 MET cc_start: 0.8815 (mmm) cc_final: 0.8483 (mmm) REVERT: B 236 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: B 271 GLU cc_start: 0.7164 (tp30) cc_final: 0.6930 (tp30) REVERT: B 489 GLN cc_start: 0.7979 (mt0) cc_final: 0.7668 (tp40) REVERT: B 501 MET cc_start: 0.8347 (mtt) cc_final: 0.8037 (mtp) REVERT: C 94 LYS cc_start: 0.8817 (mmtt) cc_final: 0.7733 (tptt) REVERT: C 105 LYS cc_start: 0.8627 (tptt) cc_final: 0.8054 (ttpp) REVERT: C 112 MET cc_start: 0.8068 (tpp) cc_final: 0.7852 (tpp) REVERT: C 120 TYR cc_start: 0.8969 (t80) cc_final: 0.8711 (t80) REVERT: C 156 ASN cc_start: 0.8453 (t0) cc_final: 0.8119 (t0) REVERT: C 164 SER cc_start: 0.9070 (m) cc_final: 0.8703 (t) REVERT: C 179 MET cc_start: 0.8663 (mtm) cc_final: 0.8381 (mtp) REVERT: C 494 GLN cc_start: 0.8525 (mm110) cc_final: 0.7828 (tm-30) REVERT: C 501 MET cc_start: 0.7741 (mtt) cc_final: 0.7530 (mtp) REVERT: D 8 LEU cc_start: 0.5435 (tp) cc_final: 0.5008 (tp) REVERT: D 84 MET cc_start: 0.8191 (pmm) cc_final: 0.7937 (pmm) REVERT: D 103 LEU cc_start: 0.9049 (tp) cc_final: 0.8823 (tp) REVERT: D 158 MET cc_start: 0.7605 (ptt) cc_final: 0.7366 (ptt) REVERT: D 236 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: D 439 LEU cc_start: 0.9197 (tm) cc_final: 0.8974 (tp) REVERT: D 489 GLN cc_start: 0.8319 (mt0) cc_final: 0.7645 (tp40) REVERT: D 499 MET cc_start: 0.7968 (tpp) cc_final: 0.7703 (tpt) REVERT: E 105 LYS cc_start: 0.8781 (tptt) cc_final: 0.8012 (ttpp) REVERT: E 164 SER cc_start: 0.9343 (m) cc_final: 0.9026 (t) REVERT: E 220 ASP cc_start: 0.6691 (t0) cc_final: 0.6434 (t0) REVERT: E 252 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7099 (tp) REVERT: E 279 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9041 (tp) REVERT: E 284 GLU cc_start: 0.7457 (tt0) cc_final: 0.7231 (pt0) REVERT: E 406 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8297 (ttpt) REVERT: E 465 MET cc_start: 0.8564 (tpp) cc_final: 0.8325 (tmm) REVERT: E 494 GLN cc_start: 0.8487 (mm110) cc_final: 0.8186 (tm-30) REVERT: E 501 MET cc_start: 0.8611 (mtp) cc_final: 0.8096 (mtm) REVERT: E 512 MET cc_start: 0.8702 (ppp) cc_final: 0.8383 (ppp) REVERT: E 523 MET cc_start: 0.8631 (tmm) cc_final: 0.7865 (tmm) REVERT: F 465 MET cc_start: 0.8380 (tpp) cc_final: 0.7815 (tpp) REVERT: F 489 GLN cc_start: 0.7712 (mt0) cc_final: 0.7286 (tp40) REVERT: F 501 MET cc_start: 0.8678 (mtt) cc_final: 0.8433 (mtp) REVERT: G 80 MET cc_start: 0.7490 (mmm) cc_final: 0.7027 (mmt) REVERT: G 84 MET cc_start: 0.8221 (pmm) cc_final: 0.7958 (pmm) REVERT: G 105 LYS cc_start: 0.8629 (tptt) cc_final: 0.7743 (ttpp) REVERT: G 184 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8054 (mm-40) REVERT: G 199 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8227 (tm-30) REVERT: G 220 ASP cc_start: 0.6998 (t0) cc_final: 0.6741 (t70) REVERT: G 289 MET cc_start: 0.8391 (mtt) cc_final: 0.8059 (mtp) REVERT: G 326 ASP cc_start: 0.8075 (m-30) cc_final: 0.7644 (m-30) REVERT: G 423 GLU cc_start: 0.8396 (pm20) cc_final: 0.8059 (pm20) REVERT: G 461 ILE cc_start: 0.8824 (mt) cc_final: 0.8544 (mt) REVERT: G 472 ASN cc_start: 0.8898 (t0) cc_final: 0.8677 (t0) REVERT: G 494 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8033 (tm-30) REVERT: G 499 MET cc_start: 0.8526 (tpp) cc_final: 0.8048 (tpp) REVERT: G 501 MET cc_start: 0.8510 (mtp) cc_final: 0.7789 (mtp) REVERT: G 508 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8742 (pt) REVERT: H 240 SER cc_start: 0.7876 (m) cc_final: 0.7608 (p) REVERT: H 478 THR cc_start: 0.5526 (OUTLIER) cc_final: 0.5219 (p) REVERT: H 489 GLN cc_start: 0.7900 (mt0) cc_final: 0.7186 (tp40) REVERT: H 499 MET cc_start: 0.8817 (tpp) cc_final: 0.8364 (tpp) REVERT: H 501 MET cc_start: 0.8602 (mtt) cc_final: 0.8392 (mtp) REVERT: I 84 MET cc_start: 0.8165 (pmm) cc_final: 0.7791 (pmm) REVERT: I 94 LYS cc_start: 0.8778 (mmtt) cc_final: 0.7722 (tptt) REVERT: I 105 LYS cc_start: 0.8771 (tptt) cc_final: 0.8096 (ttpp) REVERT: I 120 TYR cc_start: 0.9075 (t80) cc_final: 0.8791 (t80) REVERT: I 182 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7566 (ttt90) REVERT: I 240 SER cc_start: 0.7989 (m) cc_final: 0.7486 (p) REVERT: I 268 TYR cc_start: 0.8483 (t80) cc_final: 0.7992 (t80) REVERT: I 271 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6705 (mt-10) REVERT: I 404 LEU cc_start: 0.9253 (mt) cc_final: 0.9027 (mt) REVERT: I 465 MET cc_start: 0.8794 (tpp) cc_final: 0.8549 (tpp) REVERT: I 477 ASP cc_start: 0.6808 (p0) cc_final: 0.6562 (p0) REVERT: I 494 GLN cc_start: 0.8590 (mm110) cc_final: 0.8219 (tm-30) REVERT: J 23 ASP cc_start: 0.8151 (t70) cc_final: 0.7934 (t0) REVERT: J 118 MET cc_start: 0.8824 (mmm) cc_final: 0.8563 (mmm) REVERT: J 230 GLU cc_start: 0.7787 (pm20) cc_final: 0.7502 (pm20) REVERT: J 252 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8783 (pp) REVERT: J 383 ASP cc_start: 0.7288 (m-30) cc_final: 0.7056 (m-30) REVERT: J 418 PRO cc_start: 0.7847 (Cg_endo) cc_final: 0.7602 (Cg_exo) REVERT: J 465 MET cc_start: 0.8388 (tpp) cc_final: 0.7930 (tpp) REVERT: J 489 GLN cc_start: 0.7586 (mt0) cc_final: 0.7059 (tp40) REVERT: K 18 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7996 (mt-10) REVERT: K 105 LYS cc_start: 0.8773 (tptt) cc_final: 0.8312 (mtpt) REVERT: K 120 TYR cc_start: 0.8852 (t80) cc_final: 0.8604 (t80) REVERT: K 235 MET cc_start: 0.5816 (ttm) cc_final: 0.5491 (ttm) REVERT: K 400 LEU cc_start: 0.9401 (tt) cc_final: 0.9125 (tt) REVERT: K 404 LEU cc_start: 0.9493 (mt) cc_final: 0.9218 (mt) REVERT: K 477 ASP cc_start: 0.7974 (p0) cc_final: 0.7623 (p0) REVERT: K 494 GLN cc_start: 0.8532 (mm-40) cc_final: 0.7960 (tm-30) REVERT: L 23 ASP cc_start: 0.8032 (t70) cc_final: 0.7763 (t0) REVERT: L 91 TYR cc_start: 0.8190 (t80) cc_final: 0.7766 (t80) REVERT: L 118 MET cc_start: 0.8962 (mmm) cc_final: 0.8682 (mmm) REVERT: L 127 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8204 (mmt-90) REVERT: L 228 ARG cc_start: 0.8292 (tmt170) cc_final: 0.7999 (tmm160) REVERT: L 236 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: L 252 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8832 (pp) REVERT: L 315 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8393 (tp40) REVERT: L 455 MET cc_start: 0.8670 (mpp) cc_final: 0.7752 (mtt) REVERT: L 465 MET cc_start: 0.8472 (tpp) cc_final: 0.7900 (tpp) REVERT: L 489 GLN cc_start: 0.7431 (mt0) cc_final: 0.7069 (tp40) REVERT: L 501 MET cc_start: 0.8529 (mtt) cc_final: 0.8294 (mtp) REVERT: L 508 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8830 (pp) outliers start: 165 outliers final: 54 residues processed: 1367 average time/residue: 0.4522 time to fit residues: 1044.9992 Evaluate side-chains 1066 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 999 time to evaluate : 4.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 512 MET Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 263 SER Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain J residue 252 ILE Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 331 GLN Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain L residue 230 GLU Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 315 GLN Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 508 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 471 optimal weight: 0.0670 chunk 385 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 567 optimal weight: 0.7980 chunk 613 optimal weight: 0.9980 chunk 505 optimal weight: 0.7980 chunk 562 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 455 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN C 68 ASN C 407 GLN C 498 GLN C 503 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN E 33 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 503 ASN F 472 ASN ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 487 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN L 119 ASN ** L 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 49440 Z= 0.218 Angle : 0.783 11.645 66912 Z= 0.388 Chirality : 0.046 0.402 7572 Planarity : 0.005 0.061 8832 Dihedral : 6.476 41.833 6878 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.65 % Favored : 91.89 % Rotamer: Outliers : 4.01 % Allowed : 16.07 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.10), residues: 6252 helix: -0.88 (0.09), residues: 3000 sheet: -2.03 (0.18), residues: 612 loop : -2.40 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 83 HIS 0.003 0.002 HIS A 216 PHE 0.021 0.002 PHE E 78 TYR 0.024 0.002 TYR G 389 ARG 0.005 0.001 ARG H 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 1103 time to evaluate : 4.095 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: A 75 LEU cc_start: 0.8958 (tt) cc_final: 0.8746 (mm) REVERT: A 84 MET cc_start: 0.8019 (pmm) cc_final: 0.7616 (pmm) REVERT: A 94 LYS cc_start: 0.8744 (mmtt) cc_final: 0.7857 (tptt) REVERT: A 105 LYS cc_start: 0.8743 (tptt) cc_final: 0.7911 (ttpp) REVERT: A 164 SER cc_start: 0.9326 (m) cc_final: 0.9058 (t) REVERT: A 279 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9136 (tp) REVERT: A 395 GLU cc_start: 0.7688 (tp30) cc_final: 0.7414 (mm-30) REVERT: A 477 ASP cc_start: 0.7427 (p0) cc_final: 0.7214 (p0) REVERT: A 494 GLN cc_start: 0.8685 (mm110) cc_final: 0.8249 (tm-30) REVERT: B 23 ASP cc_start: 0.8198 (t70) cc_final: 0.7927 (t70) REVERT: B 80 MET cc_start: 0.6269 (tpt) cc_final: 0.5915 (tpt) REVERT: B 118 MET cc_start: 0.8683 (mmm) cc_final: 0.8444 (mmm) REVERT: B 230 GLU cc_start: 0.7770 (pm20) cc_final: 0.7565 (pm20) REVERT: B 236 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6032 (mp0) REVERT: B 444 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7836 (ttp80) REVERT: B 456 ARG cc_start: 0.8397 (mtm180) cc_final: 0.8181 (mtm180) REVERT: B 477 ASP cc_start: 0.5734 (p0) cc_final: 0.5411 (p0) REVERT: B 489 GLN cc_start: 0.8066 (mt0) cc_final: 0.7647 (tp40) REVERT: B 501 MET cc_start: 0.8501 (mtt) cc_final: 0.8214 (mtp) REVERT: C 94 LYS cc_start: 0.8718 (mmtt) cc_final: 0.7786 (tptt) REVERT: C 105 LYS cc_start: 0.8667 (tptt) cc_final: 0.7991 (ttpp) REVERT: C 120 TYR cc_start: 0.8999 (t80) cc_final: 0.8590 (t80) REVERT: C 156 ASN cc_start: 0.8757 (t0) cc_final: 0.8390 (t0) REVERT: C 164 SER cc_start: 0.9215 (m) cc_final: 0.8852 (t) REVERT: C 179 MET cc_start: 0.8761 (mtm) cc_final: 0.8560 (mtp) REVERT: C 338 PHE cc_start: 0.8399 (t80) cc_final: 0.8190 (t80) REVERT: C 357 MET cc_start: 0.7943 (mmm) cc_final: 0.7633 (mmm) REVERT: C 494 GLN cc_start: 0.8592 (mm110) cc_final: 0.7893 (tm-30) REVERT: C 501 MET cc_start: 0.7876 (mtt) cc_final: 0.7597 (mtp) REVERT: D 8 LEU cc_start: 0.5231 (tp) cc_final: 0.4713 (tp) REVERT: D 103 LEU cc_start: 0.8925 (tp) cc_final: 0.8680 (tp) REVERT: D 118 MET cc_start: 0.8864 (mmm) cc_final: 0.8499 (mmm) REVERT: D 158 MET cc_start: 0.7708 (ptt) cc_final: 0.7496 (ptt) REVERT: D 236 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: D 406 LYS cc_start: 0.8728 (tttt) cc_final: 0.8507 (ttpt) REVERT: D 465 MET cc_start: 0.8559 (tpt) cc_final: 0.7978 (tpp) REVERT: D 501 MET cc_start: 0.8670 (mtm) cc_final: 0.8391 (mtp) REVERT: E 80 MET cc_start: 0.7672 (mmm) cc_final: 0.7127 (mmm) REVERT: E 94 LYS cc_start: 0.8698 (mmtt) cc_final: 0.7857 (tptt) REVERT: E 105 LYS cc_start: 0.8829 (tptt) cc_final: 0.8093 (ttpp) REVERT: E 252 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7361 (tp) REVERT: E 279 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9255 (tp) REVERT: E 494 GLN cc_start: 0.8673 (mm110) cc_final: 0.8288 (tm-30) REVERT: E 523 MET cc_start: 0.8649 (tmm) cc_final: 0.7961 (tmm) REVERT: F 118 MET cc_start: 0.8969 (mmm) cc_final: 0.8614 (mmm) REVERT: F 179 MET cc_start: 0.8194 (mtm) cc_final: 0.7966 (mtm) REVERT: F 228 ARG cc_start: 0.8184 (tmm160) cc_final: 0.7893 (ttt-90) REVERT: F 236 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: F 465 MET cc_start: 0.8455 (tpp) cc_final: 0.8104 (tpp) REVERT: F 489 GLN cc_start: 0.7801 (mt0) cc_final: 0.7204 (tp40) REVERT: G 80 MET cc_start: 0.7471 (mmm) cc_final: 0.7148 (mmt) REVERT: G 84 MET cc_start: 0.8485 (pmm) cc_final: 0.8254 (pmm) REVERT: G 105 LYS cc_start: 0.8576 (tptt) cc_final: 0.7701 (ttpp) REVERT: G 118 MET cc_start: 0.8635 (mmm) cc_final: 0.8351 (mmm) REVERT: G 120 TYR cc_start: 0.9036 (t80) cc_final: 0.8540 (t80) REVERT: G 164 SER cc_start: 0.9260 (m) cc_final: 0.9024 (t) REVERT: G 289 MET cc_start: 0.8456 (mtt) cc_final: 0.8126 (mtp) REVERT: G 397 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: G 461 ILE cc_start: 0.8927 (mt) cc_final: 0.8626 (mt) REVERT: G 465 MET cc_start: 0.8460 (tpp) cc_final: 0.8193 (tpp) REVERT: G 472 ASN cc_start: 0.8666 (t0) cc_final: 0.8233 (t0) REVERT: G 494 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8193 (tm-30) REVERT: G 501 MET cc_start: 0.8732 (mtp) cc_final: 0.7957 (mtm) REVERT: H 195 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7685 (mtp85) REVERT: H 240 SER cc_start: 0.7787 (m) cc_final: 0.7344 (p) REVERT: H 477 ASP cc_start: 0.5795 (p0) cc_final: 0.5430 (p0) REVERT: H 489 GLN cc_start: 0.8082 (mt0) cc_final: 0.7273 (tp40) REVERT: H 492 MET cc_start: 0.8320 (ttm) cc_final: 0.7975 (ttm) REVERT: H 499 MET cc_start: 0.8791 (tpp) cc_final: 0.8583 (tpp) REVERT: H 512 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8182 (ptm) REVERT: I 94 LYS cc_start: 0.8654 (mmtt) cc_final: 0.7711 (tptt) REVERT: I 105 LYS cc_start: 0.8667 (tptt) cc_final: 0.7951 (ttpp) REVERT: I 120 TYR cc_start: 0.9145 (t80) cc_final: 0.8935 (t80) REVERT: I 182 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7669 (ttt90) REVERT: I 240 SER cc_start: 0.8088 (m) cc_final: 0.7683 (p) REVERT: I 241 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6747 (t0) REVERT: I 268 TYR cc_start: 0.8483 (t80) cc_final: 0.8203 (t80) REVERT: I 465 MET cc_start: 0.8752 (tpp) cc_final: 0.8511 (tpp) REVERT: I 494 GLN cc_start: 0.8606 (mm110) cc_final: 0.8271 (tm-30) REVERT: I 501 MET cc_start: 0.8294 (mtp) cc_final: 0.7882 (mtm) REVERT: J 23 ASP cc_start: 0.8181 (t70) cc_final: 0.7930 (t0) REVERT: J 91 TYR cc_start: 0.8174 (t80) cc_final: 0.7445 (t80) REVERT: J 112 MET cc_start: 0.8214 (tpp) cc_final: 0.7976 (tpp) REVERT: J 179 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7453 (mpp) REVERT: J 236 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: J 240 SER cc_start: 0.8394 (m) cc_final: 0.7970 (p) REVERT: J 252 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8668 (pp) REVERT: J 465 MET cc_start: 0.8469 (tpp) cc_final: 0.7947 (tpp) REVERT: J 489 GLN cc_start: 0.8056 (mt0) cc_final: 0.7347 (tp40) REVERT: K 18 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8042 (mt-10) REVERT: K 75 LEU cc_start: 0.8817 (tp) cc_final: 0.8520 (mt) REVERT: K 94 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8002 (tptt) REVERT: K 105 LYS cc_start: 0.8887 (tptt) cc_final: 0.8340 (mtpt) REVERT: K 118 MET cc_start: 0.8865 (mmm) cc_final: 0.8361 (mmm) REVERT: K 164 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8554 (t) REVERT: K 373 GLU cc_start: 0.6087 (mm-30) cc_final: 0.5754 (tm-30) REVERT: K 400 LEU cc_start: 0.9329 (tt) cc_final: 0.9015 (tt) REVERT: K 477 ASP cc_start: 0.7633 (p0) cc_final: 0.7053 (p0) REVERT: K 494 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8017 (tm-30) REVERT: K 501 MET cc_start: 0.8638 (mtp) cc_final: 0.8308 (mtm) REVERT: L 23 ASP cc_start: 0.8072 (t70) cc_final: 0.7822 (t0) REVERT: L 91 TYR cc_start: 0.8357 (t80) cc_final: 0.7897 (t80) REVERT: L 112 MET cc_start: 0.7900 (tpp) cc_final: 0.7690 (tpp) REVERT: L 158 MET cc_start: 0.7749 (ptt) cc_final: 0.7425 (ptt) REVERT: L 230 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: L 236 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: L 252 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8784 (pp) REVERT: L 325 GLU cc_start: 0.7865 (pm20) cc_final: 0.7606 (pt0) REVERT: L 455 MET cc_start: 0.8758 (mpp) cc_final: 0.7873 (mtt) REVERT: L 465 MET cc_start: 0.8528 (tpp) cc_final: 0.7949 (tpp) REVERT: L 489 GLN cc_start: 0.7759 (mt0) cc_final: 0.7230 (tp40) outliers start: 209 outliers final: 99 residues processed: 1254 average time/residue: 0.4371 time to fit residues: 936.1029 Evaluate side-chains 1071 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 956 time to evaluate : 4.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 397 GLN Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 263 SER Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 512 MET Chi-restraints excluded: chain H residue 532 LEU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 391 ILE Chi-restraints excluded: chain I residue 392 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 252 ILE Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 331 GLN Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 391 ILE Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 390 SER Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 230 GLU Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain L residue 263 SER Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 315 GLN Chi-restraints excluded: chain L residue 391 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 2.9990 chunk 426 optimal weight: 2.9990 chunk 294 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 270 optimal weight: 0.7980 chunk 381 optimal weight: 0.9990 chunk 569 optimal weight: 6.9990 chunk 603 optimal weight: 1.9990 chunk 297 optimal weight: 0.6980 chunk 539 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 GLN ** K 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 49440 Z= 0.229 Angle : 0.765 14.148 66912 Z= 0.377 Chirality : 0.045 0.358 7572 Planarity : 0.005 0.064 8832 Dihedral : 6.167 40.441 6878 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.77 % Favored : 91.79 % Rotamer: Outliers : 4.11 % Allowed : 17.55 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.10), residues: 6252 helix: -0.15 (0.09), residues: 3000 sheet: -1.64 (0.19), residues: 612 loop : -2.23 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 83 HIS 0.003 0.002 HIS A 216 PHE 0.019 0.002 PHE K 338 TYR 0.024 0.002 TYR G 389 ARG 0.006 0.001 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 1052 time to evaluate : 4.133 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: A 75 LEU cc_start: 0.9010 (tt) cc_final: 0.8785 (mm) REVERT: A 94 LYS cc_start: 0.8941 (mmtt) cc_final: 0.7808 (tptt) REVERT: A 105 LYS cc_start: 0.8787 (tptt) cc_final: 0.7919 (ttpp) REVERT: A 118 MET cc_start: 0.8907 (mmm) cc_final: 0.8408 (mmm) REVERT: A 164 SER cc_start: 0.9203 (m) cc_final: 0.8989 (t) REVERT: A 173 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: A 218 TYR cc_start: 0.9072 (p90) cc_final: 0.8831 (p90) REVERT: A 279 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9148 (tp) REVERT: A 351 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8369 (ptt180) REVERT: A 395 GLU cc_start: 0.7838 (tp30) cc_final: 0.7579 (tp30) REVERT: A 494 GLN cc_start: 0.8702 (mm110) cc_final: 0.8159 (tm-30) REVERT: B 23 ASP cc_start: 0.8205 (t70) cc_final: 0.7919 (t70) REVERT: B 236 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6086 (mp0) REVERT: B 406 LYS cc_start: 0.8485 (tttt) cc_final: 0.8255 (ttpp) REVERT: B 456 ARG cc_start: 0.8414 (mtm180) cc_final: 0.8186 (mtm180) REVERT: B 489 GLN cc_start: 0.8279 (mt0) cc_final: 0.7936 (tp40) REVERT: C 94 LYS cc_start: 0.8846 (mmtt) cc_final: 0.7827 (tptt) REVERT: C 95 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8031 (mm-40) REVERT: C 105 LYS cc_start: 0.8725 (tptt) cc_final: 0.8047 (ttpp) REVERT: C 118 MET cc_start: 0.8661 (mmm) cc_final: 0.8076 (mmm) REVERT: C 120 TYR cc_start: 0.9019 (t80) cc_final: 0.8730 (t80) REVERT: C 164 SER cc_start: 0.9242 (m) cc_final: 0.8876 (t) REVERT: C 455 MET cc_start: 0.8559 (mtm) cc_final: 0.8346 (ttm) REVERT: C 494 GLN cc_start: 0.8673 (mm110) cc_final: 0.7932 (tm-30) REVERT: D 118 MET cc_start: 0.8877 (mmm) cc_final: 0.8397 (mmm) REVERT: D 158 MET cc_start: 0.7790 (ptt) cc_final: 0.7580 (ptt) REVERT: D 235 MET cc_start: 0.7080 (ttm) cc_final: 0.6506 (ttm) REVERT: D 236 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6026 (mp0) REVERT: D 291 MET cc_start: 0.8805 (mmt) cc_final: 0.8545 (mmm) REVERT: D 385 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8243 (tt) REVERT: D 465 MET cc_start: 0.8607 (tpt) cc_final: 0.8003 (tpp) REVERT: D 477 ASP cc_start: 0.5864 (p0) cc_final: 0.5560 (p0) REVERT: D 489 GLN cc_start: 0.8479 (mt0) cc_final: 0.7665 (tp40) REVERT: D 501 MET cc_start: 0.8718 (mtm) cc_final: 0.8465 (mtp) REVERT: E 92 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7940 (mt-10) REVERT: E 94 LYS cc_start: 0.8816 (mmtt) cc_final: 0.7865 (tptt) REVERT: E 105 LYS cc_start: 0.8893 (tptt) cc_final: 0.8125 (ttpp) REVERT: E 158 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.7800 (ptp) REVERT: E 279 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9246 (tp) REVERT: E 494 GLN cc_start: 0.8632 (mm110) cc_final: 0.8222 (tm-30) REVERT: E 501 MET cc_start: 0.8542 (mtp) cc_final: 0.8194 (mtm) REVERT: E 523 MET cc_start: 0.8654 (tmm) cc_final: 0.7934 (tmm) REVERT: F 112 MET cc_start: 0.7851 (tpp) cc_final: 0.7621 (tpp) REVERT: F 118 MET cc_start: 0.9076 (mmm) cc_final: 0.8659 (mmm) REVERT: F 158 MET cc_start: 0.7993 (ptt) cc_final: 0.7689 (ptt) REVERT: F 179 MET cc_start: 0.8397 (mtm) cc_final: 0.8184 (mtm) REVERT: F 230 GLU cc_start: 0.7625 (pm20) cc_final: 0.7390 (pm20) REVERT: F 236 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: F 455 MET cc_start: 0.8149 (mtt) cc_final: 0.7864 (mtt) REVERT: F 465 MET cc_start: 0.8497 (tpp) cc_final: 0.8155 (tpp) REVERT: F 477 ASP cc_start: 0.5588 (p0) cc_final: 0.5325 (p0) REVERT: F 489 GLN cc_start: 0.7976 (mt0) cc_final: 0.7364 (tp40) REVERT: F 494 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8342 (tm-30) REVERT: G 80 MET cc_start: 0.7508 (mmm) cc_final: 0.7246 (mmt) REVERT: G 94 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8090 (tptt) REVERT: G 105 LYS cc_start: 0.8640 (tptt) cc_final: 0.7742 (ttpp) REVERT: G 118 MET cc_start: 0.8694 (mmm) cc_final: 0.8164 (mmm) REVERT: G 164 SER cc_start: 0.9262 (m) cc_final: 0.9004 (t) REVERT: G 173 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6519 (m-80) REVERT: G 220 ASP cc_start: 0.6461 (t70) cc_final: 0.6201 (t0) REVERT: G 461 ILE cc_start: 0.8962 (mt) cc_final: 0.8604 (mt) REVERT: G 465 MET cc_start: 0.8384 (tpp) cc_final: 0.8135 (tpp) REVERT: G 494 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8219 (tm-30) REVERT: G 495 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: G 498 GLN cc_start: 0.9155 (tp40) cc_final: 0.8909 (tp-100) REVERT: G 501 MET cc_start: 0.8689 (mtp) cc_final: 0.8067 (mtp) REVERT: H 118 MET cc_start: 0.8865 (mmm) cc_final: 0.8534 (mmm) REVERT: H 195 ARG cc_start: 0.8304 (mtm110) cc_final: 0.7434 (mtp85) REVERT: H 240 SER cc_start: 0.7934 (m) cc_final: 0.7210 (p) REVERT: H 465 MET cc_start: 0.8606 (tpp) cc_final: 0.8364 (tpt) REVERT: H 482 LEU cc_start: 0.8878 (pt) cc_final: 0.8661 (pp) REVERT: H 489 GLN cc_start: 0.8119 (mt0) cc_final: 0.7370 (tp40) REVERT: H 492 MET cc_start: 0.8446 (ttm) cc_final: 0.8171 (ttm) REVERT: H 512 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8174 (ptm) REVERT: I 94 LYS cc_start: 0.8612 (mmtt) cc_final: 0.7736 (tptt) REVERT: I 105 LYS cc_start: 0.8696 (tptt) cc_final: 0.7966 (ttpp) REVERT: I 112 MET cc_start: 0.8145 (tpp) cc_final: 0.7842 (tpp) REVERT: I 118 MET cc_start: 0.8731 (mmm) cc_final: 0.8253 (mmm) REVERT: I 240 SER cc_start: 0.8042 (m) cc_final: 0.7580 (p) REVERT: I 241 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6805 (t0) REVERT: I 455 MET cc_start: 0.8657 (mtt) cc_final: 0.8317 (mtt) REVERT: I 465 MET cc_start: 0.8797 (tpp) cc_final: 0.8573 (tpp) REVERT: I 494 GLN cc_start: 0.8699 (mm110) cc_final: 0.8299 (tm-30) REVERT: I 501 MET cc_start: 0.8224 (mtp) cc_final: 0.7743 (ttp) REVERT: J 23 ASP cc_start: 0.7953 (t70) cc_final: 0.7683 (t0) REVERT: J 91 TYR cc_start: 0.8342 (t80) cc_final: 0.7513 (t80) REVERT: J 118 MET cc_start: 0.8834 (mmm) cc_final: 0.8446 (mmm) REVERT: J 158 MET cc_start: 0.8152 (ptt) cc_final: 0.7776 (ptt) REVERT: J 236 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: J 240 SER cc_start: 0.8447 (m) cc_final: 0.8193 (p) REVERT: J 465 MET cc_start: 0.8599 (tpp) cc_final: 0.8060 (tpp) REVERT: J 489 GLN cc_start: 0.8184 (mt0) cc_final: 0.7428 (tp40) REVERT: K 18 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8158 (mt-10) REVERT: K 94 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8039 (tptt) REVERT: K 105 LYS cc_start: 0.8961 (tptt) cc_final: 0.8326 (mtpt) REVERT: K 118 MET cc_start: 0.8719 (mmm) cc_final: 0.8501 (mmm) REVERT: K 120 TYR cc_start: 0.8966 (t80) cc_final: 0.8711 (t80) REVERT: K 164 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8636 (t) REVERT: K 373 GLU cc_start: 0.6321 (mm-30) cc_final: 0.5992 (tm-30) REVERT: K 477 ASP cc_start: 0.7174 (p0) cc_final: 0.6608 (p0) REVERT: K 494 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8106 (tm-30) REVERT: K 499 MET cc_start: 0.8563 (tmm) cc_final: 0.7849 (tmm) REVERT: K 501 MET cc_start: 0.8619 (mtp) cc_final: 0.8419 (mtm) REVERT: L 23 ASP cc_start: 0.8092 (t70) cc_final: 0.7841 (t0) REVERT: L 158 MET cc_start: 0.7839 (ptt) cc_final: 0.7538 (ptt) REVERT: L 179 MET cc_start: 0.8178 (mtm) cc_final: 0.7885 (mtm) REVERT: L 236 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: L 252 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8848 (pp) REVERT: L 325 GLU cc_start: 0.7952 (pm20) cc_final: 0.7691 (pt0) REVERT: L 455 MET cc_start: 0.8599 (mpp) cc_final: 0.7807 (mtt) REVERT: L 465 MET cc_start: 0.8616 (tpp) cc_final: 0.8039 (tpp) REVERT: L 489 GLN cc_start: 0.7861 (mt0) cc_final: 0.7275 (tp40) REVERT: L 492 MET cc_start: 0.8173 (mmp) cc_final: 0.7939 (mmm) outliers start: 214 outliers final: 136 residues processed: 1189 average time/residue: 0.4458 time to fit residues: 909.3708 Evaluate side-chains 1115 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 962 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 325 GLU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 495 GLN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 263 SER Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 445 CYS Chi-restraints excluded: chain H residue 512 MET Chi-restraints excluded: chain H residue 532 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 357 MET Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 391 ILE Chi-restraints excluded: chain I residue 392 LEU Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 173 PHE Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 391 ILE Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 325 GLU Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 392 LEU Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 466 ILE Chi-restraints excluded: chain K residue 508 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain L residue 263 SER Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 315 GLN Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 391 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 2.9990 chunk 342 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 449 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 514 optimal weight: 1.9990 chunk 416 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 0.2980 chunk 541 optimal weight: 0.0470 chunk 152 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 GLN ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 49440 Z= 0.207 Angle : 0.746 13.006 66912 Z= 0.367 Chirality : 0.045 0.282 7572 Planarity : 0.005 0.059 8832 Dihedral : 5.943 39.448 6878 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.08 % Favored : 91.55 % Rotamer: Outliers : 4.30 % Allowed : 18.72 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.10), residues: 6252 helix: 0.27 (0.10), residues: 3000 sheet: -1.24 (0.21), residues: 528 loop : -2.13 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 83 HIS 0.003 0.002 HIS G 216 PHE 0.022 0.002 PHE E 78 TYR 0.023 0.002 TYR G 389 ARG 0.006 0.001 ARG F 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 1033 time to evaluate : 4.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8301 (pmm) cc_final: 0.7889 (pmm) REVERT: A 94 LYS cc_start: 0.8866 (mmtt) cc_final: 0.7734 (tptt) REVERT: A 105 LYS cc_start: 0.8731 (tptt) cc_final: 0.7791 (ttpp) REVERT: A 164 SER cc_start: 0.9206 (m) cc_final: 0.8947 (t) REVERT: A 173 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: A 279 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9118 (tp) REVERT: A 494 GLN cc_start: 0.8681 (mm110) cc_final: 0.8185 (tm-30) REVERT: A 501 MET cc_start: 0.8324 (mtm) cc_final: 0.7891 (ptp) REVERT: A 523 MET cc_start: 0.8112 (ttp) cc_final: 0.7286 (tmm) REVERT: B 23 ASP cc_start: 0.8192 (t70) cc_final: 0.7913 (t70) REVERT: B 236 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6163 (mp0) REVERT: B 333 GLU cc_start: 0.7502 (tp30) cc_final: 0.7253 (tp30) REVERT: B 406 LYS cc_start: 0.8598 (tttt) cc_final: 0.8315 (ttpt) REVERT: B 456 ARG cc_start: 0.8413 (mtm180) cc_final: 0.8186 (mtm180) REVERT: B 460 ASP cc_start: 0.8197 (t0) cc_final: 0.7956 (t0) REVERT: B 489 GLN cc_start: 0.8343 (mt0) cc_final: 0.7969 (tp40) REVERT: C 47 SER cc_start: 0.8498 (t) cc_final: 0.8277 (t) REVERT: C 94 LYS cc_start: 0.8808 (mmtt) cc_final: 0.7782 (tptt) REVERT: C 105 LYS cc_start: 0.8700 (tptt) cc_final: 0.8018 (ttpp) REVERT: C 118 MET cc_start: 0.8576 (mmm) cc_final: 0.8309 (mmm) REVERT: C 120 TYR cc_start: 0.9042 (t80) cc_final: 0.8763 (t80) REVERT: C 455 MET cc_start: 0.8607 (mtm) cc_final: 0.8272 (ttm) REVERT: C 501 MET cc_start: 0.8495 (mtp) cc_final: 0.7538 (mtp) REVERT: C 508 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9050 (pt) REVERT: D 118 MET cc_start: 0.8910 (mmm) cc_final: 0.8319 (mmm) REVERT: D 158 MET cc_start: 0.7817 (ptt) cc_final: 0.7573 (ptt) REVERT: D 235 MET cc_start: 0.7121 (ttm) cc_final: 0.6567 (ttm) REVERT: D 236 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.5977 (mp0) REVERT: D 385 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8294 (tt) REVERT: D 465 MET cc_start: 0.8696 (tpt) cc_final: 0.8048 (tpp) REVERT: D 477 ASP cc_start: 0.5719 (p0) cc_final: 0.5465 (p0) REVERT: D 501 MET cc_start: 0.8667 (mtm) cc_final: 0.8460 (mtp) REVERT: E 94 LYS cc_start: 0.8942 (mmtt) cc_final: 0.7962 (tptt) REVERT: E 105 LYS cc_start: 0.8906 (tptt) cc_final: 0.8112 (ttpp) REVERT: E 158 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7678 (ptp) REVERT: E 235 MET cc_start: 0.6088 (ppp) cc_final: 0.5870 (ppp) REVERT: E 279 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9225 (tp) REVERT: E 465 MET cc_start: 0.8698 (tmm) cc_final: 0.8276 (tmm) REVERT: E 494 GLN cc_start: 0.8622 (mm110) cc_final: 0.8217 (tm-30) REVERT: E 523 MET cc_start: 0.8682 (tmm) cc_final: 0.7968 (tmm) REVERT: F 112 MET cc_start: 0.7872 (tpp) cc_final: 0.7612 (tpp) REVERT: F 118 MET cc_start: 0.9109 (mmm) cc_final: 0.8847 (mmm) REVERT: F 179 MET cc_start: 0.8398 (mtm) cc_final: 0.8163 (mtm) REVERT: F 236 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: F 271 GLU cc_start: 0.7277 (tp30) cc_final: 0.7036 (tp30) REVERT: F 440 ASP cc_start: 0.8044 (t70) cc_final: 0.7754 (p0) REVERT: F 455 MET cc_start: 0.8128 (mtt) cc_final: 0.7762 (mtt) REVERT: F 465 MET cc_start: 0.8554 (tpp) cc_final: 0.8204 (tpp) REVERT: F 489 GLN cc_start: 0.8069 (mt0) cc_final: 0.7350 (tp40) REVERT: F 494 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8333 (tm-30) REVERT: G 47 SER cc_start: 0.8548 (t) cc_final: 0.8241 (t) REVERT: G 80 MET cc_start: 0.7516 (mmm) cc_final: 0.7302 (mmt) REVERT: G 94 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8129 (tptt) REVERT: G 105 LYS cc_start: 0.8669 (tptt) cc_final: 0.7726 (ttpp) REVERT: G 164 SER cc_start: 0.9265 (m) cc_final: 0.8979 (t) REVERT: G 173 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: G 206 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8465 (tppt) REVERT: G 461 ILE cc_start: 0.8954 (mt) cc_final: 0.8636 (mt) REVERT: G 465 MET cc_start: 0.8408 (tpp) cc_final: 0.8189 (tpp) REVERT: G 494 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8245 (tm-30) REVERT: G 495 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: G 498 GLN cc_start: 0.9102 (tp40) cc_final: 0.8820 (tp-100) REVERT: H 118 MET cc_start: 0.8818 (mmm) cc_final: 0.8606 (mmm) REVERT: H 195 ARG cc_start: 0.8326 (mtm110) cc_final: 0.7822 (mtp85) REVERT: H 238 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7382 (pt0) REVERT: H 240 SER cc_start: 0.7992 (m) cc_final: 0.7423 (p) REVERT: H 323 ARG cc_start: 0.8464 (mtm180) cc_final: 0.8207 (mtm110) REVERT: H 461 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8749 (tp) REVERT: H 465 MET cc_start: 0.8562 (tpp) cc_final: 0.8270 (tpt) REVERT: H 482 LEU cc_start: 0.8531 (pt) cc_final: 0.8292 (pp) REVERT: H 489 GLN cc_start: 0.8135 (mt0) cc_final: 0.7416 (tp40) REVERT: H 512 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8040 (ptm) REVERT: I 94 LYS cc_start: 0.8671 (mmtt) cc_final: 0.7834 (tptt) REVERT: I 95 GLN cc_start: 0.8640 (mm110) cc_final: 0.8438 (mm-40) REVERT: I 105 LYS cc_start: 0.8711 (tptt) cc_final: 0.7959 (ttpp) REVERT: I 112 MET cc_start: 0.8213 (tpp) cc_final: 0.7983 (tpp) REVERT: I 118 MET cc_start: 0.8695 (mmm) cc_final: 0.8015 (mmm) REVERT: I 241 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6748 (t0) REVERT: I 299 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8981 (mp) REVERT: I 455 MET cc_start: 0.8636 (mtt) cc_final: 0.8339 (mtt) REVERT: I 465 MET cc_start: 0.8799 (tpp) cc_final: 0.8566 (tpp) REVERT: I 494 GLN cc_start: 0.8686 (mm110) cc_final: 0.8209 (tm-30) REVERT: I 501 MET cc_start: 0.8360 (mtp) cc_final: 0.7989 (ttp) REVERT: J 8 LEU cc_start: 0.4874 (tp) cc_final: 0.4418 (tp) REVERT: J 118 MET cc_start: 0.8799 (mmm) cc_final: 0.8455 (mmm) REVERT: J 158 MET cc_start: 0.8150 (ptt) cc_final: 0.7605 (ptt) REVERT: J 179 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7488 (mpp) REVERT: J 236 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: J 240 SER cc_start: 0.8322 (m) cc_final: 0.8021 (p) REVERT: J 262 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6930 (mt-10) REVERT: J 465 MET cc_start: 0.8649 (tpp) cc_final: 0.8022 (tpp) REVERT: J 489 GLN cc_start: 0.8236 (mt0) cc_final: 0.7537 (tp40) REVERT: J 521 GLU cc_start: 0.8517 (pm20) cc_final: 0.8308 (pm20) REVERT: K 94 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8069 (tptt) REVERT: K 105 LYS cc_start: 0.8904 (tptt) cc_final: 0.8317 (mtpt) REVERT: K 118 MET cc_start: 0.8783 (mmm) cc_final: 0.8466 (mmm) REVERT: K 164 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8692 (t) REVERT: K 241 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7170 (t0) REVERT: K 373 GLU cc_start: 0.6475 (mm-30) cc_final: 0.6022 (tm-30) REVERT: K 494 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8104 (tm-30) REVERT: K 499 MET cc_start: 0.8673 (tmm) cc_final: 0.7979 (tmm) REVERT: K 501 MET cc_start: 0.8476 (mtp) cc_final: 0.7823 (ttm) REVERT: K 523 MET cc_start: 0.7873 (ttp) cc_final: 0.7646 (mtm) REVERT: L 23 ASP cc_start: 0.8093 (t70) cc_final: 0.7846 (t0) REVERT: L 91 TYR cc_start: 0.8473 (t80) cc_final: 0.8012 (t80) REVERT: L 94 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8610 (mptt) REVERT: L 158 MET cc_start: 0.7858 (ptt) cc_final: 0.7495 (ptt) REVERT: L 179 MET cc_start: 0.8146 (mtm) cc_final: 0.7900 (mtm) REVERT: L 236 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: L 246 LYS cc_start: 0.8353 (ttmm) cc_final: 0.8099 (mttm) REVERT: L 325 GLU cc_start: 0.8033 (pm20) cc_final: 0.7814 (pt0) REVERT: L 455 MET cc_start: 0.8542 (mpp) cc_final: 0.7686 (mtp) REVERT: L 465 MET cc_start: 0.8695 (tpp) cc_final: 0.8099 (tpp) REVERT: L 489 GLN cc_start: 0.7915 (mt0) cc_final: 0.7272 (tp40) REVERT: L 492 MET cc_start: 0.8243 (mmp) cc_final: 0.7996 (mmm) REVERT: L 499 MET cc_start: 0.7903 (ttm) cc_final: 0.7665 (ttt) outliers start: 224 outliers final: 142 residues processed: 1186 average time/residue: 0.4384 time to fit residues: 893.6977 Evaluate side-chains 1105 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 943 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 325 GLU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 495 GLN Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 263 SER Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 445 CYS Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 512 MET Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 357 MET Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 391 ILE Chi-restraints excluded: chain I residue 392 LEU Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 173 PHE Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 391 ILE Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 325 GLU Chi-restraints excluded: chain K residue 390 SER Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 392 LEU Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 440 ASP Chi-restraints excluded: chain K residue 442 LEU Chi-restraints excluded: chain K residue 508 LEU Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 263 SER Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 315 GLN Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 357 MET Chi-restraints excluded: chain L residue 391 ILE Chi-restraints excluded: chain L residue 406 LYS Chi-restraints excluded: chain L residue 481 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 0.0470 chunk 543 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 354 optimal weight: 2.9990 chunk 148 optimal weight: 0.0010 chunk 603 optimal weight: 0.0970 chunk 501 optimal weight: 0.7980 chunk 279 optimal weight: 0.0980 chunk 50 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 316 optimal weight: 4.9990 overall best weight: 0.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN C 498 GLN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** L 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 49440 Z= 0.169 Angle : 0.730 11.301 66912 Z= 0.356 Chirality : 0.044 0.218 7572 Planarity : 0.005 0.057 8832 Dihedral : 5.666 38.837 6878 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.82 % Favored : 91.79 % Rotamer: Outliers : 3.49 % Allowed : 20.39 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.11), residues: 6252 helix: 0.79 (0.10), residues: 2928 sheet: -0.95 (0.21), residues: 528 loop : -2.02 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 83 HIS 0.003 0.001 HIS E 216 PHE 0.029 0.001 PHE E 78 TYR 0.023 0.001 TYR G 389 ARG 0.006 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1270 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 1088 time to evaluate : 4.398 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: A 94 LYS cc_start: 0.8759 (mmtt) cc_final: 0.7658 (tptt) REVERT: A 105 LYS cc_start: 0.8731 (tptt) cc_final: 0.7787 (ttpp) REVERT: A 118 MET cc_start: 0.8760 (mmm) cc_final: 0.8411 (mmm) REVERT: A 164 SER cc_start: 0.9075 (m) cc_final: 0.8774 (t) REVERT: A 494 GLN cc_start: 0.8678 (mm110) cc_final: 0.8221 (tm-30) REVERT: A 501 MET cc_start: 0.8293 (mtm) cc_final: 0.8013 (ptp) REVERT: A 523 MET cc_start: 0.8069 (ttp) cc_final: 0.7325 (tmm) REVERT: B 23 ASP cc_start: 0.8257 (t70) cc_final: 0.7971 (t70) REVERT: B 118 MET cc_start: 0.8835 (mmm) cc_final: 0.8593 (mmm) REVERT: B 145 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8551 (pt) REVERT: B 158 MET cc_start: 0.7933 (ptt) cc_final: 0.7582 (ptt) REVERT: B 238 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7610 (pt0) REVERT: B 240 SER cc_start: 0.8271 (p) cc_final: 0.7992 (m) REVERT: B 460 ASP cc_start: 0.8052 (t0) cc_final: 0.7808 (t0) REVERT: B 489 GLN cc_start: 0.8276 (mt0) cc_final: 0.8054 (tp40) REVERT: C 47 SER cc_start: 0.8499 (t) cc_final: 0.8272 (t) REVERT: C 94 LYS cc_start: 0.8689 (mmtt) cc_final: 0.7783 (tptt) REVERT: C 97 LEU cc_start: 0.8989 (tp) cc_final: 0.8784 (tt) REVERT: C 105 LYS cc_start: 0.8720 (tptt) cc_final: 0.8049 (ttpp) REVERT: C 118 MET cc_start: 0.8547 (mmm) cc_final: 0.8225 (mmm) REVERT: C 120 TYR cc_start: 0.9015 (t80) cc_final: 0.8761 (t80) REVERT: C 357 MET cc_start: 0.7837 (mmm) cc_final: 0.7486 (tpp) REVERT: C 501 MET cc_start: 0.8775 (mtp) cc_final: 0.8139 (mtm) REVERT: D 48 ASP cc_start: 0.7306 (m-30) cc_final: 0.7083 (m-30) REVERT: D 118 MET cc_start: 0.8939 (mmm) cc_final: 0.8271 (mmm) REVERT: D 158 MET cc_start: 0.7667 (ptt) cc_final: 0.7222 (ptt) REVERT: D 225 GLU cc_start: 0.8160 (mp0) cc_final: 0.7938 (mp0) REVERT: D 235 MET cc_start: 0.6896 (ttm) cc_final: 0.6419 (ttm) REVERT: D 236 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5715 (mp0) REVERT: D 238 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7536 (tm-30) REVERT: D 385 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8347 (tt) REVERT: D 465 MET cc_start: 0.8704 (tpt) cc_final: 0.8067 (tpp) REVERT: E 92 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7833 (mt-10) REVERT: E 94 LYS cc_start: 0.8863 (mmtt) cc_final: 0.7936 (tptt) REVERT: E 105 LYS cc_start: 0.8848 (tptt) cc_final: 0.8036 (ttpp) REVERT: E 158 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7629 (ptp) REVERT: E 279 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9230 (tp) REVERT: E 465 MET cc_start: 0.8688 (tmm) cc_final: 0.8233 (tmm) REVERT: E 494 GLN cc_start: 0.8642 (mm110) cc_final: 0.8221 (tm-30) REVERT: E 501 MET cc_start: 0.8259 (mtm) cc_final: 0.7713 (ptp) REVERT: E 523 MET cc_start: 0.8611 (tmm) cc_final: 0.7875 (tmm) REVERT: F 112 MET cc_start: 0.7887 (tpp) cc_final: 0.7657 (tpp) REVERT: F 118 MET cc_start: 0.9119 (mmm) cc_final: 0.8894 (mmm) REVERT: F 158 MET cc_start: 0.7464 (ptt) cc_final: 0.6972 (ptt) REVERT: F 179 MET cc_start: 0.8261 (mtm) cc_final: 0.8036 (mtm) REVERT: F 235 MET cc_start: 0.6842 (ttm) cc_final: 0.6495 (ttm) REVERT: F 236 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: F 440 ASP cc_start: 0.8057 (t70) cc_final: 0.7769 (p0) REVERT: F 455 MET cc_start: 0.8015 (mtt) cc_final: 0.7785 (mtt) REVERT: F 461 ILE cc_start: 0.9161 (mm) cc_final: 0.8815 (tp) REVERT: F 465 MET cc_start: 0.8433 (tpp) cc_final: 0.7831 (tpp) REVERT: F 489 GLN cc_start: 0.7974 (mt0) cc_final: 0.7344 (tp40) REVERT: F 494 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8259 (tm-30) REVERT: G 47 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.8054 (t) REVERT: G 80 MET cc_start: 0.7426 (mmm) cc_final: 0.7123 (mmm) REVERT: G 94 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8054 (tptt) REVERT: G 105 LYS cc_start: 0.8675 (tptt) cc_final: 0.7742 (ttpp) REVERT: G 118 MET cc_start: 0.8709 (mmm) cc_final: 0.8371 (mmm) REVERT: G 164 SER cc_start: 0.9240 (m) cc_final: 0.8955 (t) REVERT: G 173 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: G 238 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7581 (mp10) REVERT: G 461 ILE cc_start: 0.8883 (mt) cc_final: 0.8559 (mt) REVERT: G 494 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8263 (tm-30) REVERT: G 497 MET cc_start: 0.8102 (tpp) cc_final: 0.7866 (mtt) REVERT: G 498 GLN cc_start: 0.9248 (tp40) cc_final: 0.8921 (tp-100) REVERT: G 501 MET cc_start: 0.8346 (ttp) cc_final: 0.7938 (ptp) REVERT: H 118 MET cc_start: 0.8806 (mmm) cc_final: 0.8473 (mmm) REVERT: H 195 ARG cc_start: 0.8315 (mtm110) cc_final: 0.7632 (mtp85) REVERT: H 325 GLU cc_start: 0.8063 (pm20) cc_final: 0.7585 (pm20) REVERT: H 482 LEU cc_start: 0.8459 (pt) cc_final: 0.8209 (pp) REVERT: H 489 GLN cc_start: 0.8042 (mt0) cc_final: 0.7321 (tp40) REVERT: H 512 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8160 (ptm) REVERT: I 18 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8126 (mt-10) REVERT: I 94 LYS cc_start: 0.8553 (mmtt) cc_final: 0.7792 (tptt) REVERT: I 105 LYS cc_start: 0.8675 (tptt) cc_final: 0.7925 (ttpp) REVERT: I 331 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: I 494 GLN cc_start: 0.8666 (mm110) cc_final: 0.8205 (tm-30) REVERT: I 501 MET cc_start: 0.8264 (mtp) cc_final: 0.7737 (ptp) REVERT: J 8 LEU cc_start: 0.4787 (tp) cc_final: 0.4390 (tp) REVERT: J 23 ASP cc_start: 0.7518 (t70) cc_final: 0.7275 (t0) REVERT: J 118 MET cc_start: 0.8771 (mmm) cc_final: 0.8522 (mmm) REVERT: J 158 MET cc_start: 0.7938 (ptt) cc_final: 0.7172 (ptt) REVERT: J 179 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7309 (mpp) REVERT: J 185 ILE cc_start: 0.8866 (mt) cc_final: 0.8446 (mt) REVERT: J 236 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5802 (mp0) REVERT: J 357 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7024 (mmp) REVERT: J 461 ILE cc_start: 0.9180 (mm) cc_final: 0.8979 (tp) REVERT: J 465 MET cc_start: 0.8578 (tpp) cc_final: 0.7997 (tpp) REVERT: J 489 GLN cc_start: 0.8194 (mt0) cc_final: 0.7480 (tp40) REVERT: K 94 LYS cc_start: 0.8740 (mmtt) cc_final: 0.7988 (tptt) REVERT: K 105 LYS cc_start: 0.8912 (tptt) cc_final: 0.8256 (mtpt) REVERT: K 118 MET cc_start: 0.8763 (mmm) cc_final: 0.8373 (mmm) REVERT: K 145 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8991 (pt) REVERT: K 158 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8051 (ppp) REVERT: K 173 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: K 373 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5943 (tm-30) REVERT: K 395 GLU cc_start: 0.7785 (tp30) cc_final: 0.7525 (mm-30) REVERT: K 465 MET cc_start: 0.8708 (tpp) cc_final: 0.8431 (tmm) REVERT: K 494 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8164 (tm-30) REVERT: K 499 MET cc_start: 0.8705 (tmm) cc_final: 0.8009 (tmm) REVERT: K 501 MET cc_start: 0.8475 (mtp) cc_final: 0.7879 (ttm) REVERT: K 523 MET cc_start: 0.8051 (ttp) cc_final: 0.7260 (tmm) REVERT: L 23 ASP cc_start: 0.8048 (t70) cc_final: 0.7780 (t0) REVERT: L 91 TYR cc_start: 0.8441 (t80) cc_final: 0.7982 (t80) REVERT: L 158 MET cc_start: 0.7754 (ptt) cc_final: 0.7487 (ptt) REVERT: L 236 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: L 325 GLU cc_start: 0.8028 (pm20) cc_final: 0.7817 (pt0) REVERT: L 440 ASP cc_start: 0.8048 (t70) cc_final: 0.7770 (p0) REVERT: L 455 MET cc_start: 0.8525 (mpp) cc_final: 0.7665 (mtt) REVERT: L 461 ILE cc_start: 0.8795 (mm) cc_final: 0.8409 (tp) REVERT: L 465 MET cc_start: 0.8649 (tpp) cc_final: 0.8245 (tpp) REVERT: L 482 LEU cc_start: 0.8358 (pp) cc_final: 0.8155 (pp) REVERT: L 489 GLN cc_start: 0.7799 (mt0) cc_final: 0.7265 (tp40) REVERT: L 492 MET cc_start: 0.8184 (mmp) cc_final: 0.7936 (mmm) outliers start: 182 outliers final: 105 residues processed: 1210 average time/residue: 0.4422 time to fit residues: 916.5777 Evaluate side-chains 1079 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 957 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 445 CYS Chi-restraints excluded: chain H residue 512 MET Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 331 GLN Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 357 MET Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 391 ILE Chi-restraints excluded: chain I residue 392 LEU Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 145 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 173 PHE Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 481 ILE Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 158 MET Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 392 LEU Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 440 ASP Chi-restraints excluded: chain K residue 442 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 315 GLN Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 391 ILE Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 481 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 440 optimal weight: 4.9990 chunk 341 optimal weight: 2.9990 chunk 508 optimal weight: 5.9990 chunk 337 optimal weight: 0.0000 chunk 601 optimal weight: 0.5980 chunk 376 optimal weight: 0.3980 chunk 366 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN C 487 GLN ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 49440 Z= 0.219 Angle : 0.747 12.327 66912 Z= 0.365 Chirality : 0.045 0.305 7572 Planarity : 0.005 0.057 8832 Dihedral : 5.551 35.845 6876 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.05 % Favored : 91.57 % Rotamer: Outliers : 3.61 % Allowed : 20.99 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.11), residues: 6252 helix: 0.93 (0.10), residues: 2964 sheet: -0.93 (0.22), residues: 528 loop : -2.02 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 83 HIS 0.002 0.001 HIS C 216 PHE 0.026 0.002 PHE A 78 TYR 0.021 0.001 TYR K 120 ARG 0.007 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 993 time to evaluate : 4.170 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: A 94 LYS cc_start: 0.8804 (mmtt) cc_final: 0.7673 (tptt) REVERT: A 105 LYS cc_start: 0.8738 (tptt) cc_final: 0.7824 (ttpp) REVERT: A 164 SER cc_start: 0.9103 (m) cc_final: 0.8810 (t) REVERT: A 241 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7207 (t0) REVERT: A 268 TYR cc_start: 0.8543 (t80) cc_final: 0.8287 (t80) REVERT: A 494 GLN cc_start: 0.8705 (mm110) cc_final: 0.8252 (tm-30) REVERT: A 523 MET cc_start: 0.8090 (ttp) cc_final: 0.7327 (tmm) REVERT: B 23 ASP cc_start: 0.8288 (t70) cc_final: 0.7988 (t70) REVERT: B 118 MET cc_start: 0.8836 (mmm) cc_final: 0.8618 (mmm) REVERT: B 238 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7337 (tm-30) REVERT: B 240 SER cc_start: 0.8391 (p) cc_final: 0.8139 (m) REVERT: B 460 ASP cc_start: 0.8143 (t0) cc_final: 0.7880 (t0) REVERT: B 489 GLN cc_start: 0.8422 (mt0) cc_final: 0.8018 (tp40) REVERT: C 94 LYS cc_start: 0.8746 (mmtt) cc_final: 0.7824 (tptt) REVERT: C 105 LYS cc_start: 0.8757 (tptt) cc_final: 0.8045 (ttpp) REVERT: C 118 MET cc_start: 0.8540 (mmm) cc_final: 0.8148 (mmm) REVERT: C 240 SER cc_start: 0.7755 (m) cc_final: 0.7419 (m) REVERT: C 501 MET cc_start: 0.8627 (mtp) cc_final: 0.7731 (ptm) REVERT: D 118 MET cc_start: 0.8941 (mmm) cc_final: 0.8324 (mmm) REVERT: D 235 MET cc_start: 0.6987 (ttm) cc_final: 0.6513 (ttm) REVERT: D 236 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.5821 (mp0) REVERT: D 238 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7543 (tm-30) REVERT: D 357 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7188 (mmp) REVERT: D 465 MET cc_start: 0.8719 (tpt) cc_final: 0.8079 (tpp) REVERT: E 94 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8002 (tptt) REVERT: E 105 LYS cc_start: 0.8734 (tptt) cc_final: 0.7923 (ttpp) REVERT: E 158 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7863 (ptp) REVERT: E 240 SER cc_start: 0.8217 (m) cc_final: 0.7959 (p) REVERT: E 279 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9180 (tp) REVERT: E 289 MET cc_start: 0.8218 (mtt) cc_final: 0.8011 (mtt) REVERT: E 465 MET cc_start: 0.8697 (tmm) cc_final: 0.8276 (tmm) REVERT: E 494 GLN cc_start: 0.8627 (mm110) cc_final: 0.8231 (tm-30) REVERT: E 501 MET cc_start: 0.8252 (mtm) cc_final: 0.7728 (ptp) REVERT: E 523 MET cc_start: 0.8581 (tmm) cc_final: 0.7794 (tmm) REVERT: F 118 MET cc_start: 0.9112 (mmm) cc_final: 0.8867 (mmm) REVERT: F 179 MET cc_start: 0.8402 (mtm) cc_final: 0.8171 (mtm) REVERT: F 235 MET cc_start: 0.6848 (ttm) cc_final: 0.6504 (ttm) REVERT: F 236 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: F 440 ASP cc_start: 0.8040 (t70) cc_final: 0.7736 (p0) REVERT: F 455 MET cc_start: 0.8212 (mtt) cc_final: 0.7923 (mtt) REVERT: F 461 ILE cc_start: 0.9171 (mm) cc_final: 0.8796 (tp) REVERT: F 465 MET cc_start: 0.8464 (tpp) cc_final: 0.7836 (tpp) REVERT: F 489 GLN cc_start: 0.8112 (mt0) cc_final: 0.7700 (tp40) REVERT: G 47 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8151 (t) REVERT: G 94 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8053 (tptt) REVERT: G 105 LYS cc_start: 0.8759 (tptt) cc_final: 0.7790 (ttpp) REVERT: G 118 MET cc_start: 0.8763 (mmm) cc_final: 0.8376 (mmm) REVERT: G 164 SER cc_start: 0.9271 (m) cc_final: 0.8985 (t) REVERT: G 173 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.6883 (m-80) REVERT: G 238 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7585 (mp-120) REVERT: G 461 ILE cc_start: 0.8807 (mt) cc_final: 0.8502 (mt) REVERT: G 494 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8266 (tm-30) REVERT: G 498 GLN cc_start: 0.9148 (tp40) cc_final: 0.8748 (tp-100) REVERT: G 501 MET cc_start: 0.8395 (ttp) cc_final: 0.8056 (ptm) REVERT: H 195 ARG cc_start: 0.8338 (mtm110) cc_final: 0.7689 (mtp85) REVERT: H 240 SER cc_start: 0.7738 (m) cc_final: 0.7520 (p) REVERT: H 325 GLU cc_start: 0.8091 (pm20) cc_final: 0.7820 (pm20) REVERT: H 482 LEU cc_start: 0.8381 (pt) cc_final: 0.8137 (pp) REVERT: H 489 GLN cc_start: 0.8227 (mt0) cc_final: 0.7522 (tp40) REVERT: H 512 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: I 94 LYS cc_start: 0.8691 (mmtt) cc_final: 0.7849 (tptt) REVERT: I 105 LYS cc_start: 0.8751 (tptt) cc_final: 0.7998 (ttpp) REVERT: I 118 MET cc_start: 0.8761 (mmm) cc_final: 0.8243 (mmm) REVERT: I 241 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6804 (t0) REVERT: I 494 GLN cc_start: 0.8658 (mm110) cc_final: 0.8184 (tm-30) REVERT: I 501 MET cc_start: 0.8303 (mtp) cc_final: 0.7760 (ptp) REVERT: J 8 LEU cc_start: 0.4991 (tp) cc_final: 0.4471 (tp) REVERT: J 23 ASP cc_start: 0.7597 (t70) cc_final: 0.7364 (t0) REVERT: J 118 MET cc_start: 0.8798 (mmm) cc_final: 0.8589 (mmm) REVERT: J 158 MET cc_start: 0.8145 (ptt) cc_final: 0.7698 (ptt) REVERT: J 179 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7467 (mpp) REVERT: J 236 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5762 (mp0) REVERT: J 455 MET cc_start: 0.8696 (mpp) cc_final: 0.7997 (mtp) REVERT: J 465 MET cc_start: 0.8630 (tpp) cc_final: 0.8025 (tpp) REVERT: J 468 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9288 (tt) REVERT: J 489 GLN cc_start: 0.8241 (mt0) cc_final: 0.7641 (tp40) REVERT: J 521 GLU cc_start: 0.8477 (pm20) cc_final: 0.8220 (pm20) REVERT: K 94 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8018 (tptt) REVERT: K 105 LYS cc_start: 0.8929 (tptt) cc_final: 0.8332 (mtpt) REVERT: K 118 MET cc_start: 0.8756 (mmm) cc_final: 0.8303 (mmm) REVERT: K 145 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9064 (pt) REVERT: K 158 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8076 (ppp) REVERT: K 164 SER cc_start: 0.9192 (t) cc_final: 0.8937 (t) REVERT: K 173 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: K 241 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7149 (t0) REVERT: K 395 GLU cc_start: 0.7828 (tp30) cc_final: 0.7607 (tp30) REVERT: K 461 ILE cc_start: 0.8514 (mt) cc_final: 0.8301 (mt) REVERT: K 465 MET cc_start: 0.8697 (tpp) cc_final: 0.8435 (tmm) REVERT: K 494 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8189 (tm-30) REVERT: K 499 MET cc_start: 0.8698 (tmm) cc_final: 0.8033 (tmm) REVERT: K 501 MET cc_start: 0.8477 (mtp) cc_final: 0.8010 (ttm) REVERT: K 523 MET cc_start: 0.8017 (ttp) cc_final: 0.7594 (mtm) REVERT: L 23 ASP cc_start: 0.8092 (t70) cc_final: 0.7828 (t0) REVERT: L 91 TYR cc_start: 0.8519 (t80) cc_final: 0.8174 (t80) REVERT: L 118 MET cc_start: 0.8955 (mmm) cc_final: 0.8607 (mmm) REVERT: L 158 MET cc_start: 0.7908 (ptt) cc_final: 0.7479 (ptt) REVERT: L 236 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5833 (mp0) REVERT: L 246 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8066 (mttm) REVERT: L 315 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8392 (tp40) REVERT: L 325 GLU cc_start: 0.8084 (pm20) cc_final: 0.7856 (pt0) REVERT: L 440 ASP cc_start: 0.8102 (t70) cc_final: 0.7813 (p0) REVERT: L 455 MET cc_start: 0.8574 (mpp) cc_final: 0.7729 (mtt) REVERT: L 461 ILE cc_start: 0.8848 (mm) cc_final: 0.8448 (tp) REVERT: L 465 MET cc_start: 0.8700 (tpp) cc_final: 0.8069 (tpp) REVERT: L 482 LEU cc_start: 0.8304 (pp) cc_final: 0.8096 (pp) REVERT: L 489 GLN cc_start: 0.7909 (mt0) cc_final: 0.7466 (tp40) REVERT: L 494 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8317 (tm-30) outliers start: 188 outliers final: 131 residues processed: 1119 average time/residue: 0.4343 time to fit residues: 834.4421 Evaluate side-chains 1064 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 914 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 325 GLU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 263 SER Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 445 CYS Chi-restraints excluded: chain H residue 512 MET Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 305 ILE Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 333 GLU Chi-restraints excluded: chain I residue 357 MET Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 391 ILE Chi-restraints excluded: chain I residue 392 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 419 LYS Chi-restraints excluded: chain J residue 145 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 173 PHE Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 468 LEU Chi-restraints excluded: chain J residue 481 ILE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 158 MET Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 390 SER Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 440 ASP Chi-restraints excluded: chain K residue 442 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 315 GLN Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 357 MET Chi-restraints excluded: chain L residue 391 ILE Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 481 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 359 optimal weight: 0.0570 chunk 181 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 chunk 382 optimal weight: 4.9990 chunk 409 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 472 optimal weight: 3.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN D 472 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 GLN ** L 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 49440 Z= 0.253 Angle : 0.767 12.094 66912 Z= 0.376 Chirality : 0.045 0.265 7572 Planarity : 0.005 0.058 8832 Dihedral : 5.609 35.041 6876 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.29 % Favored : 91.33 % Rotamer: Outliers : 3.88 % Allowed : 21.20 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.11), residues: 6252 helix: 0.97 (0.10), residues: 2976 sheet: -0.95 (0.22), residues: 528 loop : -2.01 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 83 HIS 0.003 0.001 HIS I 216 PHE 0.024 0.002 PHE A 78 TYR 0.021 0.002 TYR G 389 ARG 0.007 0.001 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 963 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8882 (mmtt) cc_final: 0.7769 (tptt) REVERT: A 105 LYS cc_start: 0.8808 (tptt) cc_final: 0.7908 (ttpp) REVERT: A 118 MET cc_start: 0.8855 (mmm) cc_final: 0.8439 (mmm) REVERT: A 164 SER cc_start: 0.9162 (m) cc_final: 0.8890 (t) REVERT: A 173 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: A 465 MET cc_start: 0.8552 (tpp) cc_final: 0.7947 (tpp) REVERT: A 494 GLN cc_start: 0.8703 (mm110) cc_final: 0.8268 (tm-30) REVERT: A 523 MET cc_start: 0.8120 (ttp) cc_final: 0.7322 (tmm) REVERT: B 23 ASP cc_start: 0.8154 (t70) cc_final: 0.7890 (t70) REVERT: B 158 MET cc_start: 0.8104 (ptt) cc_final: 0.7782 (ptt) REVERT: B 238 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7400 (tm-30) REVERT: B 455 MET cc_start: 0.8240 (mtp) cc_final: 0.8017 (mtt) REVERT: B 489 GLN cc_start: 0.8635 (mt0) cc_final: 0.8119 (tm-30) REVERT: B 490 GLN cc_start: 0.8373 (pm20) cc_final: 0.7923 (pm20) REVERT: C 94 LYS cc_start: 0.8787 (mmtt) cc_final: 0.7819 (tptt) REVERT: C 105 LYS cc_start: 0.8801 (tptt) cc_final: 0.8061 (ttpp) REVERT: C 118 MET cc_start: 0.8530 (mmm) cc_final: 0.8079 (mmm) REVERT: C 240 SER cc_start: 0.7951 (m) cc_final: 0.6770 (m) REVERT: C 498 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8551 (tp40) REVERT: C 501 MET cc_start: 0.8648 (mtp) cc_final: 0.8078 (ptp) REVERT: D 118 MET cc_start: 0.8927 (mmm) cc_final: 0.8498 (mmm) REVERT: D 195 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7434 (mtp85) REVERT: D 235 MET cc_start: 0.7064 (ttm) cc_final: 0.6525 (ttm) REVERT: D 236 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5926 (mp0) REVERT: D 238 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7480 (tm-30) REVERT: D 357 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7307 (mmp) REVERT: D 465 MET cc_start: 0.8734 (tpt) cc_final: 0.8057 (tpp) REVERT: D 492 MET cc_start: 0.7730 (ppp) cc_final: 0.7088 (ppp) REVERT: E 94 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8040 (tptt) REVERT: E 105 LYS cc_start: 0.8763 (tptt) cc_final: 0.7938 (ttpp) REVERT: E 158 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.7960 (ptp) REVERT: E 173 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: E 240 SER cc_start: 0.7768 (m) cc_final: 0.7544 (p) REVERT: E 279 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9188 (tp) REVERT: E 289 MET cc_start: 0.8189 (mtt) cc_final: 0.7986 (mtt) REVERT: E 494 GLN cc_start: 0.8617 (mm110) cc_final: 0.8235 (tm-30) REVERT: E 501 MET cc_start: 0.8257 (mtm) cc_final: 0.7697 (ptp) REVERT: E 523 MET cc_start: 0.8595 (tmm) cc_final: 0.7860 (tmm) REVERT: F 118 MET cc_start: 0.9097 (mmm) cc_final: 0.8856 (mmm) REVERT: F 158 MET cc_start: 0.7762 (ptt) cc_final: 0.7454 (ptt) REVERT: F 179 MET cc_start: 0.8415 (mtm) cc_final: 0.8168 (mtm) REVERT: F 440 ASP cc_start: 0.7912 (t70) cc_final: 0.7614 (p0) REVERT: F 455 MET cc_start: 0.8273 (mtt) cc_final: 0.7995 (mtt) REVERT: F 465 MET cc_start: 0.8477 (tpp) cc_final: 0.7861 (tpp) REVERT: F 489 GLN cc_start: 0.8282 (mt0) cc_final: 0.7659 (tp40) REVERT: F 494 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8152 (tp-100) REVERT: G 47 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8030 (t) REVERT: G 94 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8103 (tptt) REVERT: G 105 LYS cc_start: 0.8778 (tptt) cc_final: 0.7823 (ttpp) REVERT: G 164 SER cc_start: 0.9276 (m) cc_final: 0.8970 (t) REVERT: G 173 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7058 (m-80) REVERT: G 461 ILE cc_start: 0.8811 (mt) cc_final: 0.8514 (mt) REVERT: G 465 MET cc_start: 0.8524 (tpp) cc_final: 0.7930 (tpp) REVERT: G 494 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8276 (tm-30) REVERT: G 498 GLN cc_start: 0.8954 (tp40) cc_final: 0.8580 (tp-100) REVERT: G 501 MET cc_start: 0.8321 (ttp) cc_final: 0.7864 (ptm) REVERT: H 118 MET cc_start: 0.8813 (mmm) cc_final: 0.8479 (mmm) REVERT: H 195 ARG cc_start: 0.8295 (mtm110) cc_final: 0.7643 (mtp85) REVERT: H 461 ILE cc_start: 0.8819 (tp) cc_final: 0.8484 (tp) REVERT: H 482 LEU cc_start: 0.8250 (pt) cc_final: 0.8004 (pp) REVERT: H 489 GLN cc_start: 0.8308 (mt0) cc_final: 0.7601 (tp40) REVERT: H 512 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8008 (ptm) REVERT: I 94 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8001 (tptt) REVERT: I 105 LYS cc_start: 0.8740 (tptt) cc_final: 0.7947 (ttpp) REVERT: I 118 MET cc_start: 0.8765 (mmm) cc_final: 0.8115 (mmm) REVERT: I 241 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.6908 (t0) REVERT: I 331 GLN cc_start: 0.7998 (pt0) cc_final: 0.7647 (mt0) REVERT: I 494 GLN cc_start: 0.8678 (mm110) cc_final: 0.8218 (tm-30) REVERT: I 501 MET cc_start: 0.8376 (mtp) cc_final: 0.7612 (ttp) REVERT: J 118 MET cc_start: 0.8685 (mmm) cc_final: 0.8349 (mmm) REVERT: J 158 MET cc_start: 0.8232 (ptt) cc_final: 0.7905 (ptt) REVERT: J 179 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7571 (mpp) REVERT: J 236 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.5937 (mp0) REVERT: J 383 ASP cc_start: 0.6827 (m-30) cc_final: 0.6550 (m-30) REVERT: J 405 LEU cc_start: 0.8803 (mt) cc_final: 0.8593 (mp) REVERT: J 455 MET cc_start: 0.8876 (mpp) cc_final: 0.8173 (mtp) REVERT: J 465 MET cc_start: 0.8650 (tpp) cc_final: 0.8029 (tpp) REVERT: J 489 GLN cc_start: 0.8364 (mt0) cc_final: 0.7672 (tp40) REVERT: K 94 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8052 (tptt) REVERT: K 105 LYS cc_start: 0.8914 (tptt) cc_final: 0.8247 (mtpt) REVERT: K 118 MET cc_start: 0.8744 (mmm) cc_final: 0.8232 (mmm) REVERT: K 145 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9033 (pt) REVERT: K 158 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8046 (ppp) REVERT: K 173 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: K 241 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7155 (t0) REVERT: K 395 GLU cc_start: 0.7982 (tp30) cc_final: 0.7684 (tp30) REVERT: K 465 MET cc_start: 0.8683 (tpp) cc_final: 0.8439 (tmm) REVERT: K 494 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8219 (tm-30) REVERT: K 501 MET cc_start: 0.8435 (mtp) cc_final: 0.7534 (ttm) REVERT: K 523 MET cc_start: 0.8050 (ttp) cc_final: 0.7786 (mtm) REVERT: L 23 ASP cc_start: 0.8110 (t70) cc_final: 0.7830 (t0) REVERT: L 91 TYR cc_start: 0.8620 (t80) cc_final: 0.8272 (t80) REVERT: L 158 MET cc_start: 0.8012 (ptt) cc_final: 0.7590 (ptt) REVERT: L 236 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.5825 (mp0) REVERT: L 246 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8050 (mttm) REVERT: L 315 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8436 (tp40) REVERT: L 325 GLU cc_start: 0.8117 (pm20) cc_final: 0.7824 (pt0) REVERT: L 406 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7941 (pttm) REVERT: L 455 MET cc_start: 0.8643 (mpp) cc_final: 0.7872 (mtt) REVERT: L 461 ILE cc_start: 0.8913 (mm) cc_final: 0.8520 (tp) REVERT: L 465 MET cc_start: 0.8688 (tpp) cc_final: 0.8087 (tpp) REVERT: L 489 GLN cc_start: 0.8132 (mt0) cc_final: 0.7495 (tp40) REVERT: L 494 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8221 (tm-30) outliers start: 202 outliers final: 151 residues processed: 1093 average time/residue: 0.4418 time to fit residues: 832.2324 Evaluate side-chains 1089 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 919 time to evaluate : 4.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 325 GLU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 263 SER Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 445 CYS Chi-restraints excluded: chain H residue 512 MET Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 333 GLU Chi-restraints excluded: chain I residue 357 MET Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 391 ILE Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 145 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 173 PHE Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 240 SER Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 481 ILE Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 158 MET Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 390 SER Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 440 ASP Chi-restraints excluded: chain K residue 442 LEU Chi-restraints excluded: chain K residue 508 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 315 GLN Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 357 MET Chi-restraints excluded: chain L residue 391 ILE Chi-restraints excluded: chain L residue 406 LYS Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 481 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 0.5980 chunk 576 optimal weight: 0.7980 chunk 525 optimal weight: 0.9990 chunk 560 optimal weight: 0.8980 chunk 337 optimal weight: 2.9990 chunk 244 optimal weight: 0.0570 chunk 440 optimal weight: 0.4980 chunk 171 optimal weight: 0.0570 chunk 506 optimal weight: 0.6980 chunk 530 optimal weight: 0.8980 chunk 558 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN D 472 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 GLN F 495 GLN ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 49440 Z= 0.188 Angle : 0.760 11.396 66912 Z= 0.370 Chirality : 0.044 0.271 7572 Planarity : 0.004 0.056 8832 Dihedral : 5.444 33.655 6876 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.00 % Favored : 91.63 % Rotamer: Outliers : 3.21 % Allowed : 22.14 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.11), residues: 6252 helix: 0.95 (0.10), residues: 3060 sheet: -0.83 (0.22), residues: 528 loop : -2.04 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 83 HIS 0.002 0.001 HIS I 216 PHE 0.024 0.002 PHE G 78 TYR 0.024 0.001 TYR F 389 ARG 0.008 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1006 time to evaluate : 4.145 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: A 94 LYS cc_start: 0.8777 (mmtt) cc_final: 0.7725 (tptt) REVERT: A 105 LYS cc_start: 0.8749 (tptt) cc_final: 0.7891 (ttpp) REVERT: A 118 MET cc_start: 0.8896 (mmm) cc_final: 0.8497 (mmm) REVERT: A 158 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8023 (ppp) REVERT: A 164 SER cc_start: 0.9044 (m) cc_final: 0.8716 (t) REVERT: A 494 GLN cc_start: 0.8761 (mm110) cc_final: 0.8292 (tm-30) REVERT: A 523 MET cc_start: 0.8024 (ttp) cc_final: 0.7352 (tmm) REVERT: B 23 ASP cc_start: 0.8251 (t70) cc_final: 0.7955 (t70) REVERT: B 80 MET cc_start: 0.6302 (tpt) cc_final: 0.5988 (tpt) REVERT: B 158 MET cc_start: 0.7771 (ptt) cc_final: 0.7378 (ptt) REVERT: B 230 GLU cc_start: 0.8213 (pm20) cc_final: 0.7513 (pm20) REVERT: B 238 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7305 (tm-30) REVERT: B 489 GLN cc_start: 0.8571 (mt0) cc_final: 0.8109 (tm-30) REVERT: B 490 GLN cc_start: 0.8385 (pm20) cc_final: 0.7956 (pm20) REVERT: C 94 LYS cc_start: 0.8659 (mmtt) cc_final: 0.7777 (tptt) REVERT: C 105 LYS cc_start: 0.8741 (tptt) cc_final: 0.7902 (ttpp) REVERT: C 118 MET cc_start: 0.8533 (mmm) cc_final: 0.8066 (mmm) REVERT: C 121 ILE cc_start: 0.9234 (mt) cc_final: 0.9000 (mt) REVERT: C 501 MET cc_start: 0.8491 (mtp) cc_final: 0.7619 (ptp) REVERT: D 118 MET cc_start: 0.8966 (mmm) cc_final: 0.8458 (mmm) REVERT: D 185 ILE cc_start: 0.8602 (mt) cc_final: 0.8273 (mt) REVERT: D 195 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7434 (mtp85) REVERT: D 225 GLU cc_start: 0.8119 (mp0) cc_final: 0.7794 (mp0) REVERT: D 235 MET cc_start: 0.6919 (ttm) cc_final: 0.6509 (ttm) REVERT: D 236 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5818 (mp0) REVERT: D 238 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7329 (tm-30) REVERT: D 357 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7215 (mmp) REVERT: D 465 MET cc_start: 0.8682 (tpt) cc_final: 0.7951 (tpp) REVERT: E 94 LYS cc_start: 0.8892 (mmtt) cc_final: 0.7975 (tptt) REVERT: E 105 LYS cc_start: 0.8712 (tptt) cc_final: 0.7882 (ttpp) REVERT: E 158 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7720 (ptp) REVERT: E 173 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: E 279 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9147 (tp) REVERT: E 338 PHE cc_start: 0.8214 (t80) cc_final: 0.8005 (t80) REVERT: E 494 GLN cc_start: 0.8631 (mm110) cc_final: 0.8251 (tm-30) REVERT: E 501 MET cc_start: 0.8144 (mtm) cc_final: 0.7721 (ptp) REVERT: E 523 MET cc_start: 0.8550 (tmm) cc_final: 0.7906 (tmm) REVERT: F 96 LEU cc_start: 0.9097 (mt) cc_final: 0.8798 (pp) REVERT: F 236 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: F 461 ILE cc_start: 0.9083 (mm) cc_final: 0.8768 (tp) REVERT: F 489 GLN cc_start: 0.8195 (mt0) cc_final: 0.7589 (tp40) REVERT: F 490 GLN cc_start: 0.7976 (pm20) cc_final: 0.7454 (pm20) REVERT: G 47 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.7937 (t) REVERT: G 94 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8093 (tptt) REVERT: G 105 LYS cc_start: 0.8735 (tptt) cc_final: 0.7785 (ttpp) REVERT: G 164 SER cc_start: 0.9048 (m) cc_final: 0.8822 (t) REVERT: G 173 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: G 182 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7524 (ttm-80) REVERT: G 238 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7488 (mp-120) REVERT: G 461 ILE cc_start: 0.8763 (mt) cc_final: 0.8466 (mt) REVERT: G 465 MET cc_start: 0.8502 (tpp) cc_final: 0.7928 (tpp) REVERT: G 494 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8254 (tm-30) REVERT: G 498 GLN cc_start: 0.8786 (tp40) cc_final: 0.8529 (tp-100) REVERT: G 501 MET cc_start: 0.8327 (ttp) cc_final: 0.7853 (ptm) REVERT: H 158 MET cc_start: 0.7876 (ptt) cc_final: 0.7646 (ptt) REVERT: H 195 ARG cc_start: 0.8251 (mtm110) cc_final: 0.7570 (mtp85) REVERT: H 325 GLU cc_start: 0.8148 (pm20) cc_final: 0.7873 (pm20) REVERT: H 461 ILE cc_start: 0.8832 (tp) cc_final: 0.8493 (tp) REVERT: H 482 LEU cc_start: 0.8164 (pt) cc_final: 0.7956 (pp) REVERT: H 489 GLN cc_start: 0.8274 (mt0) cc_final: 0.7569 (tp40) REVERT: I 94 LYS cc_start: 0.8648 (mmtt) cc_final: 0.7894 (tptt) REVERT: I 105 LYS cc_start: 0.8693 (tptt) cc_final: 0.7894 (ttpp) REVERT: I 118 MET cc_start: 0.8740 (mmm) cc_final: 0.8106 (mmm) REVERT: I 241 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6806 (t0) REVERT: I 331 GLN cc_start: 0.7914 (pt0) cc_final: 0.7643 (mt0) REVERT: I 465 MET cc_start: 0.8638 (tpp) cc_final: 0.8062 (tpp) REVERT: I 494 GLN cc_start: 0.8668 (mm110) cc_final: 0.8242 (tm-30) REVERT: I 501 MET cc_start: 0.8278 (mtp) cc_final: 0.7713 (ttp) REVERT: I 523 MET cc_start: 0.8520 (tmm) cc_final: 0.7968 (tmm) REVERT: J 8 LEU cc_start: 0.4893 (tp) cc_final: 0.4381 (tp) REVERT: J 158 MET cc_start: 0.8102 (ptt) cc_final: 0.7380 (ptt) REVERT: J 185 ILE cc_start: 0.8840 (mt) cc_final: 0.8558 (mt) REVERT: J 201 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7439 (tm-30) REVERT: J 236 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.5901 (mp0) REVERT: J 326 ASP cc_start: 0.8499 (m-30) cc_final: 0.8212 (m-30) REVERT: J 455 MET cc_start: 0.8824 (mpp) cc_final: 0.8037 (mtp) REVERT: J 465 MET cc_start: 0.8540 (tpp) cc_final: 0.7872 (tpp) REVERT: J 468 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9236 (tt) REVERT: J 489 GLN cc_start: 0.8281 (mt0) cc_final: 0.7619 (tp40) REVERT: K 94 LYS cc_start: 0.8717 (mmtt) cc_final: 0.7982 (tptt) REVERT: K 105 LYS cc_start: 0.8945 (tptt) cc_final: 0.8349 (mtpt) REVERT: K 156 ASN cc_start: 0.8620 (t0) cc_final: 0.8296 (t0) REVERT: K 173 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: K 465 MET cc_start: 0.8657 (tpp) cc_final: 0.8389 (tmm) REVERT: K 494 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8196 (tm-30) REVERT: K 501 MET cc_start: 0.8453 (mtp) cc_final: 0.8081 (ptm) REVERT: L 23 ASP cc_start: 0.8070 (t70) cc_final: 0.7823 (t0) REVERT: L 91 TYR cc_start: 0.8570 (t80) cc_final: 0.8239 (t80) REVERT: L 158 MET cc_start: 0.7777 (ptt) cc_final: 0.7490 (ptt) REVERT: L 236 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: L 246 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8093 (mttm) REVERT: L 325 GLU cc_start: 0.8143 (pm20) cc_final: 0.7836 (pt0) REVERT: L 406 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7870 (pttm) REVERT: L 440 ASP cc_start: 0.7822 (t70) cc_final: 0.7622 (p0) REVERT: L 455 MET cc_start: 0.8594 (mpp) cc_final: 0.8272 (mpp) REVERT: L 461 ILE cc_start: 0.8919 (mm) cc_final: 0.8573 (tp) REVERT: L 465 MET cc_start: 0.8715 (tpp) cc_final: 0.8024 (tpp) REVERT: L 489 GLN cc_start: 0.8111 (mt0) cc_final: 0.7524 (tp40) REVERT: L 490 GLN cc_start: 0.7898 (pm20) cc_final: 0.7626 (pm20) REVERT: L 494 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8210 (tm-30) outliers start: 167 outliers final: 113 residues processed: 1127 average time/residue: 0.4385 time to fit residues: 847.7117 Evaluate side-chains 1063 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 934 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 445 CYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 357 MET Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 391 ILE Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 145 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 173 PHE Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 240 SER Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 468 LEU Chi-restraints excluded: chain J residue 481 ILE Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 390 SER Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 440 ASP Chi-restraints excluded: chain K residue 442 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 357 MET Chi-restraints excluded: chain L residue 406 LYS Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 445 CYS Chi-restraints excluded: chain L residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 0.8980 chunk 592 optimal weight: 0.9980 chunk 361 optimal weight: 0.9980 chunk 281 optimal weight: 0.9990 chunk 411 optimal weight: 0.0270 chunk 621 optimal weight: 0.9980 chunk 572 optimal weight: 0.8980 chunk 495 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 382 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 49440 Z= 0.220 Angle : 0.776 12.434 66912 Z= 0.378 Chirality : 0.045 0.238 7572 Planarity : 0.005 0.059 8832 Dihedral : 5.402 32.325 6876 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.21 % Favored : 91.46 % Rotamer: Outliers : 2.71 % Allowed : 23.08 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 6252 helix: 1.22 (0.10), residues: 2964 sheet: -1.03 (0.20), residues: 660 loop : -1.95 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 83 HIS 0.002 0.001 HIS A 216 PHE 0.039 0.002 PHE K 78 TYR 0.020 0.001 TYR F 389 ARG 0.008 0.000 ARG C 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 942 time to evaluate : 4.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8860 (mmtt) cc_final: 0.7770 (tptt) REVERT: A 105 LYS cc_start: 0.8752 (tptt) cc_final: 0.7875 (ttpp) REVERT: A 118 MET cc_start: 0.8865 (mmm) cc_final: 0.8436 (mmm) REVERT: A 158 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8031 (ppp) REVERT: A 164 SER cc_start: 0.9066 (m) cc_final: 0.8769 (t) REVERT: A 352 LEU cc_start: 0.9063 (tp) cc_final: 0.8804 (tp) REVERT: A 419 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7269 (ptpp) REVERT: A 465 MET cc_start: 0.8526 (tpp) cc_final: 0.8007 (tpp) REVERT: A 494 GLN cc_start: 0.8673 (mm110) cc_final: 0.8299 (tm-30) REVERT: A 523 MET cc_start: 0.8046 (ttp) cc_final: 0.7380 (tmm) REVERT: B 80 MET cc_start: 0.6269 (tpt) cc_final: 0.5983 (tpt) REVERT: B 118 MET cc_start: 0.8901 (mmm) cc_final: 0.8535 (mmm) REVERT: B 158 MET cc_start: 0.7936 (ptt) cc_final: 0.7577 (ptt) REVERT: B 238 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7303 (tm-30) REVERT: B 489 GLN cc_start: 0.8588 (mt0) cc_final: 0.7906 (tm-30) REVERT: B 490 GLN cc_start: 0.8366 (pm20) cc_final: 0.7948 (pm20) REVERT: C 94 LYS cc_start: 0.8694 (mmtt) cc_final: 0.7791 (tptt) REVERT: C 105 LYS cc_start: 0.8743 (tptt) cc_final: 0.7938 (ttpp) REVERT: C 118 MET cc_start: 0.8487 (mmm) cc_final: 0.8008 (mmm) REVERT: C 120 TYR cc_start: 0.8955 (t80) cc_final: 0.8531 (t80) REVERT: C 121 ILE cc_start: 0.9172 (mt) cc_final: 0.8933 (mt) REVERT: C 143 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8817 (m) REVERT: C 501 MET cc_start: 0.8561 (mtp) cc_final: 0.8094 (ttm) REVERT: D 118 MET cc_start: 0.8965 (mmm) cc_final: 0.8506 (mmm) REVERT: D 185 ILE cc_start: 0.8676 (mt) cc_final: 0.8333 (mt) REVERT: D 195 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7431 (mtp85) REVERT: D 357 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7154 (mmp) REVERT: D 465 MET cc_start: 0.8690 (tpt) cc_final: 0.7908 (tpp) REVERT: E 94 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8027 (tptt) REVERT: E 105 LYS cc_start: 0.8731 (tptt) cc_final: 0.7892 (ttpp) REVERT: E 158 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7871 (ptp) REVERT: E 173 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: E 279 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9142 (tp) REVERT: E 494 GLN cc_start: 0.8820 (mm110) cc_final: 0.8338 (tm-30) REVERT: E 501 MET cc_start: 0.8129 (mtm) cc_final: 0.7768 (ptp) REVERT: E 523 MET cc_start: 0.8575 (tmm) cc_final: 0.7836 (tmm) REVERT: F 96 LEU cc_start: 0.9104 (mt) cc_final: 0.8835 (pp) REVERT: F 179 MET cc_start: 0.8358 (mtm) cc_final: 0.8127 (mtm) REVERT: F 236 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: F 461 ILE cc_start: 0.9120 (mm) cc_final: 0.8783 (tp) REVERT: F 489 GLN cc_start: 0.8191 (mt0) cc_final: 0.7527 (tm-30) REVERT: F 490 GLN cc_start: 0.7658 (pm20) cc_final: 0.7447 (pm20) REVERT: F 494 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8211 (mm-40) REVERT: G 47 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.7994 (t) REVERT: G 94 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8114 (tptt) REVERT: G 105 LYS cc_start: 0.8782 (tptt) cc_final: 0.7812 (ttpp) REVERT: G 164 SER cc_start: 0.9233 (m) cc_final: 0.8945 (t) REVERT: G 173 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: G 182 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7558 (ttm-80) REVERT: G 238 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7488 (mp10) REVERT: G 256 MET cc_start: 0.8709 (tpp) cc_final: 0.8483 (tpp) REVERT: G 461 ILE cc_start: 0.8751 (mt) cc_final: 0.8459 (mt) REVERT: G 494 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8266 (tm-30) REVERT: G 498 GLN cc_start: 0.8653 (tp40) cc_final: 0.8414 (tp-100) REVERT: G 501 MET cc_start: 0.8347 (ttp) cc_final: 0.7867 (ptm) REVERT: H 195 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7562 (mtp85) REVERT: H 325 GLU cc_start: 0.8173 (pm20) cc_final: 0.7820 (pm20) REVERT: H 461 ILE cc_start: 0.8857 (tp) cc_final: 0.8537 (tp) REVERT: H 482 LEU cc_start: 0.8142 (pt) cc_final: 0.7918 (pp) REVERT: H 489 GLN cc_start: 0.8357 (mt0) cc_final: 0.7681 (tp40) REVERT: H 494 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8301 (tm-30) REVERT: I 94 LYS cc_start: 0.8650 (mmtt) cc_final: 0.7846 (tptt) REVERT: I 105 LYS cc_start: 0.8703 (tptt) cc_final: 0.7894 (ttpp) REVERT: I 241 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6738 (t0) REVERT: I 331 GLN cc_start: 0.7976 (pt0) cc_final: 0.7665 (mt0) REVERT: I 494 GLN cc_start: 0.8674 (mm110) cc_final: 0.8274 (tm-30) REVERT: I 501 MET cc_start: 0.8313 (mtp) cc_final: 0.7757 (ttp) REVERT: I 523 MET cc_start: 0.8507 (tmm) cc_final: 0.7966 (tmm) REVERT: J 8 LEU cc_start: 0.4885 (tp) cc_final: 0.4362 (tp) REVERT: J 118 MET cc_start: 0.8732 (mmm) cc_final: 0.8428 (mmm) REVERT: J 158 MET cc_start: 0.8163 (ptt) cc_final: 0.7797 (ptt) REVERT: J 185 ILE cc_start: 0.8832 (mt) cc_final: 0.8499 (mt) REVERT: J 201 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7465 (tm-30) REVERT: J 236 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: J 455 MET cc_start: 0.8682 (mpp) cc_final: 0.8095 (mtt) REVERT: J 465 MET cc_start: 0.8565 (tpp) cc_final: 0.7865 (tpp) REVERT: J 468 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9277 (tt) REVERT: J 489 GLN cc_start: 0.8338 (mt0) cc_final: 0.7644 (tp40) REVERT: J 521 GLU cc_start: 0.8515 (pm20) cc_final: 0.8226 (pm20) REVERT: K 94 LYS cc_start: 0.8774 (mmtt) cc_final: 0.7990 (tptt) REVERT: K 105 LYS cc_start: 0.8950 (tptt) cc_final: 0.8322 (mtpt) REVERT: K 156 ASN cc_start: 0.8667 (t0) cc_final: 0.8322 (t0) REVERT: K 158 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8119 (ppp) REVERT: K 173 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: K 494 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8267 (tm-30) REVERT: L 23 ASP cc_start: 0.8098 (t70) cc_final: 0.7854 (t0) REVERT: L 112 MET cc_start: 0.8997 (tmm) cc_final: 0.8783 (tmm) REVERT: L 158 MET cc_start: 0.7924 (ptt) cc_final: 0.7448 (ptt) REVERT: L 219 LEU cc_start: 0.8473 (tp) cc_final: 0.8248 (tt) REVERT: L 236 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: L 246 LYS cc_start: 0.8400 (ttmm) cc_final: 0.8137 (mttm) REVERT: L 325 GLU cc_start: 0.8151 (pm20) cc_final: 0.7838 (pt0) REVERT: L 406 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7926 (pttm) REVERT: L 440 ASP cc_start: 0.7846 (t70) cc_final: 0.7604 (p0) REVERT: L 455 MET cc_start: 0.8594 (mpp) cc_final: 0.8258 (mpp) REVERT: L 465 MET cc_start: 0.8725 (tpp) cc_final: 0.8016 (tpp) REVERT: L 489 GLN cc_start: 0.8183 (mt0) cc_final: 0.7661 (tp40) REVERT: L 494 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8164 (tm-30) outliers start: 141 outliers final: 111 residues processed: 1043 average time/residue: 0.4459 time to fit residues: 801.9270 Evaluate side-chains 1034 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 905 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 445 CYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 357 MET Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 391 ILE Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 145 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 173 PHE Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 240 SER Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 468 LEU Chi-restraints excluded: chain J residue 481 ILE Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 158 MET Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 390 SER Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 440 ASP Chi-restraints excluded: chain K residue 442 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 357 MET Chi-restraints excluded: chain L residue 406 LYS Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 435 ARG Chi-restraints excluded: chain L residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 0.9990 chunk 527 optimal weight: 0.0980 chunk 151 optimal weight: 1.9990 chunk 456 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 495 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 509 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.131590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107000 restraints weight = 87629.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110093 restraints weight = 41498.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112064 restraints weight = 25558.710| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 49440 Z= 0.215 Angle : 0.774 13.309 66912 Z= 0.377 Chirality : 0.045 0.231 7572 Planarity : 0.005 0.056 8832 Dihedral : 5.371 32.364 6876 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.09 % Favored : 91.59 % Rotamer: Outliers : 2.92 % Allowed : 22.95 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.11), residues: 6252 helix: 1.08 (0.10), residues: 3048 sheet: -0.71 (0.21), residues: 600 loop : -2.07 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 83 HIS 0.002 0.001 HIS E 216 PHE 0.036 0.002 PHE K 78 TYR 0.024 0.001 TYR J 251 ARG 0.008 0.000 ARG C 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13166.12 seconds wall clock time: 229 minutes 26.99 seconds (13766.99 seconds total)