Starting phenix.real_space_refine on Sun Feb 25 04:03:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bou_30134/02_2024/7bou_30134.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bou_30134/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bou_30134/02_2024/7bou_30134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bou_30134/02_2024/7bou_30134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bou_30134/02_2024/7bou_30134.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bou_30134/02_2024/7bou_30134.pdb" } 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 Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48708 Number of models: 1 Model: "" Number of chains: 12 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 Chain: "B" 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Chain: "F" 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 Chain: "G" 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 Chain: "H" 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 Chain: "I" 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 Chain: "J" 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 Chain: "K" 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 Chain: "L" 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 Time building chain proxies: 24.82, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 18.72 Conformation dependent library (CDL) restraints added in 9.2 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: 4.83 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: 18.20 Time building geometry restraints manager: 19.78 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: 98.06 - 105.26: 1237 105.26 - 112.46: 23802 112.46 - 119.66: 18223 119.66 - 126.87: 23160 126.87 - 134.07: 490 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 2.440 nonbonded pdb=" OG1 THR L 181 " pdb=" OG1 THR L 215 " model vdw 2.311 2.440 nonbonded pdb=" OG1 THR B 181 " pdb=" OG1 THR B 215 " model vdw 2.311 2.440 nonbonded pdb=" OG1 THR K 181 " pdb=" OG1 THR K 215 " model vdw 2.312 2.440 nonbonded pdb=" OG1 THR G 181 " pdb=" OG1 THR G 215 " model vdw 2.312 2.440 ... (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 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 11.410 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 120.900 Find NCS groups from input model: 3.550 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.860 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 48 poor density : 1814 time to evaluate : 6.153 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: 0.6070 time to fit residues: 1825.5656 Evaluate side-chains 1089 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1087 time to evaluate : 5.174 ------------------------------------------------------------------------------- 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: 0.7980 chunk 472 optimal weight: 0.9980 chunk 262 optimal weight: 0.6980 chunk 161 optimal weight: 0.7980 chunk 319 optimal weight: 0.0980 chunk 252 optimal weight: 5.9990 chunk 489 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 297 optimal weight: 0.5980 chunk 364 optimal weight: 0.0980 chunk 566 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 283 GLN A 472 ASN A 503 ASN B 119 ASN B 184 GLN B 283 GLN B 472 ASN B 503 ASN C 33 ASN C 68 ASN C 281 ASN C 315 GLN C 397 GLN C 503 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN D 281 ASN D 283 GLN D 472 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 184 GLN E 283 GLN E 472 ASN E 503 ASN F 68 ASN F 119 ASN F 184 GLN F 283 GLN ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN G 283 GLN 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 283 GLN H 472 ASN H 487 GLN H 503 ASN I 283 GLN I 397 GLN I 409 GLN I 472 ASN ** I 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 GLN J 397 GLN J 472 ASN J 503 ASN K 33 ASN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 281 ASN K 283 GLN K 315 GLN K 397 GLN K 472 ASN L 68 ASN L 184 GLN L 283 GLN L 472 ASN L 487 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 49440 Z= 0.205 Angle : 0.810 12.373 66912 Z= 0.404 Chirality : 0.047 0.438 7572 Planarity : 0.006 0.064 8832 Dihedral : 7.188 38.767 6880 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.34 % Favored : 91.92 % Rotamer: Outliers : 3.21 % Allowed : 14.54 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.84 (0.09), residues: 6252 helix: -2.33 (0.07), residues: 3036 sheet: -2.04 (0.18), residues: 696 loop : -2.81 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 449 HIS 0.002 0.001 HIS K 216 PHE 0.018 0.002 PHE L 78 TYR 0.020 0.002 TYR D 389 ARG 0.007 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 1419 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1252 time to evaluate : 5.362 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: 0.8984 (tt) cc_final: 0.8746 (mm) REVERT: A 80 MET cc_start: 0.7514 (mmm) cc_final: 0.7070 (mmm) REVERT: A 84 MET cc_start: 0.7760 (pmm) cc_final: 0.7317 (pmm) REVERT: A 94 LYS cc_start: 0.8690 (mmtt) cc_final: 0.7645 (tptt) REVERT: A 105 LYS cc_start: 0.8662 (tptt) cc_final: 0.7931 (ttpp) REVERT: A 120 TYR cc_start: 0.9235 (t80) cc_final: 0.9006 (t80) REVERT: A 122 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 268 TYR cc_start: 0.8659 (t80) cc_final: 0.8413 (t80) REVERT: A 279 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9099 (tp) REVERT: A 390 SER cc_start: 0.8532 (t) cc_final: 0.8301 (p) REVERT: A 461 ILE cc_start: 0.8646 (mt) cc_final: 0.8344 (mt) REVERT: A 472 ASN cc_start: 0.9053 (t0) cc_final: 0.8536 (t0) REVERT: A 477 ASP cc_start: 0.7937 (p0) cc_final: 0.7451 (p0) REVERT: A 491 LYS cc_start: 0.9253 (ttmt) cc_final: 0.9031 (ttmt) REVERT: A 494 GLN cc_start: 0.8685 (mm110) cc_final: 0.7855 (tm-30) REVERT: B 23 ASP cc_start: 0.7992 (t70) cc_final: 0.7642 (t0) REVERT: B 118 MET cc_start: 0.8822 (mmm) cc_final: 0.8600 (mmm) REVERT: B 235 MET cc_start: 0.6851 (ttm) cc_final: 0.6270 (ttm) REVERT: B 236 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6073 (mp0) REVERT: B 240 SER cc_start: 0.7972 (m) cc_final: 0.7733 (p) REVERT: B 252 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8947 (pt) REVERT: B 271 GLU cc_start: 0.7148 (tp30) cc_final: 0.6909 (tp30) REVERT: B 489 GLN cc_start: 0.7959 (mt0) cc_final: 0.7491 (tp40) REVERT: B 501 MET cc_start: 0.8308 (mtt) cc_final: 0.7977 (mtp) REVERT: B 503 ASN cc_start: 0.9132 (t0) cc_final: 0.8837 (m-40) REVERT: C 94 LYS cc_start: 0.8782 (mmtt) cc_final: 0.7717 (tptt) REVERT: C 105 LYS cc_start: 0.8720 (tptt) cc_final: 0.8089 (ttpp) REVERT: C 120 TYR cc_start: 0.8962 (t80) cc_final: 0.8732 (t80) REVERT: C 156 ASN cc_start: 0.8434 (t0) cc_final: 0.8121 (t0) REVERT: C 164 SER cc_start: 0.8942 (m) cc_final: 0.8578 (t) REVERT: C 179 MET cc_start: 0.8590 (mtm) cc_final: 0.8294 (mtp) REVERT: C 182 ARG cc_start: 0.8169 (ttt90) cc_final: 0.7838 (ttt90) REVERT: C 501 MET cc_start: 0.7783 (mtt) cc_final: 0.7314 (mtp) REVERT: D 103 LEU cc_start: 0.9024 (tp) cc_final: 0.8778 (tp) REVERT: D 158 MET cc_start: 0.7655 (ptt) cc_final: 0.7433 (ptt) REVERT: D 227 LEU cc_start: 0.8783 (mt) cc_final: 0.8513 (mt) REVERT: D 236 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6272 (mp0) REVERT: D 439 LEU cc_start: 0.9098 (tm) cc_final: 0.8835 (tp) REVERT: D 494 GLN cc_start: 0.8405 (mm110) cc_final: 0.8202 (tm-30) REVERT: E 80 MET cc_start: 0.7786 (mmm) cc_final: 0.7298 (mmm) REVERT: E 84 MET cc_start: 0.8398 (pmm) cc_final: 0.8184 (pmm) REVERT: E 105 LYS cc_start: 0.8780 (tptt) cc_final: 0.7994 (ttpp) REVERT: E 164 SER cc_start: 0.9347 (m) cc_final: 0.8997 (t) REVERT: E 252 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.6977 (tp) REVERT: E 279 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9007 (tp) REVERT: E 284 GLU cc_start: 0.7587 (tt0) cc_final: 0.7358 (pt0) REVERT: E 406 LYS cc_start: 0.8560 (ttpt) cc_final: 0.8275 (ttpt) REVERT: E 494 GLN cc_start: 0.8539 (mm110) cc_final: 0.8176 (tm-30) REVERT: E 501 MET cc_start: 0.8605 (mtp) cc_final: 0.8133 (mtm) REVERT: E 523 MET cc_start: 0.8657 (tmm) cc_final: 0.7900 (tmm) REVERT: F 11 ASP cc_start: 0.7110 (p0) cc_final: 0.6753 (p0) REVERT: F 465 MET cc_start: 0.8276 (tpp) cc_final: 0.7709 (tpp) REVERT: F 489 GLN cc_start: 0.7611 (mt0) cc_final: 0.7322 (tp40) REVERT: F 501 MET cc_start: 0.8675 (mtt) cc_final: 0.8437 (mtp) REVERT: G 84 MET cc_start: 0.8160 (pmm) cc_final: 0.7900 (pmm) REVERT: G 105 LYS cc_start: 0.8629 (tptt) cc_final: 0.7770 (ttpp) REVERT: G 184 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: G 199 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8225 (tm-30) REVERT: G 289 MET cc_start: 0.8337 (mtt) cc_final: 0.8017 (mtp) REVERT: G 423 GLU cc_start: 0.8539 (pm20) cc_final: 0.8178 (pm20) REVERT: G 461 ILE cc_start: 0.8795 (mt) cc_final: 0.8523 (mt) REVERT: G 465 MET cc_start: 0.8411 (tpp) cc_final: 0.8121 (tpp) REVERT: G 472 ASN cc_start: 0.8869 (t0) cc_final: 0.8309 (t0) REVERT: G 489 GLN cc_start: 0.9258 (mp10) cc_final: 0.9024 (mp10) REVERT: G 494 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8057 (tm-30) REVERT: G 508 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8721 (pt) REVERT: H 240 SER cc_start: 0.7862 (m) cc_final: 0.7627 (p) REVERT: H 291 MET cc_start: 0.8316 (mmm) cc_final: 0.8013 (mmm) REVERT: H 489 GLN cc_start: 0.7876 (mt0) cc_final: 0.7173 (tp40) REVERT: H 499 MET cc_start: 0.8777 (tpp) cc_final: 0.8338 (tpp) REVERT: H 501 MET cc_start: 0.8564 (mtt) cc_final: 0.8348 (mtp) REVERT: I 94 LYS cc_start: 0.8718 (mmtt) cc_final: 0.7723 (tptt) REVERT: I 105 LYS cc_start: 0.8753 (tptt) cc_final: 0.7966 (ttpp) REVERT: I 120 TYR cc_start: 0.9044 (t80) cc_final: 0.8674 (t80) REVERT: I 240 SER cc_start: 0.7998 (m) cc_final: 0.7507 (p) REVERT: I 268 TYR cc_start: 0.8430 (t80) cc_final: 0.7843 (t80) REVERT: I 271 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6744 (mt-10) REVERT: I 465 MET cc_start: 0.8797 (tpp) cc_final: 0.8525 (tpp) REVERT: I 494 GLN cc_start: 0.8605 (mm110) cc_final: 0.8185 (tm-30) REVERT: J 23 ASP cc_start: 0.8091 (t70) cc_final: 0.7647 (t70) REVERT: J 118 MET cc_start: 0.8824 (mmm) cc_final: 0.8511 (mmm) REVERT: J 230 GLU cc_start: 0.7982 (pm20) cc_final: 0.7753 (pm20) REVERT: J 252 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8790 (pp) REVERT: J 383 ASP cc_start: 0.7312 (m-30) cc_final: 0.7059 (m-30) REVERT: J 418 PRO cc_start: 0.7875 (Cg_endo) cc_final: 0.7668 (Cg_exo) REVERT: J 465 MET cc_start: 0.8385 (tpp) cc_final: 0.7935 (tpp) REVERT: J 489 GLN cc_start: 0.7465 (mt0) cc_final: 0.7060 (tp40) REVERT: K 18 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7967 (mt-10) REVERT: K 22 ASN cc_start: 0.7747 (p0) cc_final: 0.7522 (m-40) REVERT: K 92 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8101 (mt-10) REVERT: K 105 LYS cc_start: 0.8766 (tptt) cc_final: 0.8317 (mtpt) REVERT: K 235 MET cc_start: 0.5812 (ttm) cc_final: 0.5485 (ttm) REVERT: K 400 LEU cc_start: 0.9387 (tt) cc_final: 0.9113 (tt) REVERT: K 404 LEU cc_start: 0.9473 (mt) cc_final: 0.9196 (mt) REVERT: K 477 ASP cc_start: 0.7938 (p0) cc_final: 0.7692 (p0) REVERT: K 494 GLN cc_start: 0.8548 (mm-40) cc_final: 0.7871 (tm-30) REVERT: L 11 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8027 (p0) REVERT: L 23 ASP cc_start: 0.7990 (t70) cc_final: 0.7789 (t0) REVERT: L 91 TYR cc_start: 0.8123 (t80) cc_final: 0.7711 (t80) REVERT: L 118 MET cc_start: 0.8990 (mmm) cc_final: 0.8606 (mmm) REVERT: L 127 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8108 (mmt-90) REVERT: L 211 ILE cc_start: 0.9125 (mp) cc_final: 0.8885 (mm) REVERT: L 228 ARG cc_start: 0.8250 (tmt170) cc_final: 0.7944 (tmm160) REVERT: L 252 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8782 (pp) REVERT: L 315 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8308 (tp40) REVERT: L 455 MET cc_start: 0.8628 (mpp) cc_final: 0.7718 (mtt) REVERT: L 465 MET cc_start: 0.8405 (tpp) cc_final: 0.8065 (tpp) REVERT: L 489 GLN cc_start: 0.7399 (mt0) cc_final: 0.7061 (tp40) REVERT: L 501 MET cc_start: 0.8531 (mtt) cc_final: 0.8298 (mtp) outliers start: 167 outliers final: 57 residues processed: 1360 average time/residue: 0.5756 time to fit residues: 1316.2962 Evaluate side-chains 1073 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1004 time to evaluate : 5.281 ------------------------------------------------------------------------------- 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 68 ASN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain D residue 15 SER 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 E residue 101 ASP 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 293 SER Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 512 MET Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 398 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 460 ASP 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 I residue 417 LEU Chi-restraints excluded: chain J residue 252 ILE Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 512 MET Chi-restraints excluded: chain K residue 173 PHE 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 11 ASP Chi-restraints excluded: chain L residue 208 ASP Chi-restraints excluded: chain L residue 230 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 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: 8.9990 chunk 471 optimal weight: 0.0070 chunk 385 optimal weight: 3.9990 chunk 156 optimal weight: 0.0020 chunk 567 optimal weight: 0.9990 chunk 613 optimal weight: 0.9990 chunk 505 optimal weight: 0.9980 chunk 562 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 455 optimal weight: 3.9990 overall best weight: 0.5608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 498 GLN A 503 ASN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN B 503 ASN C 407 GLN C 472 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 503 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN ** 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 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 503 ASN I 498 GLN J 487 GLN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 281 ASN ** 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 49440 Z= 0.200 Angle : 0.744 11.183 66912 Z= 0.366 Chirality : 0.045 0.407 7572 Planarity : 0.005 0.060 8832 Dihedral : 6.355 37.206 6878 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.90 % Favored : 91.67 % Rotamer: Outliers : 4.11 % Allowed : 16.07 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.32 (0.10), residues: 6252 helix: -0.67 (0.09), residues: 2892 sheet: -1.73 (0.19), residues: 588 loop : -2.43 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 83 HIS 0.003 0.002 HIS K 216 PHE 0.021 0.002 PHE E 78 TYR 0.023 0.001 TYR G 389 ARG 0.009 0.001 ARG G 182 *********************** 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 1349 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1135 time to evaluate : 5.521 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 23 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8005 (t0) REVERT: A 84 MET cc_start: 0.7883 (pmm) cc_final: 0.7532 (pmm) REVERT: A 94 LYS cc_start: 0.8656 (mmtt) cc_final: 0.7742 (tptt) REVERT: A 105 LYS cc_start: 0.8734 (tptt) cc_final: 0.7899 (ttpp) REVERT: A 120 TYR cc_start: 0.9267 (t80) cc_final: 0.9035 (t80) REVERT: A 279 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9062 (tp) REVERT: A 390 SER cc_start: 0.8687 (t) cc_final: 0.8471 (p) REVERT: A 423 GLU cc_start: 0.8437 (pm20) cc_final: 0.8083 (pm20) REVERT: A 477 ASP cc_start: 0.8040 (p0) cc_final: 0.7704 (p0) REVERT: A 494 GLN cc_start: 0.8662 (mm110) cc_final: 0.8187 (tm-30) REVERT: B 23 ASP cc_start: 0.8028 (t70) cc_final: 0.7684 (t0) REVERT: B 236 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6008 (mp0) REVERT: B 246 LYS cc_start: 0.8340 (mttm) cc_final: 0.8045 (mttm) REVERT: B 406 LYS cc_start: 0.8591 (tttt) cc_final: 0.8380 (ttpp) REVERT: B 477 ASP cc_start: 0.5938 (p0) cc_final: 0.5452 (p0) REVERT: B 489 GLN cc_start: 0.7967 (mt0) cc_final: 0.7596 (tp40) REVERT: B 501 MET cc_start: 0.8489 (mtt) cc_final: 0.8184 (mtp) REVERT: B 503 ASN cc_start: 0.9029 (t0) cc_final: 0.8784 (m-40) REVERT: C 94 LYS cc_start: 0.8747 (mmtt) cc_final: 0.7805 (tptt) REVERT: C 105 LYS cc_start: 0.8664 (tptt) cc_final: 0.7996 (ttpp) REVERT: C 120 TYR cc_start: 0.8913 (t80) cc_final: 0.8377 (t80) REVERT: C 156 ASN cc_start: 0.8756 (t0) cc_final: 0.8377 (t0) REVERT: C 164 SER cc_start: 0.9182 (m) cc_final: 0.8794 (t) REVERT: C 182 ARG cc_start: 0.8258 (ttt90) cc_final: 0.7954 (ttt90) REVERT: C 262 GLU cc_start: 0.7579 (pt0) cc_final: 0.7370 (pt0) REVERT: C 357 MET cc_start: 0.7889 (mmm) cc_final: 0.7471 (mmm) REVERT: C 469 ARG cc_start: 0.8963 (mmt90) cc_final: 0.8655 (mmm-85) REVERT: C 494 GLN cc_start: 0.8700 (mm-40) cc_final: 0.7983 (tm-30) REVERT: C 501 MET cc_start: 0.7854 (mtt) cc_final: 0.7332 (mtp) REVERT: C 517 THR cc_start: 0.6164 (OUTLIER) cc_final: 0.5323 (p) REVERT: D 103 LEU cc_start: 0.8907 (tp) cc_final: 0.8657 (tp) REVERT: D 118 MET cc_start: 0.8804 (mmm) cc_final: 0.8469 (mmm) REVERT: D 158 MET cc_start: 0.7636 (ptt) cc_final: 0.7432 (ptt) REVERT: D 173 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: D 185 ILE cc_start: 0.8664 (mt) cc_final: 0.8437 (mt) REVERT: D 227 LEU cc_start: 0.8799 (mt) cc_final: 0.8565 (mt) REVERT: D 236 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: D 465 MET cc_start: 0.8721 (tpt) cc_final: 0.7985 (tpp) REVERT: D 498 GLN cc_start: 0.8923 (tp40) cc_final: 0.8561 (tp-100) REVERT: E 80 MET cc_start: 0.7690 (mmm) cc_final: 0.7159 (mmm) REVERT: E 94 LYS cc_start: 0.8635 (mmtt) cc_final: 0.7827 (tptt) REVERT: E 105 LYS cc_start: 0.8815 (tptt) cc_final: 0.8051 (ttpp) REVERT: E 252 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7194 (tp) REVERT: E 279 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9236 (tp) REVERT: E 494 GLN cc_start: 0.8628 (mm110) cc_final: 0.8330 (tm-30) REVERT: E 523 MET cc_start: 0.8683 (tmm) cc_final: 0.7941 (tmm) REVERT: F 236 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: F 465 MET cc_start: 0.8462 (tpp) cc_final: 0.7845 (tpp) REVERT: F 489 GLN cc_start: 0.7726 (mt0) cc_final: 0.7357 (tp40) REVERT: F 499 MET cc_start: 0.8104 (mtp) cc_final: 0.7888 (mtp) REVERT: G 18 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7974 (mt-10) REVERT: G 105 LYS cc_start: 0.8499 (tptt) cc_final: 0.7673 (ttpp) REVERT: G 118 MET cc_start: 0.8600 (mmm) cc_final: 0.8369 (mmm) REVERT: G 164 SER cc_start: 0.9126 (m) cc_final: 0.8851 (t) REVERT: G 397 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: G 461 ILE cc_start: 0.8947 (mt) cc_final: 0.8676 (mt) REVERT: G 489 GLN cc_start: 0.9266 (mp10) cc_final: 0.8976 (mp10) REVERT: G 494 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8141 (tm-30) REVERT: H 240 SER cc_start: 0.7702 (m) cc_final: 0.7412 (p) REVERT: H 489 GLN cc_start: 0.7889 (mt0) cc_final: 0.7252 (tp40) REVERT: H 499 MET cc_start: 0.8795 (tpp) cc_final: 0.8558 (tpp) REVERT: H 512 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8055 (ptm) REVERT: I 80 MET cc_start: 0.7177 (mmm) cc_final: 0.6970 (mmt) REVERT: I 94 LYS cc_start: 0.8668 (mmtt) cc_final: 0.7704 (tptt) REVERT: I 105 LYS cc_start: 0.8623 (tptt) cc_final: 0.7934 (ttpp) REVERT: I 118 MET cc_start: 0.8865 (mmm) cc_final: 0.8438 (mmm) REVERT: I 120 TYR cc_start: 0.9133 (t80) cc_final: 0.8866 (t80) REVERT: I 143 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8391 (t) REVERT: I 199 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8340 (tm-30) REVERT: I 240 SER cc_start: 0.8079 (m) cc_final: 0.7682 (p) REVERT: I 241 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6699 (t0) REVERT: I 268 TYR cc_start: 0.8485 (t80) cc_final: 0.8137 (t80) REVERT: I 404 LEU cc_start: 0.9257 (mt) cc_final: 0.8845 (mt) REVERT: I 465 MET cc_start: 0.8750 (tpp) cc_final: 0.8509 (tpp) REVERT: I 494 GLN cc_start: 0.8609 (mm110) cc_final: 0.8216 (tm-30) REVERT: I 501 MET cc_start: 0.8498 (mtp) cc_final: 0.8289 (mtm) REVERT: J 23 ASP cc_start: 0.8129 (t70) cc_final: 0.7664 (t70) REVERT: J 91 TYR cc_start: 0.8090 (t80) cc_final: 0.7390 (t80) REVERT: J 118 MET cc_start: 0.8825 (mmm) cc_final: 0.8536 (mmm) REVERT: J 179 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7213 (mpp) REVERT: J 236 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: J 240 SER cc_start: 0.8463 (m) cc_final: 0.8063 (p) REVERT: J 252 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8623 (pp) REVERT: J 271 GLU cc_start: 0.6855 (tp30) cc_final: 0.6638 (tp30) REVERT: J 465 MET cc_start: 0.8459 (tpp) cc_final: 0.7906 (tpp) REVERT: J 489 GLN cc_start: 0.7623 (mt0) cc_final: 0.7173 (tp40) REVERT: K 18 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8030 (mt-10) REVERT: K 75 LEU cc_start: 0.8792 (tp) cc_final: 0.8518 (mt) REVERT: K 80 MET cc_start: 0.7474 (mmm) cc_final: 0.7188 (mmm) REVERT: K 94 LYS cc_start: 0.8764 (mmtt) cc_final: 0.7955 (tptt) REVERT: K 105 LYS cc_start: 0.8898 (tptt) cc_final: 0.8370 (mtpt) REVERT: K 118 MET cc_start: 0.8838 (mmm) cc_final: 0.8327 (mmm) REVERT: K 400 LEU cc_start: 0.9340 (tt) cc_final: 0.9078 (tt) REVERT: K 477 ASP cc_start: 0.7900 (p0) cc_final: 0.7286 (p0) REVERT: K 494 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8000 (tm-30) REVERT: K 501 MET cc_start: 0.8607 (mtp) cc_final: 0.8275 (mtm) REVERT: L 23 ASP cc_start: 0.8063 (t70) cc_final: 0.7748 (t0) REVERT: L 52 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9076 (p) REVERT: L 91 TYR cc_start: 0.8285 (t80) cc_final: 0.7800 (t80) REVERT: L 230 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: L 236 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: L 252 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8714 (pp) REVERT: L 455 MET cc_start: 0.8721 (mpp) cc_final: 0.7806 (mtt) REVERT: L 465 MET cc_start: 0.8628 (tpp) cc_final: 0.8021 (tpp) REVERT: L 489 GLN cc_start: 0.7303 (mt0) cc_final: 0.7016 (tp40) outliers start: 214 outliers final: 105 residues processed: 1283 average time/residue: 0.5458 time to fit residues: 1189.0586 Evaluate side-chains 1108 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 983 time to evaluate : 5.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 143 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 318 ASP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 333 GLU 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 68 ASN 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 86 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 330 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 517 THR Chi-restraints excluded: chain D residue 167 VAL 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 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 11 ASP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 208 ASP 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 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 75 LEU Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 293 SER 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 391 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 ILE 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 330 LEU Chi-restraints excluded: chain G residue 332 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 417 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 167 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 296 VAL Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 503 ASN Chi-restraints excluded: chain H residue 512 MET Chi-restraints excluded: chain H residue 532 LEU Chi-restraints excluded: chain I residue 143 VAL 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 296 VAL Chi-restraints excluded: chain J residue 331 GLN Chi-restraints excluded: chain J residue 340 VAL 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 J residue 536 ILE Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 167 VAL 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 391 ILE Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 208 ASP 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 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: 0.9980 chunk 426 optimal weight: 0.6980 chunk 294 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 381 optimal weight: 2.9990 chunk 569 optimal weight: 5.9990 chunk 603 optimal weight: 0.2980 chunk 297 optimal weight: 5.9990 chunk 539 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 472 ASN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 515 GLN E 33 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN G 472 ASN G 494 GLN G 498 GLN G 503 ASN ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 498 GLN ** K 68 ASN ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4660 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= 0.210 Angle : 0.730 12.950 66912 Z= 0.356 Chirality : 0.044 0.310 7572 Planarity : 0.005 0.058 8832 Dihedral : 5.988 35.450 6878 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.19 % Favored : 91.44 % Rotamer: Outliers : 4.65 % Allowed : 17.32 % Favored : 78.03 % 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: -1.61 (0.10), residues: 6252 helix: 0.04 (0.09), residues: 2964 sheet: -1.37 (0.19), residues: 588 loop : -2.28 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 449 HIS 0.003 0.001 HIS G 216 PHE 0.018 0.002 PHE E 78 TYR 0.023 0.001 TYR G 389 ARG 0.007 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 1306 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1064 time to evaluate : 5.349 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: A 84 MET cc_start: 0.8075 (pmm) cc_final: 0.7819 (pmm) REVERT: A 94 LYS cc_start: 0.8931 (mmtt) cc_final: 0.7717 (tptt) REVERT: A 105 LYS cc_start: 0.8743 (tptt) cc_final: 0.7880 (ttpp) REVERT: A 173 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: A 351 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8288 (ptt180) REVERT: A 423 GLU cc_start: 0.8411 (pm20) cc_final: 0.8202 (pm20) REVERT: A 494 GLN cc_start: 0.8696 (mm110) cc_final: 0.8126 (tm-30) REVERT: A 501 MET cc_start: 0.8578 (mtp) cc_final: 0.8085 (mtm) REVERT: A 523 MET cc_start: 0.8169 (ttp) cc_final: 0.7291 (tmm) REVERT: B 23 ASP cc_start: 0.8050 (t70) cc_final: 0.7674 (t0) REVERT: B 236 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6038 (mp0) REVERT: B 357 MET cc_start: 0.7866 (mmp) cc_final: 0.7599 (mmp) REVERT: B 460 ASP cc_start: 0.8011 (t0) cc_final: 0.7733 (t0) REVERT: B 477 ASP cc_start: 0.5937 (p0) cc_final: 0.5613 (p0) REVERT: B 489 GLN cc_start: 0.8117 (mt0) cc_final: 0.7860 (tp40) REVERT: B 494 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7918 (tm-30) REVERT: C 94 LYS cc_start: 0.8764 (mmtt) cc_final: 0.7799 (tptt) REVERT: C 95 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8038 (mm-40) REVERT: C 105 LYS cc_start: 0.8693 (tptt) cc_final: 0.7992 (ttpp) REVERT: C 118 MET cc_start: 0.8652 (mmm) cc_final: 0.8102 (mmm) REVERT: C 120 TYR cc_start: 0.8974 (t80) cc_final: 0.8557 (t80) REVERT: C 156 ASN cc_start: 0.8856 (t0) cc_final: 0.8419 (t0) REVERT: C 194 ILE cc_start: 0.9445 (mt) cc_final: 0.9186 (mt) REVERT: C 321 THR cc_start: 0.8828 (m) cc_final: 0.8562 (p) REVERT: C 494 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8083 (tm-30) REVERT: C 501 MET cc_start: 0.8142 (mtt) cc_final: 0.7920 (mtp) REVERT: D 11 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7661 (p0) REVERT: D 118 MET cc_start: 0.8794 (mmm) cc_final: 0.8330 (mmm) REVERT: D 158 MET cc_start: 0.7777 (ptt) cc_final: 0.7532 (ptt) REVERT: D 173 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7069 (m-80) REVERT: D 227 LEU cc_start: 0.8818 (mt) cc_final: 0.8455 (mt) REVERT: D 235 MET cc_start: 0.7070 (ttm) cc_final: 0.6466 (ttm) REVERT: D 236 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: D 291 MET cc_start: 0.8751 (mmt) cc_final: 0.8452 (mmm) REVERT: D 385 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8309 (tt) REVERT: D 465 MET cc_start: 0.8742 (tpt) cc_final: 0.8022 (tpp) REVERT: D 498 GLN cc_start: 0.8926 (tp40) cc_final: 0.8484 (tp-100) REVERT: E 92 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7722 (mt-10) REVERT: E 94 LYS cc_start: 0.8760 (mmtt) cc_final: 0.7809 (tptt) REVERT: E 105 LYS cc_start: 0.8839 (tptt) cc_final: 0.8124 (ttpp) REVERT: E 158 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8278 (ppp) REVERT: E 252 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7276 (tp) REVERT: E 279 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9232 (tp) REVERT: E 306 THR cc_start: 0.9012 (m) cc_final: 0.8676 (p) REVERT: E 494 GLN cc_start: 0.8622 (mm110) cc_final: 0.8278 (tm-30) REVERT: E 501 MET cc_start: 0.8591 (mtp) cc_final: 0.8222 (mtm) REVERT: E 523 MET cc_start: 0.8665 (tmm) cc_final: 0.7865 (tmm) REVERT: F 118 MET cc_start: 0.8995 (mmm) cc_final: 0.8748 (mmm) REVERT: F 158 MET cc_start: 0.7924 (ptt) cc_final: 0.7625 (ptt) REVERT: F 236 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: F 271 GLU cc_start: 0.6869 (tp30) cc_final: 0.6661 (tp30) REVERT: F 465 MET cc_start: 0.8517 (tpp) cc_final: 0.8142 (tpp) REVERT: F 489 GLN cc_start: 0.7945 (mt0) cc_final: 0.7405 (tp40) REVERT: F 494 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8249 (tm-30) REVERT: G 94 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8098 (tptt) REVERT: G 105 LYS cc_start: 0.8652 (tptt) cc_final: 0.7762 (ttpp) REVERT: G 173 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6578 (m-80) REVERT: G 400 LEU cc_start: 0.9221 (tp) cc_final: 0.9016 (tp) REVERT: G 423 GLU cc_start: 0.8585 (pm20) cc_final: 0.8349 (pm20) REVERT: G 461 ILE cc_start: 0.8964 (mt) cc_final: 0.8618 (mt) REVERT: G 465 MET cc_start: 0.8426 (tpp) cc_final: 0.8172 (tpp) REVERT: G 472 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7940 (m-40) REVERT: G 489 GLN cc_start: 0.9346 (mp10) cc_final: 0.9000 (mp10) REVERT: G 494 GLN cc_start: 0.8700 (mm110) cc_final: 0.8189 (tm-30) REVERT: G 498 GLN cc_start: 0.9201 (tp40) cc_final: 0.8882 (tp-100) REVERT: G 501 MET cc_start: 0.8583 (mtp) cc_final: 0.8070 (mtm) REVERT: H 118 MET cc_start: 0.8873 (mmm) cc_final: 0.8399 (mmm) REVERT: H 195 ARG cc_start: 0.8191 (mtm110) cc_final: 0.7633 (mtp85) REVERT: H 240 SER cc_start: 0.7960 (m) cc_final: 0.7485 (p) REVERT: H 325 GLU cc_start: 0.7995 (pm20) cc_final: 0.7662 (pm20) REVERT: H 326 ASP cc_start: 0.8110 (m-30) cc_final: 0.7895 (m-30) REVERT: H 477 ASP cc_start: 0.5353 (p0) cc_final: 0.5091 (p0) REVERT: H 482 LEU cc_start: 0.8877 (pt) cc_final: 0.8617 (pp) REVERT: H 489 GLN cc_start: 0.7955 (mt0) cc_final: 0.7378 (tp40) REVERT: H 492 MET cc_start: 0.8303 (ttm) cc_final: 0.8007 (ttm) REVERT: H 512 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8175 (ptm) REVERT: I 18 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8130 (mt-10) REVERT: I 80 MET cc_start: 0.7295 (mmm) cc_final: 0.7046 (mmt) REVERT: I 94 LYS cc_start: 0.8610 (mmtt) cc_final: 0.7745 (tptt) REVERT: I 95 GLN cc_start: 0.8626 (mm110) cc_final: 0.8414 (mm-40) REVERT: I 105 LYS cc_start: 0.8675 (tptt) cc_final: 0.7959 (ttpp) REVERT: I 118 MET cc_start: 0.8836 (mmm) cc_final: 0.8549 (mmm) REVERT: I 120 TYR cc_start: 0.9165 (t80) cc_final: 0.8928 (t80) REVERT: I 240 SER cc_start: 0.8030 (m) cc_final: 0.7543 (p) REVERT: I 241 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6754 (t0) REVERT: I 289 MET cc_start: 0.8524 (mtt) cc_final: 0.8315 (mtt) REVERT: I 465 MET cc_start: 0.8788 (tpp) cc_final: 0.8558 (tpp) REVERT: I 494 GLN cc_start: 0.8635 (mm110) cc_final: 0.8272 (tm-30) REVERT: J 23 ASP cc_start: 0.8099 (t70) cc_final: 0.7610 (t70) REVERT: J 91 TYR cc_start: 0.8321 (t80) cc_final: 0.7510 (t80) REVERT: J 118 MET cc_start: 0.8880 (mmm) cc_final: 0.8607 (mmm) REVERT: J 158 MET cc_start: 0.8210 (ptt) cc_final: 0.7852 (ptt) REVERT: J 179 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7471 (mpp) REVERT: J 236 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: J 240 SER cc_start: 0.8370 (m) cc_final: 0.8134 (p) REVERT: J 262 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6823 (mt-10) REVERT: J 271 GLU cc_start: 0.6929 (tp30) cc_final: 0.6704 (tp30) REVERT: J 465 MET cc_start: 0.8418 (tpp) cc_final: 0.7797 (tpp) REVERT: J 489 GLN cc_start: 0.7751 (mt0) cc_final: 0.7276 (tp40) REVERT: K 18 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8085 (mt-10) REVERT: K 80 MET cc_start: 0.7446 (mmm) cc_final: 0.7208 (mmm) REVERT: K 94 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8004 (tptt) REVERT: K 105 LYS cc_start: 0.8890 (tptt) cc_final: 0.8303 (mtpt) REVERT: K 118 MET cc_start: 0.8735 (mmm) cc_final: 0.8297 (mmm) REVERT: K 241 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7233 (t0) REVERT: K 494 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8067 (tm-30) REVERT: K 499 MET cc_start: 0.8567 (tmm) cc_final: 0.7866 (tmm) REVERT: L 23 ASP cc_start: 0.8174 (t70) cc_final: 0.7830 (t0) REVERT: L 74 MET cc_start: 0.8605 (mmm) cc_final: 0.8239 (tpt) REVERT: L 179 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7504 (mpp) REVERT: L 236 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: L 252 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8755 (pp) REVERT: L 455 MET cc_start: 0.8724 (mpp) cc_final: 0.7898 (mtt) REVERT: L 465 MET cc_start: 0.8666 (tpp) cc_final: 0.8105 (tpp) REVERT: L 477 ASP cc_start: 0.5311 (p0) cc_final: 0.5080 (p0) REVERT: L 489 GLN cc_start: 0.7624 (mt0) cc_final: 0.7264 (tp40) REVERT: L 492 MET cc_start: 0.8154 (mmp) cc_final: 0.7870 (mmm) outliers start: 242 outliers final: 145 residues processed: 1206 average time/residue: 0.5566 time to fit residues: 1146.8839 Evaluate side-chains 1122 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 956 time to evaluate : 5.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 143 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 318 ASP 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 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 472 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 318 ASP 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 497 MET Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 143 VAL 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 332 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 173 PHE 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 384 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 SER 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 11 ASP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 279 LEU 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 8 LEU Chi-restraints excluded: chain F residue 49 ASN 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 263 SER Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 293 SER 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 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 49 ASN Chi-restraints excluded: chain G residue 89 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 332 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 472 ASN Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 167 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 384 THR Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 445 CYS Chi-restraints excluded: chain H residue 503 ASN Chi-restraints excluded: chain H residue 512 MET Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 208 ASP 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 391 ILE Chi-restraints excluded: chain I residue 392 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 52 THR 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 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 J residue 517 THR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 208 ASP 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 325 GLU Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 466 ILE Chi-restraints excluded: chain K residue 508 LEU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 208 ASP Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 252 ILE 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 478 THR 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: 0.9990 chunk 8 optimal weight: 2.9990 chunk 449 optimal weight: 0.9990 chunk 248 optimal weight: 0.3980 chunk 514 optimal weight: 0.9990 chunk 416 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 307 optimal weight: 4.9990 chunk 541 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 184 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN ** F 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN H 68 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 49440 Z= 0.223 Angle : 0.720 10.753 66912 Z= 0.350 Chirality : 0.044 0.241 7572 Planarity : 0.005 0.059 8832 Dihedral : 5.803 34.330 6876 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.46 % Favored : 91.15 % Rotamer: Outliers : 4.69 % Allowed : 18.18 % Favored : 77.13 % 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: -1.14 (0.11), residues: 6252 helix: 0.58 (0.10), residues: 2904 sheet: -1.17 (0.20), residues: 588 loop : -2.17 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 83 HIS 0.003 0.001 HIS C 216 PHE 0.021 0.002 PHE K 338 TYR 0.023 0.002 TYR G 389 ARG 0.006 0.000 ARG C 456 *********************** 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 1252 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1008 time to evaluate : 5.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8819 (mmtt) cc_final: 0.7634 (tptt) REVERT: A 105 LYS cc_start: 0.8755 (tptt) cc_final: 0.7843 (ttpp) REVERT: A 118 MET cc_start: 0.8733 (mmm) cc_final: 0.8326 (mmm) REVERT: A 173 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.6887 (m-80) REVERT: A 472 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7945 (m110) REVERT: A 494 GLN cc_start: 0.8684 (mm110) cc_final: 0.8212 (tm-30) REVERT: A 523 MET cc_start: 0.8080 (ttp) cc_final: 0.7206 (tmm) REVERT: B 23 ASP cc_start: 0.8028 (t70) cc_final: 0.7624 (t0) REVERT: B 118 MET cc_start: 0.8986 (mmm) cc_final: 0.8643 (mmm) REVERT: B 357 MET cc_start: 0.7800 (mmp) cc_final: 0.7420 (mmp) REVERT: B 477 ASP cc_start: 0.6030 (p0) cc_final: 0.5713 (p0) REVERT: B 489 GLN cc_start: 0.8318 (mt0) cc_final: 0.8021 (tp40) REVERT: B 494 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 94 LYS cc_start: 0.8784 (mmtt) cc_final: 0.7815 (tptt) REVERT: C 105 LYS cc_start: 0.8749 (tptt) cc_final: 0.8072 (ttpp) REVERT: C 118 MET cc_start: 0.8550 (mmm) cc_final: 0.8270 (mmm) REVERT: C 120 TYR cc_start: 0.9035 (t80) cc_final: 0.8634 (t80) REVERT: C 240 SER cc_start: 0.7483 (m) cc_final: 0.7040 (p) REVERT: C 494 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8196 (tm-30) REVERT: C 501 MET cc_start: 0.8164 (mtt) cc_final: 0.7797 (mtp) REVERT: D 11 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7606 (p0) REVERT: D 118 MET cc_start: 0.8796 (mmm) cc_final: 0.8513 (mmm) REVERT: D 158 MET cc_start: 0.7841 (ptt) cc_final: 0.7589 (ptt) REVERT: D 227 LEU cc_start: 0.8857 (mt) cc_final: 0.8463 (mt) REVERT: D 235 MET cc_start: 0.7068 (ttm) cc_final: 0.6438 (ttm) REVERT: D 236 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6057 (mp0) REVERT: D 291 MET cc_start: 0.8679 (mmt) cc_final: 0.8436 (mmm) REVERT: D 385 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8345 (tt) REVERT: D 465 MET cc_start: 0.8759 (tpt) cc_final: 0.8105 (tpp) REVERT: D 498 GLN cc_start: 0.8926 (tp40) cc_final: 0.8460 (tp-100) REVERT: E 94 LYS cc_start: 0.8977 (mmtt) cc_final: 0.7897 (tptt) REVERT: E 105 LYS cc_start: 0.8842 (tptt) cc_final: 0.8063 (ttpp) REVERT: E 158 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8322 (ppp) REVERT: E 240 SER cc_start: 0.7716 (m) cc_final: 0.7346 (p) REVERT: E 252 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7564 (tp) REVERT: E 279 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9236 (tp) REVERT: E 465 MET cc_start: 0.8758 (tmm) cc_final: 0.8332 (tmm) REVERT: E 494 GLN cc_start: 0.8633 (mm110) cc_final: 0.8253 (tm-30) REVERT: E 501 MET cc_start: 0.8448 (mtp) cc_final: 0.7905 (ttm) REVERT: E 523 MET cc_start: 0.8621 (tmm) cc_final: 0.7884 (tmm) REVERT: F 118 MET cc_start: 0.9134 (mmm) cc_final: 0.8802 (mmm) REVERT: F 230 GLU cc_start: 0.7404 (pm20) cc_final: 0.7102 (pm20) REVERT: F 235 MET cc_start: 0.7004 (ttm) cc_final: 0.6576 (ttm) REVERT: F 236 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: F 273 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9139 (tp) REVERT: F 455 MET cc_start: 0.8317 (mmm) cc_final: 0.7373 (mtt) REVERT: F 465 MET cc_start: 0.8582 (tpp) cc_final: 0.8212 (tpp) REVERT: F 477 ASP cc_start: 0.5654 (p0) cc_final: 0.5238 (p0) REVERT: F 489 GLN cc_start: 0.8042 (mt0) cc_final: 0.7574 (tp40) REVERT: F 494 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8250 (tm-30) REVERT: G 94 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8112 (tptt) REVERT: G 105 LYS cc_start: 0.8668 (tptt) cc_final: 0.7728 (ttpp) REVERT: G 158 MET cc_start: 0.7937 (ptp) cc_final: 0.7676 (ptp) REVERT: G 173 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: G 206 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8520 (tppt) REVERT: G 423 GLU cc_start: 0.8553 (pm20) cc_final: 0.8236 (pm20) REVERT: G 461 ILE cc_start: 0.8961 (mt) cc_final: 0.8652 (mt) REVERT: G 465 MET cc_start: 0.8456 (tpp) cc_final: 0.8227 (tpp) REVERT: G 494 GLN cc_start: 0.8701 (mm110) cc_final: 0.8237 (tm-30) REVERT: G 495 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: H 195 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7553 (mtp85) REVERT: H 325 GLU cc_start: 0.8020 (pm20) cc_final: 0.7747 (pm20) REVERT: H 463 LEU cc_start: 0.8719 (mm) cc_final: 0.8392 (mt) REVERT: H 482 LEU cc_start: 0.8519 (pt) cc_final: 0.8250 (pp) REVERT: H 489 GLN cc_start: 0.8071 (mt0) cc_final: 0.7405 (tp40) REVERT: H 512 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8097 (ptm) REVERT: I 94 LYS cc_start: 0.8626 (mmtt) cc_final: 0.7830 (tptt) REVERT: I 95 GLN cc_start: 0.8628 (mm110) cc_final: 0.8422 (mm-40) REVERT: I 105 LYS cc_start: 0.8698 (tptt) cc_final: 0.7972 (ttpp) REVERT: I 199 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8351 (tm-30) REVERT: I 241 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6748 (t0) REVERT: I 299 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9045 (mp) REVERT: I 404 LEU cc_start: 0.9392 (mt) cc_final: 0.9191 (mt) REVERT: I 455 MET cc_start: 0.8760 (mtt) cc_final: 0.8466 (mtt) REVERT: I 465 MET cc_start: 0.8799 (tpp) cc_final: 0.8560 (tpp) REVERT: I 494 GLN cc_start: 0.8666 (mm110) cc_final: 0.8179 (tm-30) REVERT: I 501 MET cc_start: 0.8292 (mtm) cc_final: 0.8044 (ttp) REVERT: J 23 ASP cc_start: 0.8116 (t70) cc_final: 0.7639 (t70) REVERT: J 118 MET cc_start: 0.8882 (mmm) cc_final: 0.8597 (mmm) REVERT: J 158 MET cc_start: 0.8218 (ptt) cc_final: 0.7711 (ptt) REVERT: J 179 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7519 (mpp) REVERT: J 236 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6151 (mp0) REVERT: J 262 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6766 (mt-10) REVERT: J 465 MET cc_start: 0.8619 (tpp) cc_final: 0.8053 (tpp) REVERT: J 489 GLN cc_start: 0.8109 (mt0) cc_final: 0.7418 (tp40) REVERT: K 94 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8045 (tptt) REVERT: K 105 LYS cc_start: 0.8916 (tptt) cc_final: 0.8357 (mtpt) REVERT: K 118 MET cc_start: 0.8691 (mmm) cc_final: 0.8413 (mmm) REVERT: K 167 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9283 (m) REVERT: K 241 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7358 (t0) REVERT: K 338 PHE cc_start: 0.8345 (t80) cc_final: 0.8141 (t80) REVERT: K 494 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8105 (tm-30) REVERT: K 499 MET cc_start: 0.8669 (tmm) cc_final: 0.7931 (tmm) REVERT: L 23 ASP cc_start: 0.8194 (t70) cc_final: 0.7838 (t0) REVERT: L 94 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8583 (mptt) REVERT: L 118 MET cc_start: 0.9037 (mmm) cc_final: 0.8733 (mmm) REVERT: L 179 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7589 (mpp) REVERT: L 236 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: L 455 MET cc_start: 0.8494 (mpp) cc_final: 0.7622 (mtt) REVERT: L 465 MET cc_start: 0.8706 (tpp) cc_final: 0.8104 (tpp) REVERT: L 489 GLN cc_start: 0.7779 (mt0) cc_final: 0.7285 (tp40) outliers start: 244 outliers final: 164 residues processed: 1162 average time/residue: 0.5592 time to fit residues: 1112.7182 Evaluate side-chains 1134 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 949 time to evaluate : 6.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU 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 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 417 LEU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 11 ASP 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 293 SER Chi-restraints excluded: chain B residue 318 ASP 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 49 ASN 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 259 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 11 ASP 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 66 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 167 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 318 ASP 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 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 481 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 325 GLU Chi-restraints excluded: chain E residue 330 LEU 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 8 LEU Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 293 SER 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 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 49 ASN 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 208 ASP Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 390 SER 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 H residue 11 ASP 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 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 I residue 97 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 299 LEU 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 417 LEU Chi-restraints excluded: chain J residue 49 ASN 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 179 MET Chi-restraints excluded: chain J residue 211 ILE 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 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 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 144 LEU Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 208 ASP 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 325 GLU Chi-restraints excluded: chain K residue 385 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 K residue 440 ASP Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 179 MET 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 406 LYS Chi-restraints excluded: chain L residue 426 ILE 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: 1.9990 chunk 543 optimal weight: 0.0980 chunk 119 optimal weight: 0.0870 chunk 354 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 603 optimal weight: 0.9980 chunk 501 optimal weight: 0.0980 chunk 279 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 316 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 472 ASN ** 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 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 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** H 68 ASN H 283 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 49440 Z= 0.170 Angle : 0.695 12.885 66912 Z= 0.336 Chirality : 0.043 0.188 7572 Planarity : 0.004 0.057 8832 Dihedral : 5.541 36.311 6876 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.30 % Favored : 91.33 % Rotamer: Outliers : 4.09 % Allowed : 19.34 % Favored : 76.57 % 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: -0.83 (0.11), residues: 6252 helix: 0.88 (0.10), residues: 2940 sheet: -0.96 (0.20), residues: 588 loop : -2.13 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 83 HIS 0.002 0.001 HIS F 216 PHE 0.022 0.001 PHE G 78 TYR 0.023 0.001 TYR G 389 ARG 0.007 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 1263 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1050 time to evaluate : 5.724 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 94 LYS cc_start: 0.8714 (mmtt) cc_final: 0.7580 (tptt) REVERT: A 105 LYS cc_start: 0.8746 (tptt) cc_final: 0.7807 (ttpp) REVERT: A 472 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7890 (m110) REVERT: A 494 GLN cc_start: 0.8681 (mm110) cc_final: 0.8191 (tm-30) REVERT: A 501 MET cc_start: 0.8361 (ttp) cc_final: 0.7825 (ttp) REVERT: A 523 MET cc_start: 0.8050 (ttp) cc_final: 0.7205 (tmm) REVERT: B 23 ASP cc_start: 0.7977 (t70) cc_final: 0.7519 (t0) REVERT: B 118 MET cc_start: 0.8944 (mmm) cc_final: 0.8559 (mmm) REVERT: B 238 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7253 (tm-30) REVERT: B 240 SER cc_start: 0.8309 (p) cc_final: 0.8033 (m) REVERT: B 357 MET cc_start: 0.7853 (mmp) cc_final: 0.7545 (mmp) REVERT: B 477 ASP cc_start: 0.5908 (p0) cc_final: 0.5650 (p0) REVERT: B 489 GLN cc_start: 0.8333 (mt0) cc_final: 0.8030 (tp40) REVERT: B 494 GLN cc_start: 0.8263 (tm-30) cc_final: 0.8002 (tm-30) REVERT: C 94 LYS cc_start: 0.8755 (mmtt) cc_final: 0.7793 (tptt) REVERT: C 105 LYS cc_start: 0.8747 (tptt) cc_final: 0.8043 (ttpp) REVERT: C 118 MET cc_start: 0.8577 (mmm) cc_final: 0.8273 (mmm) REVERT: C 120 TYR cc_start: 0.9033 (t80) cc_final: 0.8737 (t80) REVERT: C 240 SER cc_start: 0.7426 (m) cc_final: 0.6968 (p) REVERT: C 395 GLU cc_start: 0.7822 (tp30) cc_final: 0.7497 (tp30) REVERT: C 494 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8146 (tm-30) REVERT: C 501 MET cc_start: 0.8051 (mtt) cc_final: 0.7746 (mtp) REVERT: C 508 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9059 (pt) REVERT: D 11 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7399 (p0) REVERT: D 118 MET cc_start: 0.8716 (mmm) cc_final: 0.8486 (mmm) REVERT: D 158 MET cc_start: 0.7787 (ptt) cc_final: 0.7554 (ptt) REVERT: D 227 LEU cc_start: 0.8815 (mt) cc_final: 0.8370 (mt) REVERT: D 235 MET cc_start: 0.7032 (ttm) cc_final: 0.6524 (ttm) REVERT: D 236 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5907 (mp0) REVERT: D 498 GLN cc_start: 0.8866 (tp40) cc_final: 0.8374 (tp-100) REVERT: D 499 MET cc_start: 0.8233 (ttt) cc_final: 0.7994 (ttt) REVERT: E 92 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7685 (mt-10) REVERT: E 94 LYS cc_start: 0.8899 (mmtt) cc_final: 0.7922 (tptt) REVERT: E 105 LYS cc_start: 0.8680 (tptt) cc_final: 0.7914 (ttpp) REVERT: E 145 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9017 (pt) REVERT: E 158 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8186 (ppp) REVERT: E 240 SER cc_start: 0.7548 (m) cc_final: 0.7028 (p) REVERT: E 252 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7286 (tp) REVERT: E 279 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9221 (tp) REVERT: E 465 MET cc_start: 0.8659 (tmm) cc_final: 0.8227 (tmm) REVERT: E 494 GLN cc_start: 0.8608 (mm110) cc_final: 0.8131 (tm-30) REVERT: E 501 MET cc_start: 0.8393 (mtp) cc_final: 0.7937 (ttm) REVERT: E 523 MET cc_start: 0.8626 (tmm) cc_final: 0.7914 (tmm) REVERT: F 112 MET cc_start: 0.7858 (tpp) cc_final: 0.7609 (tpp) REVERT: F 158 MET cc_start: 0.7606 (ptt) cc_final: 0.7068 (ptt) REVERT: F 238 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7747 (pt0) REVERT: F 273 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9095 (tp) REVERT: F 440 ASP cc_start: 0.7948 (t70) cc_final: 0.7685 (p0) REVERT: F 455 MET cc_start: 0.8366 (mmm) cc_final: 0.7739 (mtt) REVERT: F 465 MET cc_start: 0.8524 (tpp) cc_final: 0.7940 (tpp) REVERT: F 489 GLN cc_start: 0.8203 (mt0) cc_final: 0.7577 (tp40) REVERT: F 494 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8204 (tm-30) REVERT: G 94 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8064 (tptt) REVERT: G 105 LYS cc_start: 0.8688 (tptt) cc_final: 0.7762 (ttpp) REVERT: G 120 TYR cc_start: 0.9070 (t80) cc_final: 0.8706 (t80) REVERT: G 164 SER cc_start: 0.8597 (m) cc_final: 0.8367 (t) REVERT: G 238 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7813 (mp-120) REVERT: G 395 GLU cc_start: 0.7602 (tp30) cc_final: 0.7336 (tp30) REVERT: G 423 GLU cc_start: 0.8434 (pm20) cc_final: 0.8107 (pm20) REVERT: G 461 ILE cc_start: 0.8933 (mt) cc_final: 0.8598 (mt) REVERT: G 465 MET cc_start: 0.8434 (tpp) cc_final: 0.8208 (tpp) REVERT: G 494 GLN cc_start: 0.8685 (mm110) cc_final: 0.8218 (tm-30) REVERT: G 495 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: G 501 MET cc_start: 0.8530 (ttp) cc_final: 0.7747 (ttp) REVERT: H 118 MET cc_start: 0.8818 (mmm) cc_final: 0.8247 (mmm) REVERT: H 195 ARG cc_start: 0.8181 (mtm110) cc_final: 0.7607 (mtp85) REVERT: H 323 ARG cc_start: 0.8326 (mtm110) cc_final: 0.7741 (mtm180) REVERT: H 463 LEU cc_start: 0.8724 (mm) cc_final: 0.8423 (mt) REVERT: H 477 ASP cc_start: 0.5667 (p0) cc_final: 0.5347 (p0) REVERT: H 482 LEU cc_start: 0.8472 (pt) cc_final: 0.8227 (pp) REVERT: H 489 GLN cc_start: 0.8031 (mt0) cc_final: 0.7375 (tp40) REVERT: H 512 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8210 (ptm) REVERT: I 94 LYS cc_start: 0.8587 (mmtt) cc_final: 0.7828 (tptt) REVERT: I 105 LYS cc_start: 0.8722 (tptt) cc_final: 0.7969 (ttpp) REVERT: I 118 MET cc_start: 0.8769 (mmm) cc_final: 0.8150 (mmm) REVERT: I 241 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6710 (t0) REVERT: I 299 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8980 (mp) REVERT: I 395 GLU cc_start: 0.7898 (tp30) cc_final: 0.7586 (tp30) REVERT: I 494 GLN cc_start: 0.8658 (mm110) cc_final: 0.8293 (tm-30) REVERT: I 501 MET cc_start: 0.8072 (mtm) cc_final: 0.7785 (ptp) REVERT: J 8 LEU cc_start: 0.4824 (tp) cc_final: 0.4395 (tp) REVERT: J 23 ASP cc_start: 0.8065 (t70) cc_final: 0.7594 (t70) REVERT: J 158 MET cc_start: 0.8051 (ptt) cc_final: 0.7253 (ptt) REVERT: J 179 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7442 (mpp) REVERT: J 236 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6011 (mp0) REVERT: J 262 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6623 (mt-10) REVERT: J 465 MET cc_start: 0.8597 (tpp) cc_final: 0.7997 (tpp) REVERT: J 489 GLN cc_start: 0.8141 (mt0) cc_final: 0.7549 (tp40) REVERT: K 94 LYS cc_start: 0.8742 (mmtt) cc_final: 0.7990 (tptt) REVERT: K 105 LYS cc_start: 0.8942 (tptt) cc_final: 0.8288 (mtpt) REVERT: K 118 MET cc_start: 0.8674 (mmm) cc_final: 0.8318 (mmm) REVERT: K 465 MET cc_start: 0.8654 (tpp) cc_final: 0.8423 (tmm) REVERT: K 494 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8181 (tm-30) REVERT: K 499 MET cc_start: 0.8634 (tmm) cc_final: 0.8128 (tmm) REVERT: K 523 MET cc_start: 0.7889 (ttp) cc_final: 0.7228 (tmm) REVERT: L 23 ASP cc_start: 0.8326 (t70) cc_final: 0.7907 (t0) REVERT: L 118 MET cc_start: 0.9109 (mmm) cc_final: 0.8741 (mmm) REVERT: L 158 MET cc_start: 0.7640 (ptt) cc_final: 0.7246 (ptt) REVERT: L 179 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7433 (mpp) REVERT: L 236 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: L 406 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7881 (pttm) REVERT: L 455 MET cc_start: 0.8512 (mpp) cc_final: 0.7716 (mtt) REVERT: L 461 ILE cc_start: 0.8878 (mm) cc_final: 0.8464 (tp) REVERT: L 465 MET cc_start: 0.8686 (tpp) cc_final: 0.8110 (tpp) REVERT: L 489 GLN cc_start: 0.7750 (mt0) cc_final: 0.7350 (tp40) REVERT: L 492 MET cc_start: 0.8106 (mmp) cc_final: 0.7831 (mmm) outliers start: 213 outliers final: 147 residues processed: 1184 average time/residue: 0.5371 time to fit residues: 1088.7678 Evaluate side-chains 1121 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 956 time to evaluate : 5.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 318 ASP 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 472 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 11 ASP 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 293 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 417 LEU 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 49 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 392 LEU 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 11 ASP Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 167 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 318 ASP 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 481 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 296 VAL 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 452 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 293 SER 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 390 SER 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 49 ASN 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 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 11 ASP Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 240 SER 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 392 LEU Chi-restraints excluded: chain H residue 445 CYS Chi-restraints excluded: chain H residue 512 MET Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 240 SER 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 417 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 211 ILE 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 391 ILE Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 417 LEU 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 144 LEU Chi-restraints excluded: chain K residue 208 ASP Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 385 LEU 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 11 ASP Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 208 ASP Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 254 ILE 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 406 LYS Chi-restraints excluded: chain L residue 426 ILE 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: 0.7980 chunk 68 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 440 optimal weight: 0.0670 chunk 341 optimal weight: 2.9990 chunk 508 optimal weight: 1.9990 chunk 337 optimal weight: 0.0570 chunk 601 optimal weight: 0.7980 chunk 376 optimal weight: 0.3980 chunk 366 optimal weight: 0.5980 chunk 277 optimal weight: 1.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 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** H 283 GLN ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 GLN K 498 GLN L 495 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 49440 Z= 0.169 Angle : 0.698 12.173 66912 Z= 0.336 Chirality : 0.043 0.266 7572 Planarity : 0.004 0.056 8832 Dihedral : 5.400 33.484 6876 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.37 % Favored : 91.33 % Rotamer: Outliers : 3.92 % Allowed : 19.57 % Favored : 76.52 % 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: -0.60 (0.11), residues: 6252 helix: 1.12 (0.10), residues: 2976 sheet: -0.78 (0.20), residues: 588 loop : -2.14 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 83 HIS 0.002 0.001 HIS J 216 PHE 0.028 0.002 PHE E 78 TYR 0.019 0.001 TYR G 389 ARG 0.008 0.000 ARG K 64 *********************** 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 1240 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1036 time to evaluate : 6.587 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: A 94 LYS cc_start: 0.8725 (mmtt) cc_final: 0.7603 (tptt) REVERT: A 105 LYS cc_start: 0.8759 (tptt) cc_final: 0.7822 (ttpp) REVERT: A 118 MET cc_start: 0.8790 (mmm) cc_final: 0.8384 (mmm) REVERT: A 494 GLN cc_start: 0.8679 (mm110) cc_final: 0.8212 (tm-30) REVERT: A 501 MET cc_start: 0.8270 (ttp) cc_final: 0.7712 (ptm) REVERT: A 523 MET cc_start: 0.8026 (ttp) cc_final: 0.7227 (tmm) REVERT: B 23 ASP cc_start: 0.7935 (t70) cc_final: 0.7472 (t0) REVERT: B 118 MET cc_start: 0.8988 (mmm) cc_final: 0.8548 (mmm) REVERT: B 158 MET cc_start: 0.7951 (ptt) cc_final: 0.7666 (ptt) REVERT: B 238 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7287 (tm-30) REVERT: B 357 MET cc_start: 0.7807 (mmp) cc_final: 0.7461 (mmp) REVERT: B 489 GLN cc_start: 0.8347 (mt0) cc_final: 0.8063 (tp40) REVERT: B 494 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7896 (tm-30) REVERT: C 94 LYS cc_start: 0.8627 (mmtt) cc_final: 0.7768 (tptt) REVERT: C 105 LYS cc_start: 0.8778 (tptt) cc_final: 0.8080 (ttpp) REVERT: C 118 MET cc_start: 0.8556 (mmm) cc_final: 0.8191 (mmm) REVERT: C 120 TYR cc_start: 0.9040 (t80) cc_final: 0.8786 (t80) REVERT: C 240 SER cc_start: 0.7466 (m) cc_final: 0.6556 (m) REVERT: C 395 GLU cc_start: 0.7822 (tp30) cc_final: 0.7520 (tp30) REVERT: C 494 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8252 (tm-30) REVERT: C 508 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8955 (pt) REVERT: D 11 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7175 (p0) REVERT: D 118 MET cc_start: 0.8748 (mmm) cc_final: 0.8413 (mmm) REVERT: D 158 MET cc_start: 0.7742 (ptt) cc_final: 0.7481 (ptt) REVERT: D 225 GLU cc_start: 0.8259 (mp0) cc_final: 0.8000 (mp0) REVERT: D 227 LEU cc_start: 0.8810 (mt) cc_final: 0.8399 (mt) REVERT: D 235 MET cc_start: 0.6914 (ttm) cc_final: 0.6378 (ttm) REVERT: D 236 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5827 (mp0) REVERT: D 357 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7239 (mmp) REVERT: D 440 ASP cc_start: 0.7787 (t0) cc_final: 0.7506 (t0) REVERT: D 465 MET cc_start: 0.8641 (tpt) cc_final: 0.7943 (tpp) REVERT: D 477 ASP cc_start: 0.5759 (p0) cc_final: 0.5370 (p0) REVERT: D 499 MET cc_start: 0.8311 (ttt) cc_final: 0.8055 (ttt) REVERT: E 94 LYS cc_start: 0.8881 (mmtt) cc_final: 0.7945 (tptt) REVERT: E 105 LYS cc_start: 0.8677 (tptt) cc_final: 0.7878 (ttpp) REVERT: E 145 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9052 (pt) REVERT: E 158 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8079 (ppp) REVERT: E 192 GLU cc_start: 0.6326 (pm20) cc_final: 0.5860 (pm20) REVERT: E 196 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8341 (ptpt) REVERT: E 252 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7277 (tp) REVERT: E 279 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9194 (tp) REVERT: E 465 MET cc_start: 0.8689 (tmm) cc_final: 0.8242 (tmm) REVERT: E 494 GLN cc_start: 0.8768 (mm110) cc_final: 0.8267 (tm-30) REVERT: E 501 MET cc_start: 0.8274 (mtp) cc_final: 0.7910 (ttm) REVERT: E 523 MET cc_start: 0.8595 (tmm) cc_final: 0.7825 (tmm) REVERT: F 118 MET cc_start: 0.9081 (mmm) cc_final: 0.8789 (mmm) REVERT: F 158 MET cc_start: 0.7567 (ptt) cc_final: 0.7182 (ptt) REVERT: F 179 MET cc_start: 0.8341 (mtm) cc_final: 0.8127 (mtm) REVERT: F 236 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: F 238 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7735 (pt0) REVERT: F 273 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9119 (tp) REVERT: F 455 MET cc_start: 0.8330 (mmm) cc_final: 0.7630 (mtt) REVERT: F 489 GLN cc_start: 0.8156 (mt0) cc_final: 0.7542 (tm-30) REVERT: F 494 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8234 (tm-30) REVERT: G 94 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8063 (tptt) REVERT: G 105 LYS cc_start: 0.8703 (tptt) cc_final: 0.7761 (ttpp) REVERT: G 173 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6719 (m-80) REVERT: G 238 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7625 (mp10) REVERT: G 395 GLU cc_start: 0.7621 (tp30) cc_final: 0.7363 (tp30) REVERT: G 423 GLU cc_start: 0.8453 (pm20) cc_final: 0.7955 (pm20) REVERT: G 461 ILE cc_start: 0.8826 (mt) cc_final: 0.8499 (mt) REVERT: G 494 GLN cc_start: 0.8752 (mm110) cc_final: 0.8210 (tm-30) REVERT: G 495 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: G 498 GLN cc_start: 0.8868 (tp40) cc_final: 0.8503 (tp-100) REVERT: G 501 MET cc_start: 0.8456 (ttp) cc_final: 0.7825 (ptm) REVERT: H 118 MET cc_start: 0.8813 (mmm) cc_final: 0.8442 (mmm) REVERT: H 195 ARG cc_start: 0.8247 (mtm110) cc_final: 0.7667 (mtp85) REVERT: H 323 ARG cc_start: 0.8338 (mtm110) cc_final: 0.7745 (mtm180) REVERT: H 482 LEU cc_start: 0.8361 (pt) cc_final: 0.8133 (pp) REVERT: H 489 GLN cc_start: 0.8031 (mt0) cc_final: 0.7443 (tp40) REVERT: H 512 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7937 (ptm) REVERT: I 84 MET cc_start: 0.8566 (pmm) cc_final: 0.8241 (pmm) REVERT: I 94 LYS cc_start: 0.8656 (mmtt) cc_final: 0.7861 (tptt) REVERT: I 105 LYS cc_start: 0.8728 (tptt) cc_final: 0.7964 (ttpp) REVERT: I 228 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8176 (ptm-80) REVERT: I 241 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6793 (t0) REVERT: I 299 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8948 (mp) REVERT: I 331 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7640 (mt0) REVERT: I 395 GLU cc_start: 0.7844 (tp30) cc_final: 0.7549 (tp30) REVERT: I 494 GLN cc_start: 0.8653 (mm110) cc_final: 0.8276 (tm-30) REVERT: I 501 MET cc_start: 0.8133 (mtm) cc_final: 0.7877 (ptp) REVERT: I 523 MET cc_start: 0.8484 (tmm) cc_final: 0.7903 (tmm) REVERT: J 8 LEU cc_start: 0.4528 (tp) cc_final: 0.4060 (tp) REVERT: J 158 MET cc_start: 0.7968 (ptt) cc_final: 0.7236 (ptt) REVERT: J 179 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7349 (mpp) REVERT: J 236 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5774 (mp0) REVERT: J 465 MET cc_start: 0.8561 (tpp) cc_final: 0.7932 (tpp) REVERT: J 468 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9262 (tt) REVERT: J 489 GLN cc_start: 0.8124 (mt0) cc_final: 0.7590 (tp40) REVERT: K 94 LYS cc_start: 0.8769 (mmtt) cc_final: 0.7965 (tptt) REVERT: K 105 LYS cc_start: 0.8913 (tptt) cc_final: 0.8345 (mtpt) REVERT: K 118 MET cc_start: 0.8662 (mmm) cc_final: 0.8247 (mmm) REVERT: K 395 GLU cc_start: 0.7895 (tp30) cc_final: 0.7481 (tp30) REVERT: K 435 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.5748 (ptt90) REVERT: K 461 ILE cc_start: 0.8513 (mt) cc_final: 0.8289 (mt) REVERT: K 465 MET cc_start: 0.8660 (tpp) cc_final: 0.8445 (tmm) REVERT: K 494 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8169 (tm-30) REVERT: K 499 MET cc_start: 0.8661 (tmm) cc_final: 0.8153 (tmm) REVERT: K 523 MET cc_start: 0.8101 (ttp) cc_final: 0.7290 (tmm) REVERT: L 23 ASP cc_start: 0.8378 (t70) cc_final: 0.7976 (t0) REVERT: L 112 MET cc_start: 0.7971 (tpp) cc_final: 0.7767 (tpp) REVERT: L 118 MET cc_start: 0.9152 (mmm) cc_final: 0.8909 (mmm) REVERT: L 179 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7347 (mpp) REVERT: L 236 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: L 406 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7980 (pttm) REVERT: L 440 ASP cc_start: 0.7894 (t70) cc_final: 0.7679 (p0) REVERT: L 455 MET cc_start: 0.8558 (mpp) cc_final: 0.7761 (mtt) REVERT: L 461 ILE cc_start: 0.8865 (mm) cc_final: 0.8479 (tp) REVERT: L 465 MET cc_start: 0.8667 (tpp) cc_final: 0.8056 (tpp) REVERT: L 489 GLN cc_start: 0.7753 (mt0) cc_final: 0.7418 (tp40) outliers start: 204 outliers final: 140 residues processed: 1162 average time/residue: 0.5582 time to fit residues: 1112.1643 Evaluate side-chains 1112 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 948 time to evaluate : 5.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 318 ASP 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 A residue 508 LEU 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 293 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 482 LEU Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 144 LEU 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 391 ILE Chi-restraints excluded: chain C residue 392 LEU 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 11 ASP Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 167 VAL 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 318 ASP Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 296 VAL 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 E residue 452 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 293 SER 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 390 SER 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 49 ASN 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 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 439 LEU Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 495 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 293 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 143 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 299 LEU 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 J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 211 ILE 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 384 THR Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 468 LEU Chi-restraints excluded: chain J residue 481 ILE Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 208 ASP Chi-restraints excluded: chain K residue 211 ILE Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 385 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 K residue 435 ARG 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 11 ASP Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 208 ASP Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 254 ILE 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 406 LYS Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 476 ILE 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: 0.8980 chunk 240 optimal weight: 2.9990 chunk 359 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 chunk 118 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 382 optimal weight: 0.9990 chunk 409 optimal weight: 0.8980 chunk 297 optimal weight: 0.0170 chunk 56 optimal weight: 5.9990 chunk 472 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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** D 331 GLN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 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** H 283 GLN I 487 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 49440 Z= 0.182 Angle : 0.702 12.361 66912 Z= 0.338 Chirality : 0.043 0.263 7572 Planarity : 0.004 0.055 8832 Dihedral : 5.312 32.520 6876 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.46 % Favored : 91.25 % Rotamer: Outliers : 3.90 % Allowed : 20.16 % Favored : 75.94 % 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: -0.45 (0.11), residues: 6252 helix: 1.28 (0.10), residues: 2976 sheet: -0.79 (0.22), residues: 528 loop : -2.07 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 83 HIS 0.002 0.001 HIS L 216 PHE 0.025 0.002 PHE E 78 TYR 0.019 0.001 TYR G 389 ARG 0.007 0.000 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 1210 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1007 time to evaluate : 5.638 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: A 23 ASP cc_start: 0.8346 (t0) cc_final: 0.8046 (t0) REVERT: A 94 LYS cc_start: 0.8780 (mmtt) cc_final: 0.7664 (tptt) REVERT: A 105 LYS cc_start: 0.8704 (tptt) cc_final: 0.7856 (ttpp) REVERT: A 173 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6947 (m-80) REVERT: A 494 GLN cc_start: 0.8675 (mm110) cc_final: 0.8212 (tm-30) REVERT: A 501 MET cc_start: 0.8326 (ttp) cc_final: 0.7763 (ptm) REVERT: A 523 MET cc_start: 0.7965 (ttp) cc_final: 0.7275 (tmm) REVERT: B 23 ASP cc_start: 0.7938 (t70) cc_final: 0.7353 (t0) REVERT: B 118 MET cc_start: 0.8988 (mmm) cc_final: 0.8542 (mmm) REVERT: B 158 MET cc_start: 0.7677 (ptt) cc_final: 0.7438 (ptt) REVERT: B 238 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7305 (tm-30) REVERT: B 357 MET cc_start: 0.7594 (mmp) cc_final: 0.7233 (mmp) REVERT: B 489 GLN cc_start: 0.8358 (mt0) cc_final: 0.8080 (tp40) REVERT: B 494 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7910 (tm-30) REVERT: C 94 LYS cc_start: 0.8686 (mmtt) cc_final: 0.7737 (tptt) REVERT: C 105 LYS cc_start: 0.8766 (tptt) cc_final: 0.8060 (ttpp) REVERT: C 118 MET cc_start: 0.8570 (mmm) cc_final: 0.8136 (mmm) REVERT: C 120 TYR cc_start: 0.9021 (t80) cc_final: 0.8791 (t80) REVERT: C 240 SER cc_start: 0.7756 (m) cc_final: 0.6804 (m) REVERT: C 395 GLU cc_start: 0.7848 (tp30) cc_final: 0.7528 (tp30) REVERT: C 494 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8146 (tm-30) REVERT: C 501 MET cc_start: 0.8446 (mtp) cc_final: 0.7808 (mtm) REVERT: D 11 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7153 (p0) REVERT: D 118 MET cc_start: 0.8845 (mmm) cc_final: 0.8418 (mmm) REVERT: D 225 GLU cc_start: 0.8265 (mp0) cc_final: 0.7978 (mp0) REVERT: D 227 LEU cc_start: 0.8766 (mt) cc_final: 0.8316 (mt) REVERT: D 235 MET cc_start: 0.6885 (ttm) cc_final: 0.6412 (ttm) REVERT: D 236 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5683 (mp0) REVERT: D 238 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7469 (tm-30) REVERT: D 357 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7112 (mmp) REVERT: D 465 MET cc_start: 0.8695 (tpt) cc_final: 0.8017 (tpp) REVERT: D 498 GLN cc_start: 0.8821 (tp40) cc_final: 0.8084 (tm-30) REVERT: E 94 LYS cc_start: 0.8885 (mmtt) cc_final: 0.7991 (tptt) REVERT: E 105 LYS cc_start: 0.8620 (tptt) cc_final: 0.7787 (ttpp) REVERT: E 145 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9029 (pt) REVERT: E 158 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8132 (ppp) REVERT: E 252 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7358 (tp) REVERT: E 279 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9170 (tp) REVERT: E 465 MET cc_start: 0.8674 (tmm) cc_final: 0.8227 (tmm) REVERT: E 494 GLN cc_start: 0.8659 (mm110) cc_final: 0.8216 (tm-30) REVERT: E 501 MET cc_start: 0.8246 (mtp) cc_final: 0.7905 (ttm) REVERT: E 523 MET cc_start: 0.8583 (tmm) cc_final: 0.7791 (tmm) REVERT: F 96 LEU cc_start: 0.9064 (mt) cc_final: 0.8758 (pp) REVERT: F 118 MET cc_start: 0.9157 (mmm) cc_final: 0.8834 (mmm) REVERT: F 158 MET cc_start: 0.7574 (ptt) cc_final: 0.7236 (ptt) REVERT: F 179 MET cc_start: 0.8374 (mtm) cc_final: 0.8142 (mtm) REVERT: F 236 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: F 238 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7706 (pt0) REVERT: F 273 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9088 (tp) REVERT: F 455 MET cc_start: 0.8337 (mmm) cc_final: 0.7613 (mtt) REVERT: F 489 GLN cc_start: 0.8178 (mt0) cc_final: 0.7556 (tm-30) REVERT: G 94 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8049 (tptt) REVERT: G 105 LYS cc_start: 0.8748 (tptt) cc_final: 0.7764 (ttpp) REVERT: G 118 MET cc_start: 0.8768 (mmm) cc_final: 0.8382 (mmm) REVERT: G 158 MET cc_start: 0.7915 (ptp) cc_final: 0.7669 (ptp) REVERT: G 173 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.6799 (m-80) REVERT: G 206 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8645 (mmmt) REVERT: G 238 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7592 (mp10) REVERT: G 395 GLU cc_start: 0.7608 (tp30) cc_final: 0.7343 (tp30) REVERT: G 423 GLU cc_start: 0.8379 (pm20) cc_final: 0.7927 (pm20) REVERT: G 435 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.5945 (ptt90) REVERT: G 461 ILE cc_start: 0.8782 (mt) cc_final: 0.8488 (mt) REVERT: G 465 MET cc_start: 0.8515 (tpp) cc_final: 0.7927 (tpp) REVERT: G 494 GLN cc_start: 0.8744 (mm110) cc_final: 0.8222 (tm-30) REVERT: G 495 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: G 498 GLN cc_start: 0.8733 (tp40) cc_final: 0.8349 (tp-100) REVERT: G 501 MET cc_start: 0.8376 (ttp) cc_final: 0.7783 (ptm) REVERT: H 195 ARG cc_start: 0.8275 (mtm110) cc_final: 0.7544 (mtp85) REVERT: H 323 ARG cc_start: 0.8327 (mtm110) cc_final: 0.7761 (mtm180) REVERT: H 482 LEU cc_start: 0.8223 (pt) cc_final: 0.8004 (pp) REVERT: H 489 GLN cc_start: 0.8135 (mt0) cc_final: 0.7581 (tp40) REVERT: H 512 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7976 (ptm) REVERT: I 84 MET cc_start: 0.8513 (pmm) cc_final: 0.8225 (pmm) REVERT: I 94 LYS cc_start: 0.8679 (mmtt) cc_final: 0.7863 (tptt) REVERT: I 105 LYS cc_start: 0.8733 (tptt) cc_final: 0.7951 (ttpp) REVERT: I 241 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6811 (t0) REVERT: I 331 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: I 395 GLU cc_start: 0.7945 (tp30) cc_final: 0.7653 (tp30) REVERT: I 494 GLN cc_start: 0.8661 (mm110) cc_final: 0.8323 (tm-30) REVERT: I 501 MET cc_start: 0.8162 (mtm) cc_final: 0.7866 (ptp) REVERT: I 523 MET cc_start: 0.8523 (tmm) cc_final: 0.7934 (tmm) REVERT: J 8 LEU cc_start: 0.4636 (tp) cc_final: 0.4183 (tp) REVERT: J 118 MET cc_start: 0.8933 (mmm) cc_final: 0.8690 (mmm) REVERT: J 158 MET cc_start: 0.8053 (ptt) cc_final: 0.7618 (ptt) REVERT: J 179 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7456 (mpp) REVERT: J 236 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5894 (mp0) REVERT: J 455 MET cc_start: 0.8712 (mpp) cc_final: 0.8059 (mtp) REVERT: J 465 MET cc_start: 0.8548 (tpp) cc_final: 0.7881 (tpp) REVERT: J 468 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9272 (tt) REVERT: J 489 GLN cc_start: 0.8250 (mt0) cc_final: 0.7707 (tp40) REVERT: J 492 MET cc_start: 0.8511 (mpp) cc_final: 0.8135 (mpp) REVERT: K 94 LYS cc_start: 0.8766 (mmtt) cc_final: 0.7958 (tptt) REVERT: K 105 LYS cc_start: 0.8940 (tptt) cc_final: 0.8248 (ttpt) REVERT: K 118 MET cc_start: 0.8640 (mmm) cc_final: 0.8233 (mmm) REVERT: K 173 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: K 241 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7068 (t0) REVERT: K 395 GLU cc_start: 0.7910 (tp30) cc_final: 0.7500 (tp30) REVERT: K 435 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.5578 (ptt90) REVERT: K 461 ILE cc_start: 0.8608 (mt) cc_final: 0.8398 (mt) REVERT: K 465 MET cc_start: 0.8661 (tpp) cc_final: 0.8424 (tmm) REVERT: K 494 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8266 (tm-30) REVERT: K 499 MET cc_start: 0.8601 (tmm) cc_final: 0.8106 (tmm) REVERT: K 523 MET cc_start: 0.8082 (ttp) cc_final: 0.7369 (tmm) REVERT: L 23 ASP cc_start: 0.8352 (t70) cc_final: 0.7958 (t0) REVERT: L 118 MET cc_start: 0.9168 (mmm) cc_final: 0.8941 (mmm) REVERT: L 179 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7462 (mpp) REVERT: L 236 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: L 270 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8114 (tm-30) REVERT: L 315 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8434 (tp40) REVERT: L 406 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7986 (pttm) REVERT: L 455 MET cc_start: 0.8584 (mpp) cc_final: 0.7789 (mtt) REVERT: L 461 ILE cc_start: 0.8855 (mm) cc_final: 0.8477 (tp) REVERT: L 465 MET cc_start: 0.8670 (tpp) cc_final: 0.8025 (tpp) outliers start: 203 outliers final: 151 residues processed: 1132 average time/residue: 0.5583 time to fit residues: 1080.6750 Evaluate side-chains 1127 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 950 time to evaluate : 5.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 49 ASN 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 318 ASP 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 398 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 293 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 49 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 208 ASP 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 392 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 167 VAL 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 318 ASP 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 390 SER 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 101 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 252 ILE 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 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 442 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 8 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 273 LEU Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 293 SER 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 390 SER 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 49 ASN Chi-restraints excluded: chain G residue 80 MET 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 330 LEU Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 390 SER 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 435 ARG Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 495 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 293 SER Chi-restraints excluded: chain H residue 296 VAL 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 75 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 325 GLU 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 417 LEU Chi-restraints excluded: chain I residue 435 ARG 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 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 417 LEU Chi-restraints excluded: chain J residue 468 LEU Chi-restraints excluded: chain J residue 481 ILE Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 208 ASP 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 435 ARG 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 11 ASP Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 254 ILE 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 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: 1.9990 chunk 576 optimal weight: 0.0470 chunk 525 optimal weight: 2.9990 chunk 560 optimal weight: 0.6980 chunk 337 optimal weight: 0.3980 chunk 244 optimal weight: 7.9990 chunk 440 optimal weight: 0.0970 chunk 171 optimal weight: 0.9980 chunk 506 optimal weight: 1.9990 chunk 530 optimal weight: 0.8980 chunk 558 optimal weight: 0.5980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 413 GLN A 472 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 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** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5855 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= 0.171 Angle : 0.706 12.049 66912 Z= 0.339 Chirality : 0.043 0.269 7572 Planarity : 0.004 0.056 8832 Dihedral : 5.227 33.474 6876 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.53 % Favored : 91.23 % Rotamer: Outliers : 3.53 % Allowed : 21.10 % Favored : 75.36 % 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: -0.36 (0.11), residues: 6252 helix: 1.38 (0.10), residues: 2976 sheet: -0.69 (0.22), residues: 528 loop : -2.06 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 83 HIS 0.001 0.000 HIS B 216 PHE 0.038 0.002 PHE K 78 TYR 0.019 0.001 TYR K 120 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 1189 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1005 time to evaluate : 5.650 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 23 ASP cc_start: 0.8269 (t0) cc_final: 0.8019 (t0) REVERT: A 94 LYS cc_start: 0.8753 (mmtt) cc_final: 0.7664 (tptt) REVERT: A 105 LYS cc_start: 0.8723 (tptt) cc_final: 0.7867 (ttpp) REVERT: A 173 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: A 395 GLU cc_start: 0.8088 (tp30) cc_final: 0.7598 (tp30) REVERT: A 465 MET cc_start: 0.8543 (tpp) cc_final: 0.7995 (tpp) REVERT: A 494 GLN cc_start: 0.8660 (mm110) cc_final: 0.8241 (tm-30) REVERT: A 501 MET cc_start: 0.8335 (ttp) cc_final: 0.7695 (ptm) REVERT: A 523 MET cc_start: 0.7978 (ttp) cc_final: 0.7282 (tmm) REVERT: B 23 ASP cc_start: 0.7855 (t70) cc_final: 0.7320 (t70) REVERT: B 80 MET cc_start: 0.6277 (tpt) cc_final: 0.5969 (tpt) REVERT: B 118 MET cc_start: 0.8993 (mmm) cc_final: 0.8551 (mmm) REVERT: B 158 MET cc_start: 0.7787 (ptt) cc_final: 0.7380 (ptt) REVERT: B 238 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7252 (tm-30) REVERT: B 357 MET cc_start: 0.7506 (mmp) cc_final: 0.7167 (mmp) REVERT: B 489 GLN cc_start: 0.8349 (mt0) cc_final: 0.8068 (tp40) REVERT: B 494 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 94 LYS cc_start: 0.8594 (mmtt) cc_final: 0.7714 (tptt) REVERT: C 105 LYS cc_start: 0.8733 (tptt) cc_final: 0.7963 (ttpp) REVERT: C 118 MET cc_start: 0.8517 (mmm) cc_final: 0.8037 (mmm) REVERT: C 120 TYR cc_start: 0.9019 (t80) cc_final: 0.8771 (t80) REVERT: C 143 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8565 (m) REVERT: C 395 GLU cc_start: 0.7829 (tp30) cc_final: 0.7531 (tp30) REVERT: C 494 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8067 (tm-30) REVERT: C 501 MET cc_start: 0.8358 (mtp) cc_final: 0.7793 (mtm) REVERT: D 11 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7117 (p0) REVERT: D 118 MET cc_start: 0.8878 (mmm) cc_final: 0.8431 (mmm) REVERT: D 185 ILE cc_start: 0.8852 (mt) cc_final: 0.8631 (mt) REVERT: D 225 GLU cc_start: 0.8248 (mp0) cc_final: 0.7984 (mp0) REVERT: D 227 LEU cc_start: 0.8808 (mt) cc_final: 0.8374 (mt) REVERT: D 238 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7257 (tm-30) REVERT: D 357 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7095 (mmp) REVERT: D 465 MET cc_start: 0.8692 (tpt) cc_final: 0.7982 (tpp) REVERT: D 498 GLN cc_start: 0.8795 (tp40) cc_final: 0.8067 (tm-30) REVERT: E 94 LYS cc_start: 0.8885 (mmtt) cc_final: 0.7951 (tptt) REVERT: E 105 LYS cc_start: 0.8590 (tptt) cc_final: 0.7750 (ttpp) REVERT: E 145 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9006 (pt) REVERT: E 158 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8116 (ppp) REVERT: E 252 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7281 (tp) REVERT: E 279 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9178 (tp) REVERT: E 465 MET cc_start: 0.8553 (tmm) cc_final: 0.8257 (tmm) REVERT: E 494 GLN cc_start: 0.8766 (mm110) cc_final: 0.8239 (tm-30) REVERT: E 501 MET cc_start: 0.8174 (mtp) cc_final: 0.7885 (ttm) REVERT: E 523 MET cc_start: 0.8610 (tmm) cc_final: 0.7983 (tmm) REVERT: F 96 LEU cc_start: 0.9057 (mt) cc_final: 0.8803 (pp) REVERT: F 158 MET cc_start: 0.7490 (ptt) cc_final: 0.7118 (ptt) REVERT: F 179 MET cc_start: 0.8344 (mtm) cc_final: 0.8119 (mtm) REVERT: F 236 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: F 273 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9070 (tp) REVERT: F 455 MET cc_start: 0.8314 (mmm) cc_final: 0.7620 (mtt) REVERT: F 489 GLN cc_start: 0.8199 (mt0) cc_final: 0.7631 (tm-30) REVERT: G 94 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8042 (tptt) REVERT: G 105 LYS cc_start: 0.8739 (tptt) cc_final: 0.7757 (ttpp) REVERT: G 173 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6797 (m-80) REVERT: G 220 ASP cc_start: 0.6580 (t0) cc_final: 0.6318 (t0) REVERT: G 238 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7508 (mp10) REVERT: G 395 GLU cc_start: 0.7602 (tp30) cc_final: 0.7369 (tp30) REVERT: G 423 GLU cc_start: 0.8347 (pm20) cc_final: 0.7916 (pm20) REVERT: G 435 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.5880 (ptt90) REVERT: G 461 ILE cc_start: 0.8688 (mt) cc_final: 0.8348 (mt) REVERT: G 465 MET cc_start: 0.8535 (tpp) cc_final: 0.7940 (tpp) REVERT: G 494 GLN cc_start: 0.8744 (mm110) cc_final: 0.8210 (tm-30) REVERT: G 495 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: G 498 GLN cc_start: 0.8519 (tp40) cc_final: 0.8186 (tp-100) REVERT: G 501 MET cc_start: 0.8341 (ttp) cc_final: 0.7802 (ptm) REVERT: H 158 MET cc_start: 0.7869 (ptt) cc_final: 0.7612 (ptt) REVERT: H 195 ARG cc_start: 0.8243 (mtm110) cc_final: 0.7536 (mtp85) REVERT: H 323 ARG cc_start: 0.8268 (mtm110) cc_final: 0.7677 (mtm180) REVERT: H 325 GLU cc_start: 0.8241 (pm20) cc_final: 0.8022 (pt0) REVERT: H 482 LEU cc_start: 0.8169 (pt) cc_final: 0.7959 (pp) REVERT: H 489 GLN cc_start: 0.8091 (mt0) cc_final: 0.7558 (tp40) REVERT: H 512 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7984 (ptm) REVERT: I 94 LYS cc_start: 0.8596 (mmtt) cc_final: 0.7838 (tptt) REVERT: I 105 LYS cc_start: 0.8725 (tptt) cc_final: 0.7930 (ttpp) REVERT: I 241 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6630 (t0) REVERT: I 331 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7622 (mt0) REVERT: I 395 GLU cc_start: 0.7920 (tp30) cc_final: 0.7627 (tp30) REVERT: I 465 MET cc_start: 0.8812 (tpp) cc_final: 0.8238 (tpp) REVERT: I 494 GLN cc_start: 0.8652 (mm110) cc_final: 0.8348 (tm-30) REVERT: I 501 MET cc_start: 0.8153 (mtm) cc_final: 0.7907 (ptp) REVERT: I 523 MET cc_start: 0.8523 (tmm) cc_final: 0.7954 (tmm) REVERT: J 8 LEU cc_start: 0.4564 (tp) cc_final: 0.4110 (tp) REVERT: J 118 MET cc_start: 0.8966 (mmm) cc_final: 0.8737 (mmm) REVERT: J 158 MET cc_start: 0.7973 (ptt) cc_final: 0.7529 (ptt) REVERT: J 179 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7455 (mpp) REVERT: J 235 MET cc_start: 0.7315 (ttm) cc_final: 0.6893 (ttm) REVERT: J 236 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5704 (mp0) REVERT: J 252 ILE cc_start: 0.8709 (pp) cc_final: 0.8440 (tp) REVERT: J 455 MET cc_start: 0.8690 (mpp) cc_final: 0.8189 (mtp) REVERT: J 465 MET cc_start: 0.8501 (tpp) cc_final: 0.7787 (tpp) REVERT: J 468 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9239 (tt) REVERT: J 489 GLN cc_start: 0.8221 (mt0) cc_final: 0.7667 (tp40) REVERT: J 492 MET cc_start: 0.8307 (mpp) cc_final: 0.8059 (mpp) REVERT: K 94 LYS cc_start: 0.8659 (mmtt) cc_final: 0.7942 (tptt) REVERT: K 105 LYS cc_start: 0.8931 (tptt) cc_final: 0.8333 (mtpt) REVERT: K 173 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: K 395 GLU cc_start: 0.7882 (tp30) cc_final: 0.7497 (tp30) REVERT: K 435 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5793 (ptt90) REVERT: K 465 MET cc_start: 0.8635 (tpp) cc_final: 0.8406 (tmm) REVERT: K 494 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8293 (tm-30) REVERT: K 499 MET cc_start: 0.8696 (tmm) cc_final: 0.8375 (tmm) REVERT: L 23 ASP cc_start: 0.8289 (t70) cc_final: 0.7875 (t0) REVERT: L 74 MET cc_start: 0.8526 (tpt) cc_final: 0.8104 (tpt) REVERT: L 96 LEU cc_start: 0.9023 (mt) cc_final: 0.8796 (pp) REVERT: L 118 MET cc_start: 0.9202 (mmm) cc_final: 0.8948 (mmm) REVERT: L 179 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7381 (mpp) REVERT: L 236 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: L 315 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8391 (tp40) REVERT: L 325 GLU cc_start: 0.7927 (pm20) cc_final: 0.7641 (pt0) REVERT: L 406 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7988 (pttm) REVERT: L 455 MET cc_start: 0.8560 (mpp) cc_final: 0.7741 (mtt) REVERT: L 461 ILE cc_start: 0.8832 (mm) cc_final: 0.8457 (tp) REVERT: L 465 MET cc_start: 0.8697 (tpp) cc_final: 0.8122 (tpp) outliers start: 184 outliers final: 140 residues processed: 1123 average time/residue: 0.5515 time to fit residues: 1060.5181 Evaluate side-chains 1117 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 952 time to evaluate : 5.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU 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 318 ASP 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 398 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 293 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 49 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 305 ILE 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 392 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 318 ASP 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 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 84 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 252 ILE 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 390 SER Chi-restraints excluded: chain E residue 391 ILE 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 E residue 530 VAL Chi-restraints excluded: chain F residue 8 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 273 LEU Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 293 SER 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 390 SER 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 49 ASN 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 377 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 495 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 293 SER Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 318 ASP 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 143 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 331 GLN Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 391 ILE Chi-restraints excluded: chain I residue 435 ARG 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 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 384 THR Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 468 LEU Chi-restraints excluded: chain J residue 481 ILE Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 208 ASP 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 435 ARG 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 11 ASP Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 179 MET 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 406 LYS Chi-restraints excluded: chain L residue 426 ILE 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: 0.0070 chunk 592 optimal weight: 0.8980 chunk 361 optimal weight: 8.9990 chunk 281 optimal weight: 0.8980 chunk 411 optimal weight: 0.2980 chunk 621 optimal weight: 1.9990 chunk 572 optimal weight: 6.9990 chunk 495 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 382 optimal weight: 0.2980 chunk 303 optimal weight: 0.2980 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN ** 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 359 ASN ** J 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 49440 Z= 0.172 Angle : 0.719 12.717 66912 Z= 0.344 Chirality : 0.043 0.272 7572 Planarity : 0.004 0.058 8832 Dihedral : 5.149 31.862 6876 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.56 % Favored : 91.20 % Rotamer: Outliers : 3.38 % Allowed : 21.68 % Favored : 74.94 % 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: -0.29 (0.11), residues: 6252 helix: 1.46 (0.10), residues: 2976 sheet: -0.67 (0.22), residues: 528 loop : -2.05 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 83 HIS 0.002 0.001 HIS L 216 PHE 0.034 0.002 PHE K 78 TYR 0.021 0.001 TYR E 120 ARG 0.009 0.000 ARG E 195 ********************** 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 1173 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 997 time to evaluate : 5.646 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 23 ASP cc_start: 0.8225 (t0) cc_final: 0.7995 (t0) REVERT: A 94 LYS cc_start: 0.8745 (mmtt) cc_final: 0.7605 (tptt) REVERT: A 105 LYS cc_start: 0.8697 (tptt) cc_final: 0.7822 (ttpp) REVERT: A 118 MET cc_start: 0.8891 (mmm) cc_final: 0.8568 (mmm) REVERT: A 173 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: A 395 GLU cc_start: 0.8083 (tp30) cc_final: 0.7594 (tp30) REVERT: A 435 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6369 (ptt-90) REVERT: A 472 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7786 (m110) REVERT: A 494 GLN cc_start: 0.8653 (mm110) cc_final: 0.8225 (tm-30) REVERT: A 501 MET cc_start: 0.8257 (ttp) cc_final: 0.7705 (ptm) REVERT: A 523 MET cc_start: 0.7972 (ttp) cc_final: 0.7279 (tmm) REVERT: B 23 ASP cc_start: 0.7794 (t70) cc_final: 0.7255 (t0) REVERT: B 118 MET cc_start: 0.8966 (mmm) cc_final: 0.8576 (mmm) REVERT: B 158 MET cc_start: 0.7682 (ptt) cc_final: 0.7408 (ptt) REVERT: B 238 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7237 (tm-30) REVERT: B 357 MET cc_start: 0.7469 (mmp) cc_final: 0.7037 (mmp) REVERT: B 455 MET cc_start: 0.8484 (mmt) cc_final: 0.7916 (mmm) REVERT: B 465 MET cc_start: 0.8891 (tpt) cc_final: 0.8257 (tpp) REVERT: B 489 GLN cc_start: 0.8346 (mt0) cc_final: 0.8072 (tp40) REVERT: B 494 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 75 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7440 (mm) REVERT: C 94 LYS cc_start: 0.8582 (mmtt) cc_final: 0.7761 (tptt) REVERT: C 105 LYS cc_start: 0.8745 (tptt) cc_final: 0.7909 (ttpp) REVERT: C 118 MET cc_start: 0.8522 (mmm) cc_final: 0.8064 (mmm) REVERT: C 120 TYR cc_start: 0.9030 (t80) cc_final: 0.8783 (t80) REVERT: C 143 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8565 (m) REVERT: C 187 PHE cc_start: 0.8591 (t80) cc_final: 0.8283 (t80) REVERT: C 395 GLU cc_start: 0.7799 (tp30) cc_final: 0.7523 (tp30) REVERT: C 494 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8055 (tm-30) REVERT: C 501 MET cc_start: 0.8257 (mtp) cc_final: 0.7734 (mtm) REVERT: D 118 MET cc_start: 0.8889 (mmm) cc_final: 0.8562 (mmm) REVERT: D 185 ILE cc_start: 0.8834 (mt) cc_final: 0.8592 (mt) REVERT: D 225 GLU cc_start: 0.8234 (mp0) cc_final: 0.7982 (mp0) REVERT: D 227 LEU cc_start: 0.8788 (mt) cc_final: 0.8444 (mt) REVERT: D 238 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7235 (tm-30) REVERT: D 357 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7065 (mmp) REVERT: D 465 MET cc_start: 0.8685 (tpt) cc_final: 0.7974 (tpp) REVERT: D 498 GLN cc_start: 0.8728 (tp40) cc_final: 0.8085 (tm-30) REVERT: E 75 LEU cc_start: 0.8775 (mt) cc_final: 0.8541 (mt) REVERT: E 94 LYS cc_start: 0.8873 (mmtt) cc_final: 0.7965 (tptt) REVERT: E 105 LYS cc_start: 0.8462 (tptt) cc_final: 0.7636 (ttpp) REVERT: E 158 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7872 (ptp) REVERT: E 192 GLU cc_start: 0.6232 (pm20) cc_final: 0.5732 (pm20) REVERT: E 196 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8090 (ptmt) REVERT: E 252 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7245 (tp) REVERT: E 279 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9177 (tp) REVERT: E 352 LEU cc_start: 0.8965 (tp) cc_final: 0.8748 (tt) REVERT: E 465 MET cc_start: 0.8550 (tmm) cc_final: 0.8272 (tmm) REVERT: E 494 GLN cc_start: 0.8780 (mm110) cc_final: 0.8272 (tm-30) REVERT: E 523 MET cc_start: 0.8603 (tmm) cc_final: 0.7977 (tmm) REVERT: F 96 LEU cc_start: 0.9046 (mt) cc_final: 0.8835 (pp) REVERT: F 158 MET cc_start: 0.7474 (ptt) cc_final: 0.7103 (ptt) REVERT: F 179 MET cc_start: 0.8329 (mtm) cc_final: 0.8099 (mtm) REVERT: F 236 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: F 273 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9029 (tp) REVERT: F 455 MET cc_start: 0.8313 (mmm) cc_final: 0.7635 (mtt) REVERT: F 461 ILE cc_start: 0.9001 (mm) cc_final: 0.8558 (tp) REVERT: F 489 GLN cc_start: 0.8231 (mt0) cc_final: 0.7664 (tp40) REVERT: F 494 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8198 (mm-40) REVERT: G 94 LYS cc_start: 0.8974 (mmtt) cc_final: 0.7994 (tptt) REVERT: G 105 LYS cc_start: 0.8741 (tptt) cc_final: 0.7988 (mtpt) REVERT: G 120 TYR cc_start: 0.8709 (t80) cc_final: 0.8418 (t80) REVERT: G 173 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: G 206 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8566 (mmmt) REVERT: G 220 ASP cc_start: 0.6578 (t0) cc_final: 0.6316 (t0) REVERT: G 238 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7480 (mp10) REVERT: G 352 LEU cc_start: 0.8970 (tp) cc_final: 0.8667 (tp) REVERT: G 395 GLU cc_start: 0.7616 (tp30) cc_final: 0.7356 (tp30) REVERT: G 423 GLU cc_start: 0.8330 (pm20) cc_final: 0.7964 (pm20) REVERT: G 435 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.5914 (ptt90) REVERT: G 461 ILE cc_start: 0.8644 (mt) cc_final: 0.8344 (mt) REVERT: G 465 MET cc_start: 0.8460 (tpp) cc_final: 0.7851 (tpp) REVERT: G 494 GLN cc_start: 0.8759 (mm110) cc_final: 0.8241 (tm-30) REVERT: G 495 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: G 498 GLN cc_start: 0.8369 (tp40) cc_final: 0.8106 (tp-100) REVERT: G 501 MET cc_start: 0.8321 (ttp) cc_final: 0.7820 (ptm) REVERT: H 195 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7496 (mtp85) REVERT: H 323 ARG cc_start: 0.8273 (mtm110) cc_final: 0.7683 (mtm180) REVERT: H 489 GLN cc_start: 0.8138 (mt0) cc_final: 0.7663 (tp40) REVERT: H 512 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8044 (ptm) REVERT: I 94 LYS cc_start: 0.8553 (mmtt) cc_final: 0.7813 (tptt) REVERT: I 105 LYS cc_start: 0.8734 (tptt) cc_final: 0.7930 (ttpp) REVERT: I 143 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8847 (m) REVERT: I 228 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8421 (ttt-90) REVERT: I 241 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6836 (t0) REVERT: I 331 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: I 395 GLU cc_start: 0.7903 (tp30) cc_final: 0.7624 (tp30) REVERT: I 465 MET cc_start: 0.8830 (tpp) cc_final: 0.8273 (tpp) REVERT: I 494 GLN cc_start: 0.8703 (mm110) cc_final: 0.8356 (tm-30) REVERT: I 501 MET cc_start: 0.8153 (mtm) cc_final: 0.7940 (ptp) REVERT: I 523 MET cc_start: 0.8471 (tmm) cc_final: 0.7890 (tmm) REVERT: J 8 LEU cc_start: 0.4703 (tp) cc_final: 0.4269 (tp) REVERT: J 118 MET cc_start: 0.8940 (mmm) cc_final: 0.8688 (mmm) REVERT: J 158 MET cc_start: 0.7931 (ptt) cc_final: 0.7572 (ptt) REVERT: J 179 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7441 (mpp) REVERT: J 235 MET cc_start: 0.7223 (ttm) cc_final: 0.6850 (ttm) REVERT: J 236 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5572 (mp0) REVERT: J 289 MET cc_start: 0.8342 (mtt) cc_final: 0.8131 (mtt) REVERT: J 455 MET cc_start: 0.8550 (mpp) cc_final: 0.7912 (mtp) REVERT: J 468 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9210 (tt) REVERT: J 489 GLN cc_start: 0.8209 (mt0) cc_final: 0.7641 (tp40) REVERT: J 499 MET cc_start: 0.8181 (ptp) cc_final: 0.7870 (ptm) REVERT: K 94 LYS cc_start: 0.8694 (mmtt) cc_final: 0.7894 (tptt) REVERT: K 105 LYS cc_start: 0.8670 (tptt) cc_final: 0.8177 (mtmt) REVERT: K 173 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: K 241 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7075 (t0) REVERT: K 395 GLU cc_start: 0.7894 (tp30) cc_final: 0.7522 (tp30) REVERT: K 435 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.5824 (ptt90) REVERT: K 494 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8339 (tm-30) REVERT: K 499 MET cc_start: 0.8649 (tmm) cc_final: 0.8396 (tmm) REVERT: L 74 MET cc_start: 0.8548 (tpt) cc_final: 0.8159 (tpt) REVERT: L 118 MET cc_start: 0.9175 (mmm) cc_final: 0.8911 (mmm) REVERT: L 179 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7381 (mpp) REVERT: L 236 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: L 406 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7984 (pttm) REVERT: L 455 MET cc_start: 0.8549 (mpp) cc_final: 0.7779 (mtt) REVERT: L 461 ILE cc_start: 0.8870 (mm) cc_final: 0.8501 (tp) REVERT: L 465 MET cc_start: 0.8684 (tpp) cc_final: 0.8078 (tpp) REVERT: L 501 MET cc_start: 0.8343 (mtp) cc_final: 0.7746 (ptp) outliers start: 176 outliers final: 130 residues processed: 1110 average time/residue: 0.5487 time to fit residues: 1041.0396 Evaluate side-chains 1096 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 938 time to evaluate : 5.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 143 VAL 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 318 ASP 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 435 ARG Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 49 ASN 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 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 392 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 318 ASP 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 404 LEU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 252 ILE 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 333 GLU 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 E residue 530 VAL Chi-restraints excluded: chain F residue 8 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 273 LEU 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 390 SER Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain G residue 49 ASN 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 377 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 495 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 236 GLU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 318 ASP Chi-restraints excluded: chain H residue 445 CYS Chi-restraints excluded: chain H residue 512 MET Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 173 PHE Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 331 GLN Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 391 ILE Chi-restraints excluded: chain I residue 435 ARG 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 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 384 THR Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 468 LEU Chi-restraints excluded: chain J residue 481 ILE Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 208 ASP 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 435 ARG 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 11 ASP Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 236 GLU 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 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 0.6980 chunk 527 optimal weight: 0.0970 chunk 151 optimal weight: 0.3980 chunk 456 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 495 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 509 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 331 GLN ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 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** ** J 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.135752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111561 restraints weight = 87617.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114687 restraints weight = 41453.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116676 restraints weight = 25463.163| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.6135 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= 0.171 Angle : 0.722 12.821 66912 Z= 0.344 Chirality : 0.043 0.270 7572 Planarity : 0.004 0.056 8832 Dihedral : 5.099 32.007 6876 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.59 % Favored : 91.17 % Rotamer: Outliers : 3.05 % Allowed : 22.54 % Favored : 74.40 % 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: -0.21 (0.11), residues: 6252 helix: 1.54 (0.10), residues: 2976 sheet: -0.61 (0.23), residues: 528 loop : -2.05 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 83 HIS 0.002 0.000 HIS F 216 PHE 0.033 0.002 PHE E 78 TYR 0.019 0.001 TYR H 389 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: 16421.96 seconds wall clock time: 295 minutes 37.58 seconds (17737.58 seconds total)