Starting phenix.real_space_refine on Sat Jun 28 09:12:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua9_42055/06_2025/8ua9_42055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua9_42055/06_2025/8ua9_42055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ua9_42055/06_2025/8ua9_42055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua9_42055/06_2025/8ua9_42055.map" model { file = "/net/cci-nas-00/data/ceres_data/8ua9_42055/06_2025/8ua9_42055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua9_42055/06_2025/8ua9_42055.cif" } resolution = 3.0 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= 0.012 sd= 0.073 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 228 5.16 5 C 20992 2.51 5 N 5725 2.21 5 O 6161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33106 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 411} Chain: "B" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3284 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 32, 'TRANS': 385} Chain: "C" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 422 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "D" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "E" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "F" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3284 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 32, 'TRANS': 385} Chain: "G" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 422 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "H" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "I" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 411} Chain: "J" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3284 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 32, 'TRANS': 385} Chain: "K" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 422 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "L" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "M" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 411} Chain: "N" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3284 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 32, 'TRANS': 385} Chain: "O" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 422 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "P" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.60, per 1000 atoms: 0.56 Number of scatterers: 33106 At special positions: 0 Unit cell: (199.28, 203.52, 160.06, 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 228 16.00 O 6161 8.00 N 5725 7.00 C 20992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=61, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=1.92 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.43 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.13 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.14 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=1.85 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.54 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 122 " distance=2.21 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=1.68 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 103 " distance=2.00 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 263 " distance=1.99 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 223 " distance=2.60 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 217 " distance=2.58 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 16 " distance=1.76 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 56 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.12 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.32 Simple disulfide: pdb=" SG CYS E 260 " - pdb=" SG CYS E 272 " distance=2.11 Simple disulfide: pdb=" SG CYS E 302 " - pdb=" SG CYS E 377 " distance=1.90 Simple disulfide: pdb=" SG CYS E 307 " - pdb=" SG CYS E 381 " distance=1.92 Simple disulfide: pdb=" SG CYS E 329 " - pdb=" SG CYS E 371 " distance=2.84 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 122 " distance=2.19 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 27 " distance=2.28 Simple disulfide: pdb=" SG CYS F 89 " - pdb=" SG CYS F 103 " distance=1.99 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 263 " distance=1.92 Simple disulfide: pdb=" SG CYS F 199 " - pdb=" SG CYS F 223 " distance=2.26 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 217 " distance=1.91 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS G 16 " distance=1.99 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 25 " distance=1.82 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 56 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 114 " distance=1.84 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 94 " distance=2.68 Simple disulfide: pdb=" SG CYS I 68 " - pdb=" SG CYS I 78 " distance=2.81 Simple disulfide: pdb=" SG CYS I 260 " - pdb=" SG CYS I 272 " distance=2.51 Simple disulfide: pdb=" SG CYS I 302 " - pdb=" SG CYS I 377 " distance=1.97 Simple disulfide: pdb=" SG CYS I 307 " - pdb=" SG CYS I 381 " distance=1.96 Simple disulfide: pdb=" SG CYS I 329 " - pdb=" SG CYS I 371 " distance=2.68 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 122 " distance=2.37 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 27 " distance=1.67 Simple disulfide: pdb=" SG CYS J 89 " - pdb=" SG CYS J 103 " distance=2.12 Simple disulfide: pdb=" SG CYS J 150 " - pdb=" SG CYS J 263 " distance=1.87 Simple disulfide: pdb=" SG CYS J 199 " - pdb=" SG CYS J 223 " distance=2.13 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 217 " distance=2.39 Simple disulfide: pdb=" SG CYS K 7 " - pdb=" SG CYS K 16 " distance=2.65 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 56 " distance=2.04 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 114 " distance=2.03 Simple disulfide: pdb=" SG CYS M 62 " - pdb=" SG CYS M 94 " distance=2.60 Simple disulfide: pdb=" SG CYS M 63 " - pdb=" SG CYS M 96 " distance=2.55 Simple disulfide: pdb=" SG CYS M 68 " - pdb=" SG CYS M 78 " distance=2.76 Simple disulfide: pdb=" SG CYS M 260 " - pdb=" SG CYS M 272 " distance=2.70 Simple disulfide: pdb=" SG CYS M 302 " - pdb=" SG CYS M 377 " distance=2.04 Simple disulfide: pdb=" SG CYS M 307 " - pdb=" SG CYS M 381 " distance=2.03 Simple disulfide: pdb=" SG CYS M 329 " - pdb=" SG CYS M 371 " distance=1.96 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 122 " distance=2.40 Simple disulfide: pdb=" SG CYS N 89 " - pdb=" SG CYS N 103 " distance=2.00 Simple disulfide: pdb=" SG CYS N 150 " - pdb=" SG CYS N 263 " distance=2.19 Simple disulfide: pdb=" SG CYS N 199 " - pdb=" SG CYS N 223 " distance=2.29 Simple disulfide: pdb=" SG CYS N 201 " - pdb=" SG CYS N 217 " distance=1.94 Simple disulfide: pdb=" SG CYS O 7 " - pdb=" SG CYS O 16 " distance=2.41 Simple disulfide: pdb=" SG CYS O 21 " - pdb=" SG CYS O 25 " distance=2.65 Simple disulfide: pdb=" SG CYS O 24 " - pdb=" SG CYS O 56 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 134 " " NAG B 501 " - " ASN B 315 " " NAG E 501 " - " ASN E 134 " " NAG F 501 " - " ASN F 315 " " NAG G 101 " - " ASN G 11 " " NAG I 501 " - " ASN I 134 " " NAG J 501 " - " ASN J 315 " " NAG M 501 " - " ASN M 134 " " NAG N 501 " - " ASN N 315 " Time building additional restraints: 8.69 Conformation dependent library (CDL) restraints added in 4.6 seconds 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7896 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 81 sheets defined 16.3% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.887A pdb=" N SER A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 248 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.650A pdb=" N THR A 294 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 441 removed outlier: 3.953A pdb=" N ALA A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 9 through 12 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 348 through 360 Processing helix chain 'B' and resid 360 through 400 removed outlier: 3.541A pdb=" N THR B 364 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 375 " --> pdb=" O CYS B 371 " (cutoff:3.500A) Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.756A pdb=" N LEU C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 removed outlier: 3.935A pdb=" N ALA D 150 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 151 " --> pdb=" O LEU D 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 151' Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.900A pdb=" N SER E 115 " --> pdb=" O GLU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 248 Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 290 through 294 removed outlier: 3.577A pdb=" N THR E 294 " --> pdb=" O ILE E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 441 removed outlier: 3.883A pdb=" N ALA E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 10 through 12 No H-bonds generated for 'chain 'F' and resid 10 through 12' Processing helix chain 'F' and resid 348 through 360 Processing helix chain 'F' and resid 364 through 400 removed outlier: 3.795A pdb=" N ILE F 374 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE F 375 " --> pdb=" O CYS F 371 " (cutoff:3.500A) Proline residue: F 396 - end of helix Processing helix chain 'F' and resid 406 through 413 Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 45 through 55 removed outlier: 3.752A pdb=" N LEU G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 150 removed outlier: 3.548A pdb=" N ALA H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 171 Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.857A pdb=" N SER I 115 " --> pdb=" O GLU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 248 Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 257 through 260 Processing helix chain 'I' and resid 290 through 294 removed outlier: 3.667A pdb=" N THR I 294 " --> pdb=" O ILE I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 441 removed outlier: 3.814A pdb=" N ALA I 407 " --> pdb=" O ILE I 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 8 through 12 removed outlier: 4.137A pdb=" N LEU J 11 " --> pdb=" O GLN J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 219 through 221 No H-bonds generated for 'chain 'J' and resid 219 through 221' Processing helix chain 'J' and resid 348 through 360 Processing helix chain 'J' and resid 360 through 400 removed outlier: 3.652A pdb=" N THR J 364 " --> pdb=" O TYR J 360 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE J 365 " --> pdb=" O PRO J 361 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE J 366 " --> pdb=" O LEU J 362 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY J 367 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE J 374 " --> pdb=" O THR J 370 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE J 375 " --> pdb=" O CYS J 371 " (cutoff:3.500A) Proline residue: J 396 - end of helix Processing helix chain 'J' and resid 406 through 413 Processing helix chain 'K' and resid 29 through 40 Processing helix chain 'K' and resid 45 through 55 removed outlier: 3.624A pdb=" N LEU K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 150 Processing helix chain 'L' and resid 157 through 159 No H-bonds generated for 'chain 'L' and resid 157 through 159' Processing helix chain 'L' and resid 167 through 171 Processing helix chain 'M' and resid 112 through 116 removed outlier: 3.985A pdb=" N SER M 115 " --> pdb=" O GLU M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 248 Processing helix chain 'M' and resid 251 through 256 Processing helix chain 'M' and resid 257 through 260 Processing helix chain 'M' and resid 290 through 294 removed outlier: 3.614A pdb=" N THR M 294 " --> pdb=" O ILE M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 441 removed outlier: 3.885A pdb=" N ALA M 407 " --> pdb=" O ILE M 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 12 removed outlier: 3.856A pdb=" N LYS N 10 " --> pdb=" O THR N 7 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU N 11 " --> pdb=" O GLN N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 360 Processing helix chain 'N' and resid 360 through 400 removed outlier: 3.929A pdb=" N ILE N 365 " --> pdb=" O PRO N 361 " (cutoff:3.500A) Proline residue: N 396 - end of helix Processing helix chain 'N' and resid 408 through 413 Processing helix chain 'O' and resid 29 through 40 removed outlier: 3.862A pdb=" N THR O 33 " --> pdb=" O ASN O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 55 Processing helix chain 'P' and resid 157 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.518A pdb=" N LYS A 161 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21 removed outlier: 5.213A pdb=" N ARG A 21 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE A 31 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU A 33 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN A 134 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 35 " --> pdb=" O MET A 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 145 through 148 current: chain 'A' and resid 268 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 186 removed outlier: 6.397A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 101 through 110 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 307 removed outlier: 4.648A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 347 Processing sheet with id=AA8, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.530A pdb=" N GLU B 35 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 84 Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 153 Processing sheet with id=AB4, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AB5, first strand: chain 'B' and resid 166 through 167 Processing sheet with id=AB6, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.575A pdb=" N GLN B 194 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.697A pdb=" N ILE B 187 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 272 through 276 Processing sheet with id=AB9, first strand: chain 'C' and resid 6 through 9 Processing sheet with id=AC1, first strand: chain 'D' and resid 113 through 118 removed outlier: 6.257A pdb=" N PHE D 114 " --> pdb=" O TYR D 125 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR D 125 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 116 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N TYR D 125 " --> pdb=" O PRO D 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 250 through 253 removed outlier: 6.921A pdb=" N ARG D 236 " --> pdb=" O ASN D 232 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN D 232 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA D 238 " --> pdb=" O GLY D 230 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY D 230 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER D 240 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TRP D 244 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N VAL D 224 " --> pdb=" O TRP D 244 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE D 216 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ALA D 192 " --> pdb=" O PRO D 203 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE D 200 " --> pdb=" O LEU D 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 2 through 8 removed outlier: 3.604A pdb=" N LYS E 161 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 15 through 21 removed outlier: 5.406A pdb=" N ARG E 21 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA E 25 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE E 31 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU E 33 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN E 134 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN E 35 " --> pdb=" O MET E 132 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR E 128 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR E 126 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN E 43 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU E 45 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N TYR E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE E 47 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS E 120 " --> pdb=" O ILE E 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 145 through 148 current: chain 'E' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 184 through 186 current: chain 'E' and resid 215 through 216 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 215 through 216 current: chain 'E' and resid 268 through 270 Processing sheet with id=AC5, first strand: chain 'E' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 54 current: chain 'E' and resid 101 through 110 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 221 through 222 Processing sheet with id=AC7, first strand: chain 'E' and resid 297 through 307 removed outlier: 4.501A pdb=" N ASP E 299 " --> pdb=" O LYS E 322 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS E 322 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE E 316 " --> pdb=" O THR E 305 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 344 through 347 Processing sheet with id=AC9, first strand: chain 'E' and resid 388 through 389 Processing sheet with id=AD1, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AD2, first strand: chain 'F' and resid 35 through 37 removed outlier: 3.547A pdb=" N GLU F 35 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR F 64 " --> pdb=" O GLY F 54 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 82 through 84 Processing sheet with id=AD4, first strand: chain 'F' and resid 146 through 153 Processing sheet with id=AD5, first strand: chain 'F' and resid 163 through 164 Processing sheet with id=AD6, first strand: chain 'F' and resid 166 through 167 Processing sheet with id=AD7, first strand: chain 'F' and resid 172 through 173 Processing sheet with id=AD8, first strand: chain 'F' and resid 178 through 181 removed outlier: 3.637A pdb=" N ILE F 187 " --> pdb=" O HIS F 213 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 272 through 276 Processing sheet with id=AE1, first strand: chain 'G' and resid 6 through 9 Processing sheet with id=AE2, first strand: chain 'H' and resid 114 through 117 removed outlier: 5.957A pdb=" N PHE H 114 " --> pdb=" O TYR H 125 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR H 125 " --> pdb=" O PHE H 114 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE H 116 " --> pdb=" O ASN H 123 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N TYR H 125 " --> pdb=" O PRO H 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 184 through 188 removed outlier: 8.272A pdb=" N ALA H 192 " --> pdb=" O PRO H 203 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 199 through 203 current: chain 'H' and resid 223 through 233 removed outlier: 8.732A pdb=" N VAL H 224 " --> pdb=" O TRP H 244 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP H 244 " --> pdb=" O VAL H 224 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER H 240 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY H 230 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA H 238 " --> pdb=" O GLY H 230 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN H 232 " --> pdb=" O ARG H 236 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG H 236 " --> pdb=" O ASN H 232 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 2 through 8 Processing sheet with id=AE5, first strand: chain 'I' and resid 15 through 21 removed outlier: 5.308A pdb=" N ARG I 21 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA I 25 " --> pdb=" O ARG I 21 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE I 31 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR I 136 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU I 33 " --> pdb=" O ASN I 134 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN I 134 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN I 35 " --> pdb=" O MET I 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 145 through 148 current: chain 'I' and resid 268 through 270 Processing sheet with id=AE6, first strand: chain 'I' and resid 44 through 48 removed outlier: 6.812A pdb=" N ALA I 121 " --> pdb=" O GLU I 45 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE I 47 " --> pdb=" O ALA I 119 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA I 119 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 51 through 54 current: chain 'I' and resid 101 through 110 No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'I' and resid 204 through 205 Processing sheet with id=AE9, first strand: chain 'I' and resid 221 through 222 Processing sheet with id=AF1, first strand: chain 'I' and resid 297 through 307 removed outlier: 4.457A pdb=" N ASP I 299 " --> pdb=" O LYS I 322 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS I 322 " --> pdb=" O ASP I 299 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE I 316 " --> pdb=" O THR I 305 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 344 through 347 Processing sheet with id=AF3, first strand: chain 'I' and resid 388 through 389 Processing sheet with id=AF4, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AF5, first strand: chain 'J' and resid 35 through 37 removed outlier: 3.504A pdb=" N GLU J 35 " --> pdb=" O GLN J 48 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR J 64 " --> pdb=" O GLY J 54 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 82 through 84 Processing sheet with id=AF7, first strand: chain 'J' and resid 146 through 153 Processing sheet with id=AF8, first strand: chain 'J' and resid 163 through 164 Processing sheet with id=AF9, first strand: chain 'J' and resid 166 through 167 Processing sheet with id=AG1, first strand: chain 'J' and resid 171 through 173 Processing sheet with id=AG2, first strand: chain 'J' and resid 178 through 181 Processing sheet with id=AG3, first strand: chain 'J' and resid 272 through 276 Processing sheet with id=AG4, first strand: chain 'K' and resid 6 through 9 Processing sheet with id=AG5, first strand: chain 'L' and resid 113 through 118 removed outlier: 3.861A pdb=" N GLY L 124 " --> pdb=" O ILE L 116 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU L 118 " --> pdb=" O VAL L 122 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL L 122 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N TYR L 125 " --> pdb=" O PRO L 136 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 199 through 203 current: chain 'L' and resid 223 through 233 removed outlier: 8.953A pdb=" N VAL L 224 " --> pdb=" O TRP L 244 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP L 244 " --> pdb=" O VAL L 224 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 226 " --> pdb=" O VAL L 242 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N SER L 240 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY L 230 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA L 238 " --> pdb=" O GLY L 230 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN L 232 " --> pdb=" O ARG L 236 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ARG L 236 " --> pdb=" O ASN L 232 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 2 through 8 Processing sheet with id=AG8, first strand: chain 'M' and resid 15 through 21 removed outlier: 5.212A pdb=" N ARG M 21 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA M 25 " --> pdb=" O ARG M 21 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET M 132 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR M 36 " --> pdb=" O GLN M 130 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN M 130 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE M 38 " --> pdb=" O THR M 128 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR M 128 " --> pdb=" O ILE M 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 145 through 148 current: chain 'M' and resid 268 through 270 Processing sheet with id=AG9, first strand: chain 'M' and resid 184 through 186 removed outlier: 6.502A pdb=" N ALA M 119 " --> pdb=" O ILE M 47 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE M 47 " --> pdb=" O ALA M 119 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA M 121 " --> pdb=" O GLU M 45 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 51 through 54 current: chain 'M' and resid 101 through 110 No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'M' and resid 221 through 222 Processing sheet with id=AH3, first strand: chain 'M' and resid 301 through 307 removed outlier: 4.443A pdb=" N ILE M 316 " --> pdb=" O THR M 305 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 344 through 347 Processing sheet with id=AH5, first strand: chain 'M' and resid 388 through 389 Processing sheet with id=AH6, first strand: chain 'N' and resid 17 through 19 Processing sheet with id=AH7, first strand: chain 'N' and resid 35 through 37 removed outlier: 5.593A pdb=" N TYR N 97 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N ALA N 51 " --> pdb=" O HIS N 95 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N HIS N 95 " --> pdb=" O ALA N 51 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N PHE N 53 " --> pdb=" O SER N 93 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N SER N 93 " --> pdb=" O PHE N 53 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 64 through 67 Processing sheet with id=AH9, first strand: chain 'N' and resid 82 through 84 Processing sheet with id=AI1, first strand: chain 'N' and resid 146 through 153 Processing sheet with id=AI2, first strand: chain 'N' and resid 163 through 164 Processing sheet with id=AI3, first strand: chain 'N' and resid 166 through 167 Processing sheet with id=AI4, first strand: chain 'N' and resid 172 through 173 Processing sheet with id=AI5, first strand: chain 'N' and resid 178 through 180 removed outlier: 3.540A pdb=" N VAL N 185 " --> pdb=" O THR N 215 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 272 through 276 Processing sheet with id=AI7, first strand: chain 'O' and resid 6 through 9 Processing sheet with id=AI8, first strand: chain 'P' and resid 113 through 116 removed outlier: 3.768A pdb=" N GLY P 124 " --> pdb=" O ILE P 116 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU P 161 " --> pdb=" O ALA P 156 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 184 through 188 removed outlier: 8.451A pdb=" N ALA P 192 " --> pdb=" O PRO P 203 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 200 through 203 current: chain 'P' and resid 223 through 233 removed outlier: 8.740A pdb=" N VAL P 224 " --> pdb=" O TRP P 244 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP P 244 " --> pdb=" O VAL P 224 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE P 226 " --> pdb=" O VAL P 242 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER P 240 " --> pdb=" O LEU P 228 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY P 230 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA P 238 " --> pdb=" O GLY P 230 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASN P 232 " --> pdb=" O ARG P 236 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG P 236 " --> pdb=" O ASN P 232 " (cutoff:3.500A) 1153 hydrogen bonds defined for protein. 2949 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: 12.10 Time building geometry restraints manager: 9.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 11036 1.35 - 1.49: 9580 1.49 - 1.63: 13106 1.63 - 1.77: 41 1.77 - 1.91: 243 Bond restraints: 34006 Sorted by residual: bond pdb=" CB CYS M 272 " pdb=" SG CYS M 272 " ideal model delta sigma weight residual 1.808 1.648 0.160 3.30e-02 9.18e+02 2.36e+01 bond pdb=" CB CYS E 371 " pdb=" SG CYS E 371 " ideal model delta sigma weight residual 1.808 1.668 0.140 3.30e-02 9.18e+02 1.80e+01 bond pdb=" CB CYS A 329 " pdb=" SG CYS A 329 " ideal model delta sigma weight residual 1.808 1.678 0.130 3.30e-02 9.18e+02 1.55e+01 bond pdb=" CB CYS A 371 " pdb=" SG CYS A 371 " ideal model delta sigma weight residual 1.808 1.685 0.123 3.30e-02 9.18e+02 1.38e+01 bond pdb=" CB CYS I 329 " pdb=" SG CYS I 329 " ideal model delta sigma weight residual 1.808 1.686 0.122 3.30e-02 9.18e+02 1.36e+01 ... (remaining 34001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 44519 2.97 - 5.94: 1657 5.94 - 8.91: 161 8.91 - 11.88: 21 11.88 - 14.85: 5 Bond angle restraints: 46363 Sorted by residual: angle pdb=" CA PRO L 255 " pdb=" N PRO L 255 " pdb=" CD PRO L 255 " ideal model delta sigma weight residual 112.00 97.15 14.85 1.40e+00 5.10e-01 1.12e+02 angle pdb=" CA PRO B 401 " pdb=" N PRO B 401 " pdb=" CD PRO B 401 " ideal model delta sigma weight residual 112.00 100.38 11.62 1.40e+00 5.10e-01 6.89e+01 angle pdb=" CA PRO D 182 " pdb=" N PRO D 182 " pdb=" CD PRO D 182 " ideal model delta sigma weight residual 112.00 102.39 9.61 1.40e+00 5.10e-01 4.71e+01 angle pdb=" CA CYS M 260 " pdb=" CB CYS M 260 " pdb=" SG CYS M 260 " ideal model delta sigma weight residual 114.40 129.25 -14.85 2.30e+00 1.89e-01 4.17e+01 angle pdb=" CA TYR L 163 " pdb=" CB TYR L 163 " pdb=" CG TYR L 163 " ideal model delta sigma weight residual 113.90 102.55 11.35 1.80e+00 3.09e-01 3.98e+01 ... (remaining 46358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 17175 17.90 - 35.79: 2520 35.79 - 53.69: 697 53.69 - 71.58: 109 71.58 - 89.48: 31 Dihedral angle restraints: 20532 sinusoidal: 8208 harmonic: 12324 Sorted by residual: dihedral pdb=" CA GLU E 265 " pdb=" C GLU E 265 " pdb=" N PRO E 266 " pdb=" CA PRO E 266 " ideal model delta harmonic sigma weight residual -180.00 -95.14 -84.86 0 5.00e+00 4.00e-02 2.88e+02 dihedral pdb=" CA CYS B 201 " pdb=" C CYS B 201 " pdb=" N PRO B 202 " pdb=" CA PRO B 202 " ideal model delta harmonic sigma weight residual -180.00 -119.68 -60.32 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CB CYS M 329 " pdb=" SG CYS M 329 " pdb=" SG CYS M 371 " pdb=" CB CYS M 371 " ideal model delta sinusoidal sigma weight residual 93.00 -177.52 -89.48 1 1.00e+01 1.00e-02 9.51e+01 ... (remaining 20529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 4608 0.113 - 0.226: 549 0.226 - 0.339: 25 0.339 - 0.451: 7 0.451 - 0.564: 4 Chirality restraints: 5193 Sorted by residual: chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 134 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.96e+00 chirality pdb=" C1 NAG I 501 " pdb=" ND2 ASN I 134 " pdb=" C2 NAG I 501 " pdb=" O5 NAG I 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 134 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.22e+00 ... (remaining 5190 not shown) Planarity restraints: 5974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 400 " 0.110 5.00e-02 4.00e+02 1.58e-01 4.00e+01 pdb=" N PRO B 401 " -0.273 5.00e-02 4.00e+02 pdb=" CA PRO B 401 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO B 401 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 254 " 0.107 5.00e-02 4.00e+02 1.48e-01 3.49e+01 pdb=" N PRO L 255 " -0.255 5.00e-02 4.00e+02 pdb=" CA PRO L 255 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO L 255 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 181 " -0.087 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO D 182 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO D 182 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 182 " -0.067 5.00e-02 4.00e+02 ... (remaining 5971 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 369 2.57 - 3.15: 26901 3.15 - 3.73: 49813 3.73 - 4.32: 69096 4.32 - 4.90: 119827 Nonbonded interactions: 266006 Sorted by model distance: nonbonded pdb=" O CYS K 25 " pdb=" OG1 THR K 33 " model vdw 1.983 3.040 nonbonded pdb=" O CYS C 25 " pdb=" OG1 THR C 33 " model vdw 1.984 3.040 nonbonded pdb=" O ALA M 402 " pdb=" OH TYR N 356 " model vdw 1.997 3.040 nonbonded pdb=" OE2 GLU I 2 " pdb=" OG SER I 280 " model vdw 2.001 3.040 nonbonded pdb=" O PRO H 182 " pdb=" OH TYR H 186 " model vdw 2.041 3.040 ... (remaining 266001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 4 through 57) selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 71.320 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.180 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.020 0.812 34076 Z= 0.942 Angle : 1.331 66.950 46512 Z= 0.716 Chirality : 0.074 0.564 5193 Planarity : 0.012 0.158 5965 Dihedral : 17.851 88.906 12453 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.02 % Favored : 98.93 % Rotamer: Outliers : 3.56 % Allowed : 32.04 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.23 % 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: -1.54 (0.12), residues: 4224 helix: -0.34 (0.21), residues: 536 sheet: -0.69 (0.14), residues: 1336 loop : -1.37 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 384 HIS 0.025 0.003 HIS J 126 PHE 0.054 0.004 PHE J 6 TYR 0.085 0.004 TYR F 163 ARG 0.025 0.001 ARG D 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 9) link_NAG-ASN : angle 2.64710 ( 27) hydrogen bonds : bond 0.12744 ( 1153) hydrogen bonds : angle 7.35734 ( 2949) SS BOND : bond 0.34444 ( 61) SS BOND : angle 8.39793 ( 122) covalent geometry : bond 0.01397 (34006) covalent geometry : angle 1.25965 (46363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1085 time to evaluate : 3.484 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 109 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 325 LYS cc_start: 0.8604 (ptmm) cc_final: 0.8274 (pttm) REVERT: B 6 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7114 (t80) REVERT: B 19 CYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7642 (t) REVERT: B 363 THR cc_start: 0.8648 (m) cc_final: 0.8419 (t) REVERT: D 214 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7904 (mtt180) REVERT: E 156 LYS cc_start: 0.8586 (tppt) cc_final: 0.8207 (tppt) REVERT: E 255 VAL cc_start: 0.8613 (t) cc_final: 0.8387 (m) REVERT: E 440 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7855 (mtm-85) REVERT: F 111 VAL cc_start: 0.8700 (t) cc_final: 0.8439 (m) REVERT: F 157 ARG cc_start: 0.4462 (OUTLIER) cc_final: 0.4182 (mpp-170) REVERT: F 385 LEU cc_start: 0.8495 (tt) cc_final: 0.8239 (tt) REVERT: H 129 VAL cc_start: 0.8368 (t) cc_final: 0.8168 (p) REVERT: H 220 LYS cc_start: 0.8221 (mptt) cc_final: 0.7870 (mptt) REVERT: I 321 TYR cc_start: 0.8376 (p90) cc_final: 0.8033 (p90) REVERT: J 6 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7064 (t80) REVERT: J 208 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8312 (tt) REVERT: J 398 LYS cc_start: 0.8110 (tmtt) cc_final: 0.7771 (ttpt) REVERT: L 117 MET cc_start: 0.7009 (mmp) cc_final: 0.6574 (mmp) REVERT: L 242 VAL cc_start: 0.8730 (t) cc_final: 0.8318 (m) REVERT: M 61 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7824 (tppp) REVERT: M 71 LYS cc_start: 0.8149 (mttt) cc_final: 0.7946 (mttm) REVERT: M 117 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7768 (p0) REVERT: M 291 ILE cc_start: 0.8695 (tp) cc_final: 0.8440 (tt) REVERT: N 166 MET cc_start: 0.8550 (mmm) cc_final: 0.7989 (mmm) REVERT: N 227 LEU cc_start: 0.8190 (tt) cc_final: 0.7930 (tm) REVERT: N 344 ASN cc_start: 0.8450 (t0) cc_final: 0.8240 (t0) outliers start: 130 outliers final: 88 residues processed: 1175 average time/residue: 1.3695 time to fit residues: 1930.1170 Evaluate side-chains 1153 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1058 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 252 LYS Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 157 ARG Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 402 ASN Chi-restraints excluded: chain G residue 27 GLU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 256 GLU Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 125 HIS Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 400 THR Chi-restraints excluded: chain I residue 421 PHE Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 19 CYS Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 378 SER Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 387 CYS Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain M residue 97 ASP Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 125 HIS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 261 SER Chi-restraints excluded: chain M residue 302 CYS Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain N residue 8 GLN Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 305 ARG Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 240 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 381 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 67 GLN A 176 ASN B 302 ASN C 40 ASN E 28 HIS E 32 GLN E 77 GLN E 223 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 222 GLN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN I 332 HIS J 24 HIS J 69 ASN J 126 HIS L 194 GLN L 197 ASN M 9 ASN M 35 ASN M 363 HIS M 369 GLN N 8 GLN N 21 ASN ** N 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 236 ASN N 285 HIS N 344 ASN O 18 GLN O 40 ASN P 145 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114014 restraints weight = 52228.299| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.26 r_work: 0.3306 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34076 Z= 0.181 Angle : 0.734 12.965 46512 Z= 0.377 Chirality : 0.050 0.397 5193 Planarity : 0.007 0.111 5965 Dihedral : 7.709 76.296 4937 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.80 % Favored : 94.03 % Rotamer: Outliers : 6.14 % Allowed : 27.08 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.03 % 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: -1.00 (0.13), residues: 4224 helix: 0.72 (0.21), residues: 556 sheet: -0.57 (0.14), residues: 1340 loop : -1.04 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 188 HIS 0.009 0.001 HIS J 126 PHE 0.019 0.002 PHE L 134 TYR 0.024 0.002 TYR L 177 ARG 0.008 0.001 ARG H 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 9) link_NAG-ASN : angle 2.72304 ( 27) hydrogen bonds : bond 0.04169 ( 1153) hydrogen bonds : angle 5.96803 ( 2949) SS BOND : bond 0.00515 ( 61) SS BOND : angle 2.34845 ( 122) covalent geometry : bond 0.00409 (34006) covalent geometry : angle 0.72225 (46363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 1095 time to evaluate : 3.613 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: A 4 THR cc_start: 0.8642 (p) cc_final: 0.8390 (m) REVERT: A 30 GLN cc_start: 0.8462 (tt0) cc_final: 0.8257 (tt0) REVERT: A 37 ARG cc_start: 0.8960 (mpp80) cc_final: 0.8623 (mtm180) REVERT: A 50 LYS cc_start: 0.8553 (tttm) cc_final: 0.8097 (tttm) REVERT: A 54 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8140 (ttpp) REVERT: A 75 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: A 88 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7600 (ptp) REVERT: A 109 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7739 (mt-10) REVERT: A 192 GLU cc_start: 0.7087 (tt0) cc_final: 0.6791 (tt0) REVERT: A 211 SER cc_start: 0.8147 (m) cc_final: 0.7675 (p) REVERT: A 242 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 245 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8379 (mtmt) REVERT: A 279 ILE cc_start: 0.8698 (pt) cc_final: 0.8497 (pt) REVERT: B 6 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7036 (t80) REVERT: B 62 LEU cc_start: 0.8553 (mt) cc_final: 0.8284 (mt) REVERT: B 172 VAL cc_start: 0.8493 (t) cc_final: 0.8230 (p) REVERT: B 200 LYS cc_start: 0.8186 (tmtt) cc_final: 0.7927 (tmtt) REVERT: B 210 SER cc_start: 0.8331 (t) cc_final: 0.7964 (p) REVERT: B 274 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8172 (mt-10) REVERT: B 300 ASP cc_start: 0.7965 (t0) cc_final: 0.7737 (t0) REVERT: B 376 MET cc_start: 0.7217 (tpp) cc_final: 0.7006 (tpp) REVERT: B 399 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7702 (mm) REVERT: D 117 MET cc_start: 0.6294 (tmm) cc_final: 0.5951 (tmm) REVERT: D 206 VAL cc_start: 0.7005 (OUTLIER) cc_final: 0.6797 (t) REVERT: E 16 LYS cc_start: 0.8927 (mttt) cc_final: 0.8699 (mttt) REVERT: E 54 LYS cc_start: 0.8699 (tttt) cc_final: 0.8352 (tttt) REVERT: E 103 MET cc_start: 0.8545 (ttm) cc_final: 0.8336 (ttm) REVERT: E 113 GLU cc_start: 0.7704 (mp0) cc_final: 0.7275 (mp0) REVERT: E 156 LYS cc_start: 0.8645 (tppt) cc_final: 0.8297 (tppt) REVERT: E 305 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8237 (p) REVERT: F 74 LYS cc_start: 0.8892 (ptmt) cc_final: 0.8692 (tttp) REVERT: F 136 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7268 (mt-10) REVERT: F 175 HIS cc_start: 0.8307 (p-80) cc_final: 0.8095 (p90) REVERT: F 178 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8014 (mm) REVERT: F 217 CYS cc_start: 0.7485 (m) cc_final: 0.7179 (m) REVERT: F 259 VAL cc_start: 0.8696 (p) cc_final: 0.8405 (m) REVERT: F 370 THR cc_start: 0.8106 (t) cc_final: 0.7830 (p) REVERT: G 22 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6910 (mmp) REVERT: G 48 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7607 (mm-40) REVERT: H 129 VAL cc_start: 0.8331 (t) cc_final: 0.8042 (p) REVERT: H 132 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6513 (mtt90) REVERT: I 69 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8096 (p) REVERT: I 96 CYS cc_start: 0.8017 (t) cc_final: 0.7704 (t) REVERT: I 137 TYR cc_start: 0.8729 (p90) cc_final: 0.8173 (p90) REVERT: I 246 LYS cc_start: 0.8544 (pttt) cc_final: 0.8150 (ptmm) REVERT: I 296 THR cc_start: 0.8752 (p) cc_final: 0.8533 (t) REVERT: I 305 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8360 (p) REVERT: I 426 LEU cc_start: 0.8199 (mt) cc_final: 0.7974 (mm) REVERT: J 6 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6782 (t80) REVERT: J 200 LYS cc_start: 0.8088 (tppp) cc_final: 0.7873 (tppp) REVERT: K 22 MET cc_start: 0.6931 (tpp) cc_final: 0.6583 (tpp) REVERT: L 193 VAL cc_start: 0.7856 (t) cc_final: 0.7605 (m) REVERT: M 35 ASN cc_start: 0.8694 (p0) cc_final: 0.8489 (p0) REVERT: M 61 LYS cc_start: 0.8245 (mmmm) cc_final: 0.8008 (tppp) REVERT: M 75 ASP cc_start: 0.8271 (t0) cc_final: 0.7957 (t0) REVERT: M 141 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7812 (p) REVERT: M 150 ASN cc_start: 0.8355 (p0) cc_final: 0.8147 (p0) REVERT: M 175 ASP cc_start: 0.7919 (m-30) cc_final: 0.7551 (m-30) REVERT: M 214 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8210 (tt) REVERT: M 217 ASN cc_start: 0.8612 (t0) cc_final: 0.8306 (t0) REVERT: M 426 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7528 (mm) REVERT: N 65 MET cc_start: 0.7838 (ptt) cc_final: 0.7449 (ptp) REVERT: N 186 LYS cc_start: 0.8546 (tptp) cc_final: 0.8212 (tptp) REVERT: N 221 LYS cc_start: 0.8851 (ptpt) cc_final: 0.8631 (ptpt) REVERT: N 295 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8666 (ptt180) REVERT: N 302 ASN cc_start: 0.8458 (t0) cc_final: 0.8176 (t0) REVERT: N 351 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7536 (mm-30) REVERT: N 364 THR cc_start: 0.8719 (t) cc_final: 0.8513 (t) REVERT: O 22 MET cc_start: 0.5961 (tpp) cc_final: 0.5334 (tpp) outliers start: 224 outliers final: 107 residues processed: 1205 average time/residue: 1.3434 time to fit residues: 1951.0914 Evaluate side-chains 1148 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1023 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 260 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 408 TRP Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 205 ARG Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 309 GLU Chi-restraints excluded: chain J residue 378 SER Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 169 CYS Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 306 GLU Chi-restraints excluded: chain M residue 319 VAL Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 426 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 212 ASP Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 324 GLU Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 394 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 79 optimal weight: 5.9990 chunk 359 optimal weight: 20.0000 chunk 350 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 413 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 302 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 343 ASN B 151 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN B 391 ASN B 402 ASN C 40 ASN E 32 GLN E 77 GLN E 223 GLN F 8 GLN F 118 ASN F 151 ASN G 40 ASN I 223 GLN I 369 GLN I 439 HIS J 24 HIS J 69 ASN J 402 ASN K 39 GLN M 30 GLN M 100 ASN M 332 HIS M 361 ASN M 363 HIS N 151 ASN N 222 GLN N 358 ASN ** O 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 ASN P 198 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113893 restraints weight = 52843.423| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.27 r_work: 0.3308 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34076 Z= 0.160 Angle : 0.692 13.661 46512 Z= 0.352 Chirality : 0.049 0.329 5193 Planarity : 0.006 0.074 5965 Dihedral : 6.740 77.054 4819 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.14 % Favored : 94.74 % Rotamer: Outliers : 6.61 % Allowed : 27.60 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -0.82 (0.13), residues: 4224 helix: 0.93 (0.21), residues: 564 sheet: -0.49 (0.14), residues: 1436 loop : -0.91 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 188 HIS 0.008 0.001 HIS J 82 PHE 0.015 0.001 PHE L 134 TYR 0.021 0.002 TYR O 26 ARG 0.011 0.001 ARG H 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 9) link_NAG-ASN : angle 2.63551 ( 27) hydrogen bonds : bond 0.03767 ( 1153) hydrogen bonds : angle 5.63567 ( 2949) SS BOND : bond 0.00444 ( 61) SS BOND : angle 2.00713 ( 122) covalent geometry : bond 0.00372 (34006) covalent geometry : angle 0.68242 (46363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 1082 time to evaluate : 3.870 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: A 21 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8390 (ttt180) REVERT: A 30 GLN cc_start: 0.8451 (tt0) cc_final: 0.8248 (tt0) REVERT: A 37 ARG cc_start: 0.8951 (mpp80) cc_final: 0.8668 (mtm180) REVERT: A 50 LYS cc_start: 0.8571 (tttm) cc_final: 0.7995 (tttm) REVERT: A 54 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8095 (ttpp) REVERT: A 109 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7699 (mt-10) REVERT: A 192 GLU cc_start: 0.7151 (tt0) cc_final: 0.6840 (mt-10) REVERT: A 211 SER cc_start: 0.8184 (m) cc_final: 0.7693 (p) REVERT: A 242 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7830 (mt-10) REVERT: A 245 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8399 (mtmt) REVERT: A 260 CYS cc_start: 0.7603 (m) cc_final: 0.7399 (m) REVERT: B 6 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6971 (t80) REVERT: B 62 LEU cc_start: 0.8427 (mt) cc_final: 0.8127 (mt) REVERT: B 102 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8005 (mm-40) REVERT: B 172 VAL cc_start: 0.8397 (t) cc_final: 0.8057 (p) REVERT: B 200 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7972 (tmtt) REVERT: B 228 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8067 (pt) REVERT: B 249 LYS cc_start: 0.8286 (mttm) cc_final: 0.8045 (mttm) REVERT: B 274 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8183 (mt-10) REVERT: B 300 ASP cc_start: 0.8010 (t0) cc_final: 0.7781 (t0) REVERT: B 399 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7611 (mm) REVERT: D 117 MET cc_start: 0.6305 (tmm) cc_final: 0.5838 (tmm) REVERT: D 193 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8361 (t) REVERT: E 16 LYS cc_start: 0.8875 (mttt) cc_final: 0.8650 (mttt) REVERT: E 54 LYS cc_start: 0.8711 (tttt) cc_final: 0.8371 (tttt) REVERT: E 96 CYS cc_start: 0.7966 (t) cc_final: 0.7026 (m) REVERT: E 103 MET cc_start: 0.8589 (ttm) cc_final: 0.8347 (ttm) REVERT: E 113 GLU cc_start: 0.7688 (mp0) cc_final: 0.7275 (mp0) REVERT: E 156 LYS cc_start: 0.8626 (tppt) cc_final: 0.8272 (tppt) REVERT: E 305 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8137 (p) REVERT: E 367 LYS cc_start: 0.8574 (tttt) cc_final: 0.8370 (tttt) REVERT: F 73 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8296 (tm-30) REVERT: F 74 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8638 (tttp) REVERT: F 259 VAL cc_start: 0.8691 (p) cc_final: 0.8404 (m) REVERT: F 370 THR cc_start: 0.8122 (t) cc_final: 0.7818 (p) REVERT: F 402 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7408 (p0) REVERT: G 6 MET cc_start: 0.6183 (mmm) cc_final: 0.5954 (mmm) REVERT: G 48 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: H 129 VAL cc_start: 0.8285 (t) cc_final: 0.8015 (p) REVERT: H 132 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6227 (mmm-85) REVERT: H 175 LEU cc_start: 0.8338 (mm) cc_final: 0.8137 (mm) REVERT: H 247 LYS cc_start: 0.8546 (mmmm) cc_final: 0.8324 (mmmm) REVERT: I 96 CYS cc_start: 0.8061 (t) cc_final: 0.7768 (t) REVERT: I 101 THR cc_start: 0.8425 (t) cc_final: 0.8172 (p) REVERT: I 137 TYR cc_start: 0.8723 (p90) cc_final: 0.8094 (p90) REVERT: I 217 ASN cc_start: 0.8630 (t0) cc_final: 0.8416 (t0) REVERT: I 305 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.7548 (t) REVERT: I 382 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8340 (mtpp) REVERT: J 6 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6839 (t80) REVERT: J 55 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7746 (mm) REVERT: J 108 THR cc_start: 0.8400 (p) cc_final: 0.8091 (t) REVERT: J 174 ASP cc_start: 0.7900 (t0) cc_final: 0.7640 (t0) REVERT: J 200 LYS cc_start: 0.8092 (tppp) cc_final: 0.7823 (tppp) REVERT: J 208 ILE cc_start: 0.8657 (mm) cc_final: 0.8268 (tt) REVERT: J 249 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8095 (ptpt) REVERT: J 262 LYS cc_start: 0.8735 (mttp) cc_final: 0.8489 (mttm) REVERT: J 263 CYS cc_start: 0.7071 (m) cc_final: 0.6740 (m) REVERT: J 354 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8167 (p) REVERT: K 22 MET cc_start: 0.7148 (tpp) cc_final: 0.6639 (tpp) REVERT: L 117 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7162 (mmp) REVERT: L 177 TYR cc_start: 0.7902 (p90) cc_final: 0.7650 (p90) REVERT: L 193 VAL cc_start: 0.7864 (t) cc_final: 0.7591 (m) REVERT: L 204 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.7664 (ttm-80) REVERT: M 61 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8093 (tppp) REVERT: M 75 ASP cc_start: 0.8334 (t0) cc_final: 0.8063 (t0) REVERT: M 112 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8088 (mt-10) REVERT: M 156 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7961 (tmtm) REVERT: M 161 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8062 (ttpp) REVERT: M 175 ASP cc_start: 0.7872 (m-30) cc_final: 0.7593 (m-30) REVERT: M 217 ASN cc_start: 0.8682 (t0) cc_final: 0.8378 (t0) REVERT: M 300 LEU cc_start: 0.8610 (mt) cc_final: 0.8375 (mt) REVERT: N 65 MET cc_start: 0.7942 (ptt) cc_final: 0.7547 (ptp) REVERT: N 77 LYS cc_start: 0.8470 (mmmm) cc_final: 0.8248 (ttmm) REVERT: N 78 ILE cc_start: 0.8950 (mt) cc_final: 0.8722 (mp) REVERT: N 186 LYS cc_start: 0.8530 (tptp) cc_final: 0.8029 (tptp) REVERT: N 196 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8072 (tttp) REVERT: N 219 ASP cc_start: 0.8339 (t0) cc_final: 0.8125 (t0) REVERT: N 227 LEU cc_start: 0.8383 (tt) cc_final: 0.8148 (tm) REVERT: N 295 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8648 (ptt180) REVERT: N 314 VAL cc_start: 0.8745 (t) cc_final: 0.8406 (m) REVERT: N 351 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7474 (mm-30) REVERT: O 22 MET cc_start: 0.5151 (tpp) cc_final: 0.4663 (tpp) REVERT: P 129 VAL cc_start: 0.8113 (t) cc_final: 0.7768 (m) outliers start: 241 outliers final: 123 residues processed: 1199 average time/residue: 1.3163 time to fit residues: 1914.0399 Evaluate side-chains 1208 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1061 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 260 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 402 ASN Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 329 CYS Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 249 LYS Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 309 GLU Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 399 LEU Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 125 HIS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 301 GLU Chi-restraints excluded: chain M residue 306 GLU Chi-restraints excluded: chain M residue 319 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 237 SER Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain N residue 394 ILE Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 415 optimal weight: 0.0060 chunk 253 optimal weight: 4.9990 chunk 366 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 417 optimal weight: 0.0050 chunk 30 optimal weight: 2.9990 chunk 320 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.0016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 343 ASN B 151 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN B 302 ASN B 391 ASN B 402 ASN E 77 GLN E 223 GLN E 441 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN F 151 ASN I 223 GLN I 328 ASN I 439 HIS J 24 HIS J 69 ASN L 197 ASN M 32 GLN M 363 HIS N 151 ASN N 358 ASN O 29 ASN P 145 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113161 restraints weight = 52432.967| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.31 r_work: 0.3301 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34076 Z= 0.168 Angle : 0.680 14.662 46512 Z= 0.344 Chirality : 0.048 0.310 5193 Planarity : 0.006 0.069 5965 Dihedral : 6.520 79.053 4814 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.61 % Favored : 94.27 % Rotamer: Outliers : 7.13 % Allowed : 27.49 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.03 % 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: -0.81 (0.13), residues: 4224 helix: 1.00 (0.21), residues: 564 sheet: -0.53 (0.14), residues: 1360 loop : -0.89 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 188 HIS 0.008 0.001 HIS J 82 PHE 0.018 0.001 PHE I 95 TYR 0.021 0.002 TYR P 195 ARG 0.010 0.001 ARG H 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 9) link_NAG-ASN : angle 2.71059 ( 27) hydrogen bonds : bond 0.03609 ( 1153) hydrogen bonds : angle 5.51542 ( 2949) SS BOND : bond 0.00432 ( 61) SS BOND : angle 1.92588 ( 122) covalent geometry : bond 0.00386 (34006) covalent geometry : angle 0.67064 (46363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1356 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 1096 time to evaluate : 3.606 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: A 21 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8414 (ttt180) REVERT: A 37 ARG cc_start: 0.8950 (mpp80) cc_final: 0.8396 (mtm180) REVERT: A 48 THR cc_start: 0.8674 (m) cc_final: 0.8384 (t) REVERT: A 50 LYS cc_start: 0.8572 (tttm) cc_final: 0.8003 (tttm) REVERT: A 95 PHE cc_start: 0.8152 (t80) cc_final: 0.7887 (t80) REVERT: A 109 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 192 GLU cc_start: 0.7191 (tt0) cc_final: 0.6878 (mt-10) REVERT: A 211 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7711 (p) REVERT: A 235 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8377 (t) REVERT: A 242 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 245 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8391 (mtmt) REVERT: A 255 VAL cc_start: 0.8569 (t) cc_final: 0.8221 (m) REVERT: A 260 CYS cc_start: 0.7644 (m) cc_final: 0.7425 (m) REVERT: B 6 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6973 (t80) REVERT: B 62 LEU cc_start: 0.8535 (mt) cc_final: 0.8234 (mt) REVERT: B 102 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8051 (mm-40) REVERT: B 152 ARG cc_start: 0.8471 (mtp85) cc_final: 0.8218 (mtp85) REVERT: B 200 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7925 (tmtt) REVERT: B 249 LYS cc_start: 0.8309 (mttm) cc_final: 0.8091 (mttm) REVERT: B 274 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 300 ASP cc_start: 0.8060 (t0) cc_final: 0.7771 (t0) REVERT: B 399 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7751 (mm) REVERT: E 16 LYS cc_start: 0.8870 (mttt) cc_final: 0.8639 (mttt) REVERT: E 54 LYS cc_start: 0.8710 (tttt) cc_final: 0.8373 (tttt) REVERT: E 96 CYS cc_start: 0.7977 (t) cc_final: 0.7055 (m) REVERT: E 103 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8359 (ttm) REVERT: E 113 GLU cc_start: 0.7688 (mp0) cc_final: 0.7244 (mp0) REVERT: E 156 LYS cc_start: 0.8616 (tppt) cc_final: 0.8259 (tppt) REVERT: E 223 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8212 (mp10) REVERT: E 305 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8133 (p) REVERT: F 74 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8612 (tttp) REVERT: F 217 CYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7165 (m) REVERT: F 259 VAL cc_start: 0.8682 (p) cc_final: 0.8401 (m) REVERT: F 398 LYS cc_start: 0.8642 (tppp) cc_final: 0.8435 (ttmm) REVERT: G 48 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7570 (mm-40) REVERT: H 128 VAL cc_start: 0.8595 (m) cc_final: 0.8284 (m) REVERT: H 129 VAL cc_start: 0.8271 (t) cc_final: 0.8017 (p) REVERT: H 132 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6424 (mmm-85) REVERT: H 175 LEU cc_start: 0.8284 (mm) cc_final: 0.8009 (mm) REVERT: H 247 LYS cc_start: 0.8561 (mmmm) cc_final: 0.8320 (mmmm) REVERT: I 96 CYS cc_start: 0.8075 (t) cc_final: 0.7572 (m) REVERT: I 101 THR cc_start: 0.8489 (t) cc_final: 0.8240 (p) REVERT: I 130 GLN cc_start: 0.8747 (mt0) cc_final: 0.8523 (mt0) REVERT: I 137 TYR cc_start: 0.8735 (p90) cc_final: 0.8009 (p90) REVERT: I 217 ASN cc_start: 0.8630 (t0) cc_final: 0.8390 (t0) REVERT: I 305 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.7501 (t) REVERT: I 323 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7950 (t) REVERT: I 349 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8070 (mm-30) REVERT: I 382 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8339 (mtpp) REVERT: I 404 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7559 (p) REVERT: J 6 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6797 (t80) REVERT: J 108 THR cc_start: 0.8420 (p) cc_final: 0.8124 (t) REVERT: J 131 ARG cc_start: 0.8750 (mtt90) cc_final: 0.8449 (mtt90) REVERT: J 174 ASP cc_start: 0.7920 (t0) cc_final: 0.7627 (t0) REVERT: J 200 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7784 (tppp) REVERT: J 208 ILE cc_start: 0.8657 (mm) cc_final: 0.8285 (tt) REVERT: J 262 LYS cc_start: 0.8786 (mttp) cc_final: 0.8550 (mttm) REVERT: J 263 CYS cc_start: 0.7088 (m) cc_final: 0.6673 (m) REVERT: J 314 VAL cc_start: 0.8045 (t) cc_final: 0.7667 (t) REVERT: J 344 ASN cc_start: 0.8050 (t0) cc_final: 0.7494 (t0) REVERT: J 346 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7650 (m90) REVERT: J 354 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8140 (p) REVERT: L 117 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7159 (mmp) REVERT: L 193 VAL cc_start: 0.7864 (t) cc_final: 0.7592 (m) REVERT: L 204 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8160 (ttm-80) REVERT: M 75 ASP cc_start: 0.8351 (t0) cc_final: 0.8073 (t0) REVERT: M 141 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7778 (p) REVERT: M 146 ASP cc_start: 0.7944 (t0) cc_final: 0.7709 (t0) REVERT: M 156 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7977 (tmtm) REVERT: M 175 ASP cc_start: 0.7848 (m-30) cc_final: 0.7598 (m-30) REVERT: M 217 ASN cc_start: 0.8732 (t0) cc_final: 0.8394 (t0) REVERT: M 220 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8027 (pp) REVERT: M 229 ILE cc_start: 0.8647 (mm) cc_final: 0.8382 (mt) REVERT: M 293 GLU cc_start: 0.8121 (tt0) cc_final: 0.7753 (tt0) REVERT: M 300 LEU cc_start: 0.8671 (mt) cc_final: 0.8462 (mt) REVERT: M 342 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: M 400 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8156 (p) REVERT: M 439 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7691 (t-170) REVERT: N 18 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8036 (t0) REVERT: N 65 MET cc_start: 0.7963 (ptt) cc_final: 0.7693 (ptp) REVERT: N 77 LYS cc_start: 0.8472 (mmmm) cc_final: 0.8267 (ttmm) REVERT: N 186 LYS cc_start: 0.8512 (tptp) cc_final: 0.7908 (tptt) REVERT: N 196 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8066 (tttp) REVERT: N 219 ASP cc_start: 0.8307 (t0) cc_final: 0.8039 (t0) REVERT: N 295 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8591 (ptt180) REVERT: N 314 VAL cc_start: 0.8798 (t) cc_final: 0.8420 (m) REVERT: N 351 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7319 (mm-30) REVERT: O 22 MET cc_start: 0.5353 (tpp) cc_final: 0.4875 (tpp) outliers start: 260 outliers final: 147 residues processed: 1217 average time/residue: 1.4535 time to fit residues: 2138.6814 Evaluate side-chains 1246 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 1067 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 260 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 323 SER Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 309 GLU Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 399 LEU Chi-restraints excluded: chain J residue 402 ASN Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 125 HIS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 260 CYS Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 306 GLU Chi-restraints excluded: chain M residue 319 VAL Chi-restraints excluded: chain M residue 342 GLU Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 439 HIS Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 251 LYS Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 346 HIS Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 68 optimal weight: 8.9990 chunk 311 optimal weight: 4.9990 chunk 343 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 191 optimal weight: 0.0470 chunk 402 optimal weight: 0.2980 chunk 200 optimal weight: 8.9990 chunk 415 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS B 144 HIS B 151 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 236 ASN B 302 ASN B 391 ASN B 402 ASN E 77 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN F 151 ASN F 213 HIS H 194 GLN I 32 GLN I 236 GLN I 439 HIS J 24 HIS J 69 ASN M 125 HIS M 343 ASN M 363 HIS N 230 ASN N 358 ASN P 145 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111940 restraints weight = 52209.510| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.31 r_work: 0.3288 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 34076 Z= 0.199 Angle : 0.688 14.759 46512 Z= 0.348 Chirality : 0.049 0.318 5193 Planarity : 0.006 0.069 5965 Dihedral : 6.443 81.231 4810 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.68 % Favored : 94.20 % Rotamer: Outliers : 6.99 % Allowed : 28.65 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.03 % 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: -0.74 (0.13), residues: 4224 helix: 1.00 (0.21), residues: 564 sheet: -0.37 (0.14), residues: 1352 loop : -0.91 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 188 HIS 0.007 0.001 HIS N 126 PHE 0.019 0.002 PHE I 95 TYR 0.025 0.002 TYR L 177 ARG 0.007 0.000 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 9) link_NAG-ASN : angle 2.63943 ( 27) hydrogen bonds : bond 0.03637 ( 1153) hydrogen bonds : angle 5.46661 ( 2949) SS BOND : bond 0.00489 ( 61) SS BOND : angle 1.93398 ( 122) covalent geometry : bond 0.00454 (34006) covalent geometry : angle 0.67939 (46363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 1094 time to evaluate : 3.428 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 21 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8455 (ttt180) REVERT: A 37 ARG cc_start: 0.8962 (mpp80) cc_final: 0.8420 (mtm180) REVERT: A 48 THR cc_start: 0.8678 (m) cc_final: 0.8409 (t) REVERT: A 50 LYS cc_start: 0.8593 (tttm) cc_final: 0.8029 (tttm) REVERT: A 54 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8243 (ttmm) REVERT: A 211 SER cc_start: 0.8175 (OUTLIER) cc_final: 0.7708 (p) REVERT: A 221 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8117 (ttmt) REVERT: A 235 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8380 (t) REVERT: A 242 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 245 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8400 (mtmt) REVERT: A 255 VAL cc_start: 0.8621 (t) cc_final: 0.8265 (m) REVERT: A 321 TYR cc_start: 0.8306 (p90) cc_final: 0.8098 (p90) REVERT: B 6 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6938 (t80) REVERT: B 62 LEU cc_start: 0.8482 (mt) cc_final: 0.8190 (mt) REVERT: B 102 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: B 200 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8019 (tmtt) REVERT: B 228 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8081 (pt) REVERT: B 249 LYS cc_start: 0.8356 (mttm) cc_final: 0.7997 (mttm) REVERT: B 274 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8175 (mt-10) REVERT: B 300 ASP cc_start: 0.8080 (t0) cc_final: 0.7789 (t0) REVERT: B 344 ASN cc_start: 0.8100 (t0) cc_final: 0.7868 (t160) REVERT: B 399 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7649 (mm) REVERT: D 117 MET cc_start: 0.6513 (tmm) cc_final: 0.6099 (tmm) REVERT: D 186 TYR cc_start: 0.8013 (m-10) cc_final: 0.7773 (m-10) REVERT: E 54 LYS cc_start: 0.8714 (tttt) cc_final: 0.8383 (tttt) REVERT: E 96 CYS cc_start: 0.8083 (t) cc_final: 0.7108 (m) REVERT: E 103 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8402 (ttm) REVERT: E 113 GLU cc_start: 0.7691 (mp0) cc_final: 0.7223 (mp0) REVERT: E 223 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8243 (mp10) REVERT: E 382 LYS cc_start: 0.8754 (mttm) cc_final: 0.8531 (mttm) REVERT: F 74 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8617 (tttp) REVERT: F 217 CYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7148 (m) REVERT: F 259 VAL cc_start: 0.8699 (p) cc_final: 0.8412 (m) REVERT: F 376 MET cc_start: 0.7426 (ttp) cc_final: 0.7142 (ttp) REVERT: F 398 LYS cc_start: 0.8658 (tppp) cc_final: 0.8426 (ttmm) REVERT: H 128 VAL cc_start: 0.8601 (m) cc_final: 0.8269 (m) REVERT: H 129 VAL cc_start: 0.8284 (t) cc_final: 0.8049 (p) REVERT: H 132 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6442 (mmm-85) REVERT: H 175 LEU cc_start: 0.8307 (mm) cc_final: 0.8021 (mm) REVERT: H 247 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8284 (mmmm) REVERT: I 96 CYS cc_start: 0.8060 (t) cc_final: 0.7758 (t) REVERT: I 101 THR cc_start: 0.8559 (t) cc_final: 0.8301 (p) REVERT: I 137 TYR cc_start: 0.8767 (p90) cc_final: 0.7954 (p90) REVERT: I 247 ASP cc_start: 0.7415 (m-30) cc_final: 0.7049 (m-30) REVERT: I 305 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.7531 (t) REVERT: I 370 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8263 (t) REVERT: I 382 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: I 404 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7628 (p) REVERT: J 6 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6838 (t80) REVERT: J 108 THR cc_start: 0.8483 (p) cc_final: 0.8169 (t) REVERT: J 174 ASP cc_start: 0.7834 (t0) cc_final: 0.7540 (t0) REVERT: J 200 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7747 (tppp) REVERT: J 205 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7296 (mtp180) REVERT: J 208 ILE cc_start: 0.8666 (mm) cc_final: 0.8330 (tt) REVERT: J 300 ASP cc_start: 0.7812 (t0) cc_final: 0.7435 (t0) REVERT: J 314 VAL cc_start: 0.8051 (t) cc_final: 0.7679 (t) REVERT: J 344 ASN cc_start: 0.8112 (t0) cc_final: 0.7560 (t0) REVERT: J 346 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7618 (m90) REVERT: J 354 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8190 (p) REVERT: L 117 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7219 (mmp) REVERT: L 170 MET cc_start: 0.7725 (pmm) cc_final: 0.7426 (pmm) REVERT: L 193 VAL cc_start: 0.7882 (t) cc_final: 0.7666 (m) REVERT: M 32 GLN cc_start: 0.8462 (tt0) cc_final: 0.8139 (tt0) REVERT: M 75 ASP cc_start: 0.8373 (t0) cc_final: 0.8086 (t0) REVERT: M 99 GLU cc_start: 0.7590 (pt0) cc_final: 0.7354 (pt0) REVERT: M 103 MET cc_start: 0.8157 (ttp) cc_final: 0.7944 (ttp) REVERT: M 141 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7812 (p) REVERT: M 146 ASP cc_start: 0.7973 (t0) cc_final: 0.7772 (t0) REVERT: M 156 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7999 (tmtm) REVERT: M 175 ASP cc_start: 0.7877 (m-30) cc_final: 0.7573 (m-30) REVERT: M 220 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8049 (pp) REVERT: M 293 GLU cc_start: 0.8180 (tt0) cc_final: 0.7811 (tt0) REVERT: M 342 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: M 367 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8259 (ttmm) REVERT: M 400 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8260 (p) REVERT: N 24 HIS cc_start: 0.7533 (t-90) cc_final: 0.7327 (t-90) REVERT: N 65 MET cc_start: 0.8029 (ptt) cc_final: 0.7796 (ptp) REVERT: N 186 LYS cc_start: 0.8494 (tptp) cc_final: 0.7902 (tptt) REVERT: N 196 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8083 (tttp) REVERT: N 295 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8539 (ptt180) REVERT: N 314 VAL cc_start: 0.8850 (t) cc_final: 0.8464 (m) REVERT: N 351 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7184 (mm-30) REVERT: O 22 MET cc_start: 0.5319 (tpp) cc_final: 0.4871 (tpp) REVERT: P 159 TYR cc_start: 0.7656 (m-80) cc_final: 0.6877 (m-10) REVERT: P 250 THR cc_start: 0.8438 (p) cc_final: 0.8139 (p) outliers start: 255 outliers final: 157 residues processed: 1214 average time/residue: 1.5937 time to fit residues: 2348.4831 Evaluate side-chains 1242 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 1055 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain I residue 408 TRP Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 205 ARG Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 302 ASN Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 399 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 247 LYS Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 297 VAL Chi-restraints excluded: chain M residue 306 GLU Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 319 VAL Chi-restraints excluded: chain M residue 322 LYS Chi-restraints excluded: chain M residue 342 GLU Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 418 THR Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 439 HIS Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 251 LYS Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 346 HIS Chi-restraints excluded: chain N residue 366 ILE Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain N residue 394 ILE Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 80 optimal weight: 3.9990 chunk 300 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 236 GLN A 343 ASN B 151 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 236 ASN B 302 ASN B 391 ASN B 402 ASN E 77 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN F 151 ASN ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 HIS J 69 ASN ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 343 ASN M 361 ASN M 363 HIS N 151 ASN N 213 HIS N 230 ASN N 358 ASN P 145 ASN P 198 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111236 restraints weight = 51813.689| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.28 r_work: 0.3244 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 34076 Z= 0.353 Angle : 0.772 15.253 46512 Z= 0.392 Chirality : 0.053 0.365 5193 Planarity : 0.006 0.077 5965 Dihedral : 6.721 83.597 4810 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.49 % Favored : 93.37 % Rotamer: Outliers : 7.37 % Allowed : 29.03 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.03 % 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: -0.91 (0.13), residues: 4224 helix: 0.74 (0.21), residues: 564 sheet: -0.40 (0.14), residues: 1392 loop : -1.05 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 188 HIS 0.010 0.002 HIS F 175 PHE 0.022 0.002 PHE N 113 TYR 0.033 0.003 TYR H 125 ARG 0.009 0.001 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 9) link_NAG-ASN : angle 2.71287 ( 27) hydrogen bonds : bond 0.04096 ( 1153) hydrogen bonds : angle 5.60988 ( 2949) SS BOND : bond 0.00558 ( 61) SS BOND : angle 2.25237 ( 122) covalent geometry : bond 0.00800 (34006) covalent geometry : angle 0.76168 (46363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 1080 time to evaluate : 3.426 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 21 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8475 (ttt90) REVERT: A 37 ARG cc_start: 0.8993 (mpp80) cc_final: 0.8676 (mpp-170) REVERT: A 48 THR cc_start: 0.8693 (m) cc_final: 0.8426 (t) REVERT: A 50 LYS cc_start: 0.8567 (tttm) cc_final: 0.8034 (tttm) REVERT: A 54 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8058 (ttmm) REVERT: A 211 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7827 (t) REVERT: A 221 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8130 (ttmt) REVERT: A 235 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8437 (t) REVERT: A 242 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7839 (mt-10) REVERT: A 245 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8416 (mtmt) REVERT: A 255 VAL cc_start: 0.8683 (t) cc_final: 0.8349 (m) REVERT: A 279 ILE cc_start: 0.8710 (pt) cc_final: 0.8503 (pt) REVERT: A 300 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8027 (mp) REVERT: A 301 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6694 (tm-30) REVERT: A 321 TYR cc_start: 0.8546 (p90) cc_final: 0.8341 (p90) REVERT: B 6 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6910 (t80) REVERT: B 62 LEU cc_start: 0.8666 (mt) cc_final: 0.8292 (mt) REVERT: B 102 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8087 (mm-40) REVERT: B 249 LYS cc_start: 0.8408 (mttm) cc_final: 0.8074 (mttm) REVERT: B 263 CYS cc_start: 0.7490 (m) cc_final: 0.7211 (m) REVERT: B 300 ASP cc_start: 0.8145 (t0) cc_final: 0.7842 (t0) REVERT: B 344 ASN cc_start: 0.8200 (t0) cc_final: 0.7969 (t160) REVERT: B 391 ASN cc_start: 0.8828 (t0) cc_final: 0.8610 (t0) REVERT: B 398 LYS cc_start: 0.8477 (tptt) cc_final: 0.8250 (tptp) REVERT: B 399 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7587 (mm) REVERT: D 117 MET cc_start: 0.6592 (tmm) cc_final: 0.6163 (tmm) REVERT: D 135 LYS cc_start: 0.7794 (ptmm) cc_final: 0.7371 (ptpt) REVERT: E 54 LYS cc_start: 0.8701 (tttt) cc_final: 0.8124 (tttm) REVERT: E 96 CYS cc_start: 0.8233 (t) cc_final: 0.7291 (m) REVERT: E 103 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8415 (ttm) REVERT: E 113 GLU cc_start: 0.7765 (mp0) cc_final: 0.7213 (mp0) REVERT: E 223 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8093 (mp10) REVERT: E 299 ASP cc_start: 0.8357 (m-30) cc_final: 0.8127 (m-30) REVERT: E 382 LYS cc_start: 0.8770 (mttm) cc_final: 0.8529 (mttm) REVERT: F 74 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8609 (tttp) REVERT: F 217 CYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7201 (m) REVERT: F 259 VAL cc_start: 0.8731 (p) cc_final: 0.8446 (m) REVERT: F 376 MET cc_start: 0.7463 (ttp) cc_final: 0.7181 (ttp) REVERT: F 398 LYS cc_start: 0.8730 (tppp) cc_final: 0.8478 (ttmm) REVERT: H 117 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6451 (mpp) REVERT: H 128 VAL cc_start: 0.8668 (m) cc_final: 0.8277 (m) REVERT: H 129 VAL cc_start: 0.8342 (t) cc_final: 0.8113 (p) REVERT: H 132 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6732 (mtt90) REVERT: H 175 LEU cc_start: 0.8345 (mm) cc_final: 0.8003 (mm) REVERT: H 247 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8302 (mmmm) REVERT: I 96 CYS cc_start: 0.8139 (t) cc_final: 0.7717 (m) REVERT: I 101 THR cc_start: 0.8666 (t) cc_final: 0.8411 (p) REVERT: I 247 ASP cc_start: 0.7418 (m-30) cc_final: 0.7091 (m-30) REVERT: I 305 THR cc_start: 0.8667 (m) cc_final: 0.8297 (p) REVERT: I 323 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.8204 (t) REVERT: I 382 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8284 (mtpp) REVERT: I 404 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7694 (p) REVERT: J 6 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.6821 (t80) REVERT: J 174 ASP cc_start: 0.7937 (t0) cc_final: 0.7608 (t0) REVERT: J 200 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7799 (tppp) REVERT: J 208 ILE cc_start: 0.8673 (mm) cc_final: 0.8352 (tt) REVERT: J 300 ASP cc_start: 0.7871 (t0) cc_final: 0.7479 (t0) REVERT: J 314 VAL cc_start: 0.8168 (t) cc_final: 0.7786 (t) REVERT: J 333 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8148 (mtmm) REVERT: J 344 ASN cc_start: 0.8094 (t0) cc_final: 0.7540 (t0) REVERT: J 354 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8184 (p) REVERT: L 117 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7269 (mmp) REVERT: L 170 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7286 (pmm) REVERT: L 193 VAL cc_start: 0.7923 (t) cc_final: 0.7720 (m) REVERT: L 194 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: L 204 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8259 (ttm-80) REVERT: M 99 GLU cc_start: 0.7884 (pt0) cc_final: 0.7636 (pt0) REVERT: M 103 MET cc_start: 0.8329 (ttp) cc_final: 0.8105 (ttp) REVERT: M 112 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8125 (mt-10) REVERT: M 141 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7833 (p) REVERT: M 156 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8160 (tmtm) REVERT: M 220 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8205 (pp) REVERT: M 229 ILE cc_start: 0.8634 (mt) cc_final: 0.8395 (mm) REVERT: M 293 GLU cc_start: 0.8378 (tt0) cc_final: 0.8019 (tt0) REVERT: M 378 LYS cc_start: 0.8390 (pttm) cc_final: 0.8136 (pttm) REVERT: M 400 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8303 (p) REVERT: N 18 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.8024 (t0) REVERT: N 24 HIS cc_start: 0.7714 (t-90) cc_final: 0.7500 (t-90) REVERT: N 65 MET cc_start: 0.8103 (ptt) cc_final: 0.7854 (ptp) REVERT: N 68 MET cc_start: 0.8152 (mmm) cc_final: 0.7735 (mmm) REVERT: N 168 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: N 186 LYS cc_start: 0.8500 (tptp) cc_final: 0.7884 (tptp) REVERT: N 196 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7988 (tttp) REVERT: N 218 THR cc_start: 0.8289 (p) cc_final: 0.7893 (t) REVERT: N 351 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7234 (mm-30) REVERT: O 22 MET cc_start: 0.5425 (tpp) cc_final: 0.4962 (tpp) REVERT: P 190 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7754 (m90) outliers start: 269 outliers final: 168 residues processed: 1213 average time/residue: 1.3216 time to fit residues: 1933.5994 Evaluate side-chains 1267 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 1068 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 261 TRP Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 323 SER Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain I residue 408 TRP Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 249 LYS Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 302 ASN Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 380 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 399 LEU Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 194 GLN Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 223 GLN Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 260 CYS Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 297 VAL Chi-restraints excluded: chain M residue 319 VAL Chi-restraints excluded: chain M residue 397 GLU Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 418 THR Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 439 HIS Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 168 GLN Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 346 HIS Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain N residue 394 ILE Chi-restraints excluded: chain N residue 415 ILE Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 190 HIS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 258 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 407 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 246 optimal weight: 4.9990 chunk 381 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 105 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 343 ASN B 151 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN B 302 ASN B 402 ASN E 226 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN F 151 ASN I 223 GLN I 439 HIS J 24 HIS J 69 ASN J 175 HIS ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 125 HIS ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN M 343 ASN M 361 ASN M 363 HIS N 230 ASN N 358 ASN P 145 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113091 restraints weight = 52022.612| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.33 r_work: 0.3306 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34076 Z= 0.130 Angle : 0.678 16.295 46512 Z= 0.342 Chirality : 0.047 0.307 5193 Planarity : 0.006 0.068 5965 Dihedral : 6.394 84.067 4809 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.41 % Rotamer: Outliers : 5.62 % Allowed : 31.06 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.03 % 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: -0.76 (0.13), residues: 4224 helix: 1.02 (0.21), residues: 568 sheet: -0.40 (0.14), residues: 1372 loop : -0.93 (0.13), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 384 HIS 0.007 0.001 HIS F 126 PHE 0.025 0.001 PHE I 95 TYR 0.028 0.001 TYR H 163 ARG 0.010 0.001 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 9) link_NAG-ASN : angle 2.68662 ( 27) hydrogen bonds : bond 0.03373 ( 1153) hydrogen bonds : angle 5.34048 ( 2949) SS BOND : bond 0.00615 ( 61) SS BOND : angle 2.02646 ( 122) covalent geometry : bond 0.00296 (34006) covalent geometry : angle 0.66821 (46363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 1091 time to evaluate : 3.307 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 21 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8508 (ttt180) REVERT: A 37 ARG cc_start: 0.8943 (mpp80) cc_final: 0.8698 (mtm180) REVERT: A 48 THR cc_start: 0.8619 (m) cc_final: 0.8365 (t) REVERT: A 50 LYS cc_start: 0.8602 (tttm) cc_final: 0.8104 (tttm) REVERT: A 109 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7736 (mt-10) REVERT: A 211 SER cc_start: 0.8218 (m) cc_final: 0.7764 (t) REVERT: A 221 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8139 (ttmt) REVERT: A 235 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8374 (t) REVERT: A 242 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7762 (mt-10) REVERT: A 255 VAL cc_start: 0.8595 (t) cc_final: 0.8254 (m) REVERT: A 260 CYS cc_start: 0.7762 (m) cc_final: 0.7514 (m) REVERT: A 297 VAL cc_start: 0.9101 (p) cc_final: 0.8886 (m) REVERT: A 382 LYS cc_start: 0.8652 (mtpm) cc_final: 0.8429 (mttp) REVERT: B 6 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6838 (t80) REVERT: B 62 LEU cc_start: 0.8345 (mt) cc_final: 0.8068 (mt) REVERT: B 102 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8024 (mm-40) REVERT: B 300 ASP cc_start: 0.8081 (t0) cc_final: 0.7778 (t0) REVERT: B 344 ASN cc_start: 0.8087 (t0) cc_final: 0.7848 (t160) REVERT: B 376 MET cc_start: 0.7180 (tpp) cc_final: 0.6863 (tpp) REVERT: B 398 LYS cc_start: 0.8298 (tptt) cc_final: 0.8089 (tptp) REVERT: B 399 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7390 (mm) REVERT: D 117 MET cc_start: 0.6556 (tmm) cc_final: 0.6155 (tmm) REVERT: D 135 LYS cc_start: 0.7728 (ptmm) cc_final: 0.7356 (ptpt) REVERT: D 233 GLU cc_start: 0.4188 (tp30) cc_final: 0.3846 (tm-30) REVERT: E 54 LYS cc_start: 0.8685 (tttt) cc_final: 0.8115 (tttm) REVERT: E 96 CYS cc_start: 0.8003 (t) cc_final: 0.7138 (m) REVERT: E 113 GLU cc_start: 0.7742 (mp0) cc_final: 0.7249 (mp0) REVERT: E 135 ILE cc_start: 0.8652 (pt) cc_final: 0.8427 (mt) REVERT: E 223 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8241 (mp10) REVERT: E 246 LYS cc_start: 0.8407 (pttt) cc_final: 0.8126 (ptmm) REVERT: E 382 LYS cc_start: 0.8740 (mttm) cc_final: 0.8516 (mttm) REVERT: F 74 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8614 (ttmm) REVERT: F 175 HIS cc_start: 0.8293 (p90) cc_final: 0.8080 (p90) REVERT: F 217 CYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7114 (m) REVERT: F 259 VAL cc_start: 0.8677 (p) cc_final: 0.8420 (m) REVERT: F 376 MET cc_start: 0.7443 (ttp) cc_final: 0.7162 (ttp) REVERT: F 398 LYS cc_start: 0.8630 (tppp) cc_final: 0.8424 (ttmm) REVERT: H 128 VAL cc_start: 0.8594 (m) cc_final: 0.8195 (m) REVERT: H 175 LEU cc_start: 0.8285 (mm) cc_final: 0.7953 (mm) REVERT: H 220 LYS cc_start: 0.8574 (mptt) cc_final: 0.8236 (mptt) REVERT: H 247 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8281 (mmmm) REVERT: I 11 VAL cc_start: 0.8778 (t) cc_final: 0.8559 (p) REVERT: I 47 ILE cc_start: 0.8497 (mt) cc_final: 0.8099 (pp) REVERT: I 96 CYS cc_start: 0.8075 (t) cc_final: 0.7692 (m) REVERT: I 101 THR cc_start: 0.8629 (t) cc_final: 0.8375 (p) REVERT: I 137 TYR cc_start: 0.8750 (p90) cc_final: 0.8083 (p90) REVERT: I 235 THR cc_start: 0.8570 (t) cc_final: 0.8368 (m) REVERT: I 247 ASP cc_start: 0.7390 (m-30) cc_final: 0.7026 (m-30) REVERT: I 276 SER cc_start: 0.8565 (p) cc_final: 0.8267 (m) REVERT: I 323 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.7889 (t) REVERT: I 370 VAL cc_start: 0.8221 (t) cc_final: 0.7932 (p) REVERT: I 372 THR cc_start: 0.8151 (m) cc_final: 0.7926 (t) REVERT: I 382 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8284 (mtpp) REVERT: J 6 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.6789 (t80) REVERT: J 108 THR cc_start: 0.8439 (p) cc_final: 0.8124 (t) REVERT: J 131 ARG cc_start: 0.8710 (mtt90) cc_final: 0.8492 (mtt90) REVERT: J 174 ASP cc_start: 0.7954 (t0) cc_final: 0.7691 (t0) REVERT: J 200 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7690 (tppp) REVERT: J 226 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: J 251 LYS cc_start: 0.8635 (tttm) cc_final: 0.8341 (tttm) REVERT: J 300 ASP cc_start: 0.7818 (t0) cc_final: 0.7466 (t0) REVERT: J 314 VAL cc_start: 0.7997 (t) cc_final: 0.7738 (m) REVERT: J 333 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8172 (mtmm) REVERT: J 344 ASN cc_start: 0.8136 (t0) cc_final: 0.7510 (t0) REVERT: J 346 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7616 (m90) REVERT: J 354 VAL cc_start: 0.8363 (p) cc_final: 0.8139 (p) REVERT: L 117 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7122 (mmp) REVERT: L 163 TYR cc_start: 0.4934 (m-80) cc_final: 0.4543 (m-80) REVERT: L 170 MET cc_start: 0.7745 (pmm) cc_final: 0.7370 (pmm) REVERT: L 178 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7894 (m) REVERT: L 194 GLN cc_start: 0.8248 (pt0) cc_final: 0.7886 (pm20) REVERT: M 75 ASP cc_start: 0.8363 (t0) cc_final: 0.8159 (t0) REVERT: M 79 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8184 (tp40) REVERT: M 99 GLU cc_start: 0.7790 (pt0) cc_final: 0.7560 (pt0) REVERT: M 105 GLU cc_start: 0.8154 (pt0) cc_final: 0.7927 (pt0) REVERT: M 112 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8033 (mt-10) REVERT: M 156 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8036 (tmtm) REVERT: M 203 ASP cc_start: 0.8303 (p0) cc_final: 0.8093 (p0) REVERT: M 293 GLU cc_start: 0.8369 (tt0) cc_final: 0.7995 (tt0) REVERT: M 367 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8253 (ttmm) REVERT: M 378 LYS cc_start: 0.8340 (pttm) cc_final: 0.8109 (pttm) REVERT: M 399 PHE cc_start: 0.8040 (t80) cc_final: 0.7491 (t80) REVERT: M 400 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8337 (p) REVERT: N 18 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8038 (t0) REVERT: N 24 HIS cc_start: 0.7594 (t-90) cc_final: 0.7371 (t-90) REVERT: N 65 MET cc_start: 0.8043 (ptt) cc_final: 0.7841 (ptp) REVERT: N 68 MET cc_start: 0.8016 (mmm) cc_final: 0.7656 (mmm) REVERT: N 186 LYS cc_start: 0.8540 (tptp) cc_final: 0.7930 (tptp) REVERT: N 196 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8067 (tttp) REVERT: N 295 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8577 (ptt180) REVERT: N 351 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7155 (mm-30) REVERT: O 22 MET cc_start: 0.5292 (tpp) cc_final: 0.4864 (tpp) REVERT: P 159 TYR cc_start: 0.7666 (m-10) cc_final: 0.6884 (m-10) REVERT: P 214 ARG cc_start: 0.8393 (ptp-110) cc_final: 0.8082 (mtp180) outliers start: 205 outliers final: 120 residues processed: 1192 average time/residue: 1.3654 time to fit residues: 1973.6516 Evaluate side-chains 1245 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1103 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 260 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 402 ASN Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 323 SER Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 249 LYS Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 306 GLU Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 418 THR Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 439 HIS Chi-restraints excluded: chain N residue 8 GLN Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 251 LYS Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 346 HIS Chi-restraints excluded: chain N residue 366 ILE Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 146 optimal weight: 0.9980 chunk 419 optimal weight: 6.9990 chunk 231 optimal weight: 0.0370 chunk 222 optimal weight: 10.0000 chunk 349 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 281 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 236 GLN A 343 ASN B 151 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 236 ASN B 302 ASN B 402 ASN E 77 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN F 151 ASN I 223 GLN I 439 HIS J 5 HIS J 24 HIS J 69 ASN J 175 HIS ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN M 343 ASN M 363 HIS N 69 ASN ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 358 ASN ** O 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112046 restraints weight = 52152.196| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.32 r_work: 0.3288 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34076 Z= 0.174 Angle : 0.690 16.064 46512 Z= 0.346 Chirality : 0.048 0.363 5193 Planarity : 0.006 0.067 5965 Dihedral : 6.261 86.458 4805 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.97 % Favored : 93.94 % Rotamer: Outliers : 5.21 % Allowed : 31.88 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % 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: -0.74 (0.13), residues: 4224 helix: 0.98 (0.21), residues: 568 sheet: -0.24 (0.15), residues: 1316 loop : -0.99 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 188 HIS 0.007 0.001 HIS J 126 PHE 0.023 0.001 PHE I 95 TYR 0.036 0.002 TYR H 163 ARG 0.009 0.001 ARG B 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 9) link_NAG-ASN : angle 2.48377 ( 27) hydrogen bonds : bond 0.03481 ( 1153) hydrogen bonds : angle 5.30395 ( 2949) SS BOND : bond 0.00413 ( 61) SS BOND : angle 2.09035 ( 122) covalent geometry : bond 0.00404 (34006) covalent geometry : angle 0.67968 (46363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 1105 time to evaluate : 3.410 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: A 21 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8563 (ttt180) REVERT: A 37 ARG cc_start: 0.8963 (mpp80) cc_final: 0.8732 (mtm180) REVERT: A 48 THR cc_start: 0.8657 (m) cc_final: 0.8436 (t) REVERT: A 50 LYS cc_start: 0.8596 (tttm) cc_final: 0.8004 (tttm) REVERT: A 54 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8061 (ttpp) REVERT: A 109 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 156 LYS cc_start: 0.8738 (tppt) cc_final: 0.8492 (mmtm) REVERT: A 211 SER cc_start: 0.8235 (m) cc_final: 0.7788 (t) REVERT: A 221 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8127 (ttmt) REVERT: A 235 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8375 (t) REVERT: A 242 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7788 (mt-10) REVERT: A 255 VAL cc_start: 0.8632 (t) cc_final: 0.8288 (m) REVERT: A 297 VAL cc_start: 0.9094 (p) cc_final: 0.8890 (m) REVERT: A 301 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6616 (tm-30) REVERT: A 382 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8451 (mttp) REVERT: A 426 LEU cc_start: 0.8261 (mm) cc_final: 0.8034 (mm) REVERT: B 62 LEU cc_start: 0.8601 (mt) cc_final: 0.8391 (mt) REVERT: B 102 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8002 (mm-40) REVERT: B 228 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8078 (pt) REVERT: B 300 ASP cc_start: 0.8118 (t0) cc_final: 0.7798 (t0) REVERT: B 344 ASN cc_start: 0.8106 (t0) cc_final: 0.7849 (t160) REVERT: B 376 MET cc_start: 0.7202 (tpp) cc_final: 0.6906 (tpp) REVERT: B 398 LYS cc_start: 0.8318 (tptt) cc_final: 0.8075 (tptp) REVERT: B 399 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7422 (mm) REVERT: D 117 MET cc_start: 0.6623 (tmm) cc_final: 0.6198 (tmm) REVERT: D 135 LYS cc_start: 0.7772 (ptmm) cc_final: 0.7376 (ptpt) REVERT: E 16 LYS cc_start: 0.8863 (mttt) cc_final: 0.8633 (mttt) REVERT: E 54 LYS cc_start: 0.8715 (tttt) cc_final: 0.8331 (tttt) REVERT: E 96 CYS cc_start: 0.8048 (t) cc_final: 0.7178 (m) REVERT: E 113 GLU cc_start: 0.7735 (mp0) cc_final: 0.7247 (mp0) REVERT: E 135 ILE cc_start: 0.8650 (pt) cc_final: 0.8423 (mt) REVERT: E 246 LYS cc_start: 0.8432 (pttt) cc_final: 0.8128 (ptmm) REVERT: E 308 THR cc_start: 0.8717 (p) cc_final: 0.8454 (t) REVERT: F 27 CYS cc_start: 0.7069 (p) cc_final: 0.6774 (p) REVERT: F 175 HIS cc_start: 0.8208 (p90) cc_final: 0.7989 (p90) REVERT: F 217 CYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7151 (m) REVERT: F 218 THR cc_start: 0.8589 (m) cc_final: 0.8352 (p) REVERT: F 259 VAL cc_start: 0.8698 (p) cc_final: 0.8435 (m) REVERT: F 376 MET cc_start: 0.7405 (ttp) cc_final: 0.7127 (ttp) REVERT: F 398 LYS cc_start: 0.8626 (tppp) cc_final: 0.8404 (ttmm) REVERT: H 128 VAL cc_start: 0.8572 (m) cc_final: 0.8156 (m) REVERT: H 175 LEU cc_start: 0.8269 (mm) cc_final: 0.7957 (mm) REVERT: H 220 LYS cc_start: 0.8514 (mptt) cc_final: 0.8160 (mptt) REVERT: H 247 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8276 (mmmm) REVERT: I 2 GLU cc_start: 0.8011 (tp30) cc_final: 0.7798 (tp30) REVERT: I 11 VAL cc_start: 0.8791 (t) cc_final: 0.8568 (p) REVERT: I 30 GLN cc_start: 0.8739 (mt0) cc_final: 0.8446 (mt0) REVERT: I 47 ILE cc_start: 0.8525 (mt) cc_final: 0.8188 (pp) REVERT: I 96 CYS cc_start: 0.8075 (t) cc_final: 0.7719 (m) REVERT: I 101 THR cc_start: 0.8648 (t) cc_final: 0.8433 (p) REVERT: I 137 TYR cc_start: 0.8781 (p90) cc_final: 0.7979 (p90) REVERT: I 235 THR cc_start: 0.8615 (t) cc_final: 0.8408 (m) REVERT: I 247 ASP cc_start: 0.7441 (m-30) cc_final: 0.7093 (m-30) REVERT: I 276 SER cc_start: 0.8579 (p) cc_final: 0.8285 (m) REVERT: I 305 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8116 (p) REVERT: I 323 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.8017 (t) REVERT: I 370 VAL cc_start: 0.8371 (t) cc_final: 0.8091 (p) REVERT: I 372 THR cc_start: 0.8267 (m) cc_final: 0.8041 (t) REVERT: I 382 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8284 (mtpp) REVERT: J 6 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6803 (t80) REVERT: J 108 THR cc_start: 0.8478 (p) cc_final: 0.8163 (t) REVERT: J 131 ARG cc_start: 0.8735 (mtt90) cc_final: 0.8511 (mtt90) REVERT: J 174 ASP cc_start: 0.7932 (t0) cc_final: 0.7680 (t0) REVERT: J 200 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7695 (tppp) REVERT: J 226 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: J 236 ASN cc_start: 0.8401 (t0) cc_final: 0.8186 (t0) REVERT: J 251 LYS cc_start: 0.8637 (tttm) cc_final: 0.8401 (tttt) REVERT: J 300 ASP cc_start: 0.7829 (t0) cc_final: 0.7471 (t0) REVERT: J 314 VAL cc_start: 0.8044 (t) cc_final: 0.7766 (m) REVERT: J 333 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8155 (mtmm) REVERT: J 344 ASN cc_start: 0.8159 (t0) cc_final: 0.7536 (t0) REVERT: J 354 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8173 (p) REVERT: L 117 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7037 (mmp) REVERT: L 122 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8461 (t) REVERT: L 170 MET cc_start: 0.7800 (pmm) cc_final: 0.7366 (pmm) REVERT: L 194 GLN cc_start: 0.8243 (pt0) cc_final: 0.7924 (pm20) REVERT: M 32 GLN cc_start: 0.8452 (tt0) cc_final: 0.8149 (tt0) REVERT: M 79 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8248 (tp40) REVERT: M 99 GLU cc_start: 0.7847 (pt0) cc_final: 0.7641 (pt0) REVERT: M 105 GLU cc_start: 0.8191 (pt0) cc_final: 0.7928 (pt0) REVERT: M 112 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8024 (mt-10) REVERT: M 156 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8032 (tmtm) REVERT: M 203 ASP cc_start: 0.8291 (p0) cc_final: 0.8089 (p0) REVERT: M 220 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8084 (pp) REVERT: M 229 ILE cc_start: 0.8692 (mm) cc_final: 0.8419 (mt) REVERT: M 367 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8260 (ttmm) REVERT: M 378 LYS cc_start: 0.8334 (pttm) cc_final: 0.8098 (pttm) REVERT: M 399 PHE cc_start: 0.8057 (t80) cc_final: 0.7503 (t80) REVERT: M 400 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8270 (p) REVERT: N 18 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8033 (t0) REVERT: N 24 HIS cc_start: 0.7622 (t-90) cc_final: 0.7384 (t-90) REVERT: N 68 MET cc_start: 0.8044 (mmm) cc_final: 0.7690 (mmm) REVERT: N 186 LYS cc_start: 0.8528 (tptp) cc_final: 0.7919 (tptp) REVERT: N 196 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8070 (tttp) REVERT: N 218 THR cc_start: 0.8240 (p) cc_final: 0.7812 (t) REVERT: N 227 LEU cc_start: 0.8392 (tp) cc_final: 0.8172 (tm) REVERT: N 351 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7254 (mm-30) REVERT: O 22 MET cc_start: 0.5350 (tpp) cc_final: 0.4963 (tpp) outliers start: 190 outliers final: 125 residues processed: 1192 average time/residue: 1.3175 time to fit residues: 1890.0418 Evaluate side-chains 1229 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1082 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 261 TRP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 260 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 323 SER Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 322 LYS Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 418 THR Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 439 HIS Chi-restraints excluded: chain N residue 8 GLN Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 251 LYS Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 346 HIS Chi-restraints excluded: chain N residue 366 ILE Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 231 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 254 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 195 optimal weight: 0.6980 chunk 235 optimal weight: 0.7980 chunk 250 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 321 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 354 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 236 GLN A 343 ASN B 95 HIS B 151 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 236 ASN B 302 ASN B 391 ASN B 402 ASN E 32 GLN E 77 GLN E 223 GLN E 226 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN J 24 HIS J 69 ASN J 175 HIS ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 343 ASN M 363 HIS ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 358 ASN ** O 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112766 restraints weight = 52175.438| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.26 r_work: 0.3262 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 34076 Z= 0.269 Angle : 0.746 15.845 46512 Z= 0.376 Chirality : 0.051 0.393 5193 Planarity : 0.006 0.069 5965 Dihedral : 6.397 88.980 4801 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 5.04 % Allowed : 32.79 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -0.87 (0.13), residues: 4224 helix: 0.85 (0.21), residues: 568 sheet: -0.40 (0.14), residues: 1368 loop : -1.03 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 384 HIS 0.009 0.001 HIS J 126 PHE 0.023 0.002 PHE I 95 TYR 0.028 0.002 TYR H 163 ARG 0.012 0.001 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 9) link_NAG-ASN : angle 2.67837 ( 27) hydrogen bonds : bond 0.03757 ( 1153) hydrogen bonds : angle 5.39351 ( 2949) SS BOND : bond 0.00512 ( 61) SS BOND : angle 2.32038 ( 122) covalent geometry : bond 0.00615 (34006) covalent geometry : angle 0.73466 (46363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 1084 time to evaluate : 3.929 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 37 ARG cc_start: 0.8993 (mpp80) cc_final: 0.8719 (mtm180) REVERT: A 48 THR cc_start: 0.8687 (m) cc_final: 0.8469 (t) REVERT: A 50 LYS cc_start: 0.8581 (tttm) cc_final: 0.8027 (tttm) REVERT: A 109 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7818 (mt-10) REVERT: A 211 SER cc_start: 0.8287 (m) cc_final: 0.7831 (t) REVERT: A 221 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8155 (ttmt) REVERT: A 235 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8397 (t) REVERT: A 242 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 255 VAL cc_start: 0.8687 (t) cc_final: 0.8347 (m) REVERT: A 301 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6765 (tm-30) REVERT: A 418 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7792 (p) REVERT: B 62 LEU cc_start: 0.8490 (mt) cc_final: 0.8275 (mt) REVERT: B 102 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8016 (mm-40) REVERT: B 121 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8335 (m) REVERT: B 249 LYS cc_start: 0.8397 (mttm) cc_final: 0.8023 (mttm) REVERT: B 263 CYS cc_start: 0.7445 (m) cc_final: 0.7143 (m) REVERT: B 300 ASP cc_start: 0.8150 (t0) cc_final: 0.7817 (t0) REVERT: B 344 ASN cc_start: 0.8162 (t0) cc_final: 0.7908 (t160) REVERT: B 398 LYS cc_start: 0.8330 (tptt) cc_final: 0.8062 (tptp) REVERT: B 399 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7419 (mm) REVERT: D 139 VAL cc_start: 0.8832 (p) cc_final: 0.8596 (m) REVERT: E 54 LYS cc_start: 0.8725 (tttt) cc_final: 0.8348 (tttt) REVERT: E 96 CYS cc_start: 0.8157 (t) cc_final: 0.7343 (m) REVERT: E 113 GLU cc_start: 0.7788 (mp0) cc_final: 0.7256 (mp0) REVERT: E 235 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8252 (t) REVERT: F 27 CYS cc_start: 0.7117 (p) cc_final: 0.6808 (p) REVERT: F 175 HIS cc_start: 0.8178 (p90) cc_final: 0.7972 (p90) REVERT: F 217 CYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7158 (m) REVERT: F 218 THR cc_start: 0.8646 (m) cc_final: 0.8395 (p) REVERT: F 242 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7505 (ttm110) REVERT: F 259 VAL cc_start: 0.8732 (p) cc_final: 0.8455 (m) REVERT: F 376 MET cc_start: 0.7423 (ttp) cc_final: 0.7147 (ttp) REVERT: F 402 ASN cc_start: 0.7963 (m-40) cc_final: 0.7608 (p0) REVERT: H 117 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6500 (mpp) REVERT: H 128 VAL cc_start: 0.8596 (m) cc_final: 0.8151 (m) REVERT: H 175 LEU cc_start: 0.8346 (mm) cc_final: 0.8021 (mm) REVERT: H 177 TYR cc_start: 0.8465 (p90) cc_final: 0.8242 (p90) REVERT: H 220 LYS cc_start: 0.8519 (mptt) cc_final: 0.8241 (mptt) REVERT: H 247 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8287 (mmmm) REVERT: I 2 GLU cc_start: 0.8022 (tp30) cc_final: 0.7737 (tp30) REVERT: I 11 VAL cc_start: 0.8828 (t) cc_final: 0.8616 (p) REVERT: I 47 ILE cc_start: 0.8521 (mt) cc_final: 0.8189 (pp) REVERT: I 96 CYS cc_start: 0.8064 (t) cc_final: 0.7692 (m) REVERT: I 101 THR cc_start: 0.8689 (t) cc_final: 0.8457 (p) REVERT: I 247 ASP cc_start: 0.7438 (m-30) cc_final: 0.7132 (m-30) REVERT: I 276 SER cc_start: 0.8618 (p) cc_final: 0.8327 (m) REVERT: I 305 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8258 (p) REVERT: I 370 VAL cc_start: 0.8435 (t) cc_final: 0.8156 (p) REVERT: I 372 THR cc_start: 0.8339 (m) cc_final: 0.8114 (t) REVERT: I 382 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8252 (mtpp) REVERT: I 400 THR cc_start: 0.8703 (m) cc_final: 0.8446 (t) REVERT: J 6 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.6905 (t80) REVERT: J 131 ARG cc_start: 0.8750 (mtt90) cc_final: 0.8526 (mtt90) REVERT: J 174 ASP cc_start: 0.7867 (t0) cc_final: 0.7598 (t0) REVERT: J 236 ASN cc_start: 0.8405 (t0) cc_final: 0.8180 (t0) REVERT: J 300 ASP cc_start: 0.7864 (t0) cc_final: 0.7509 (t0) REVERT: J 314 VAL cc_start: 0.8115 (t) cc_final: 0.7755 (t) REVERT: J 333 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8190 (mtmm) REVERT: J 344 ASN cc_start: 0.8198 (t0) cc_final: 0.7607 (t0) REVERT: J 354 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8211 (p) REVERT: L 117 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7057 (mmp) REVERT: L 122 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8487 (t) REVERT: L 170 MET cc_start: 0.7756 (pmm) cc_final: 0.7327 (pmm) REVERT: L 194 GLN cc_start: 0.8298 (pt0) cc_final: 0.7904 (pt0) REVERT: L 204 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8083 (ttm-80) REVERT: M 79 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: M 105 GLU cc_start: 0.8031 (pt0) cc_final: 0.7817 (pt0) REVERT: M 112 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8040 (mt-10) REVERT: M 156 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8098 (tmtm) REVERT: M 203 ASP cc_start: 0.8301 (p0) cc_final: 0.8080 (p0) REVERT: M 220 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8217 (pp) REVERT: M 229 ILE cc_start: 0.8808 (mm) cc_final: 0.8576 (mm) REVERT: M 293 GLU cc_start: 0.8355 (tt0) cc_final: 0.8154 (tt0) REVERT: M 367 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8277 (ttmm) REVERT: M 399 PHE cc_start: 0.8086 (t80) cc_final: 0.7543 (t80) REVERT: M 400 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8303 (p) REVERT: N 18 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7980 (t0) REVERT: N 24 HIS cc_start: 0.7650 (t-90) cc_final: 0.7420 (t-90) REVERT: N 68 MET cc_start: 0.8069 (mmm) cc_final: 0.7725 (mmm) REVERT: N 186 LYS cc_start: 0.8542 (tptp) cc_final: 0.7927 (tptp) REVERT: N 196 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7986 (tttp) REVERT: N 218 THR cc_start: 0.8271 (p) cc_final: 0.7880 (t) REVERT: N 227 LEU cc_start: 0.8452 (tp) cc_final: 0.8247 (tm) REVERT: N 351 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7258 (mm-30) REVERT: N 383 VAL cc_start: 0.8458 (t) cc_final: 0.8207 (t) REVERT: N 415 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6341 (mp) REVERT: O 22 MET cc_start: 0.5325 (tpp) cc_final: 0.4931 (tpp) REVERT: P 145 ASN cc_start: 0.8076 (t0) cc_final: 0.7725 (t0) REVERT: P 147 GLN cc_start: 0.8176 (mt0) cc_final: 0.7901 (pp30) outliers start: 184 outliers final: 127 residues processed: 1178 average time/residue: 1.3808 time to fit residues: 1967.7066 Evaluate side-chains 1218 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1069 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 261 TRP Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 346 HIS Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 247 LYS Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 260 CYS Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 418 THR Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 439 HIS Chi-restraints excluded: chain N residue 8 GLN Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 251 LYS Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 346 HIS Chi-restraints excluded: chain N residue 366 ILE Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain N residue 415 ILE Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 15 optimal weight: 0.7980 chunk 318 optimal weight: 5.9990 chunk 273 optimal weight: 0.8980 chunk 307 optimal weight: 0.0030 chunk 293 optimal weight: 1.9990 chunk 394 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.0570 chunk 150 optimal weight: 1.9990 overall best weight: 0.5308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 236 GLN B 95 HIS B 151 ASN B 155 HIS B 175 HIS B 236 ASN B 302 ASN E 77 GLN E 223 GLN E 226 GLN E 343 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN I 223 GLN J 69 ASN J 175 HIS M 100 ASN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 363 HIS N 230 ASN N 285 HIS N 358 ASN O 29 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114090 restraints weight = 52407.648| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.33 r_work: 0.3315 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34076 Z= 0.126 Angle : 0.688 16.335 46512 Z= 0.345 Chirality : 0.048 0.325 5193 Planarity : 0.006 0.071 5965 Dihedral : 6.109 89.313 4801 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 4.14 % Allowed : 33.72 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4224 helix: 1.09 (0.22), residues: 568 sheet: -0.24 (0.15), residues: 1340 loop : -0.95 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 384 HIS 0.005 0.001 HIS N 126 PHE 0.026 0.001 PHE I 95 TYR 0.027 0.001 TYR H 177 ARG 0.009 0.001 ARG B 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 9) link_NAG-ASN : angle 2.74446 ( 27) hydrogen bonds : bond 0.03212 ( 1153) hydrogen bonds : angle 5.18008 ( 2949) SS BOND : bond 0.00369 ( 61) SS BOND : angle 1.90465 ( 122) covalent geometry : bond 0.00297 (34006) covalent geometry : angle 0.67914 (46363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1088 time to evaluate : 3.458 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: A 37 ARG cc_start: 0.8894 (mpp80) cc_final: 0.8676 (mtm180) REVERT: A 48 THR cc_start: 0.8604 (m) cc_final: 0.8390 (t) REVERT: A 50 LYS cc_start: 0.8588 (tttm) cc_final: 0.8126 (tttm) REVERT: A 109 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7918 (mt-10) REVERT: A 192 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7001 (mt-10) REVERT: A 211 SER cc_start: 0.8199 (m) cc_final: 0.7769 (t) REVERT: A 221 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8067 (ttmt) REVERT: A 235 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8339 (t) REVERT: A 242 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7797 (mt-10) REVERT: A 260 CYS cc_start: 0.7748 (m) cc_final: 0.7499 (m) REVERT: A 279 ILE cc_start: 0.8639 (pt) cc_final: 0.8423 (pt) REVERT: A 301 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6653 (tm-30) REVERT: A 382 LYS cc_start: 0.8680 (mtpm) cc_final: 0.8438 (mttp) REVERT: A 418 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7698 (p) REVERT: B 155 HIS cc_start: 0.7384 (m170) cc_final: 0.7152 (m170) REVERT: B 300 ASP cc_start: 0.8094 (t0) cc_final: 0.7769 (t0) REVERT: B 344 ASN cc_start: 0.8058 (t0) cc_final: 0.7813 (t160) REVERT: B 398 LYS cc_start: 0.8173 (tptt) cc_final: 0.7922 (tptp) REVERT: B 399 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7377 (mm) REVERT: D 135 LYS cc_start: 0.7751 (ptmm) cc_final: 0.7361 (ptpt) REVERT: D 139 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8605 (m) REVERT: E 54 LYS cc_start: 0.8733 (tttt) cc_final: 0.8311 (tttt) REVERT: E 96 CYS cc_start: 0.7969 (t) cc_final: 0.7289 (m) REVERT: E 113 GLU cc_start: 0.7713 (mp0) cc_final: 0.7249 (mp0) REVERT: E 223 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8208 (mp10) REVERT: E 246 LYS cc_start: 0.8393 (pttt) cc_final: 0.8158 (pttt) REVERT: F 27 CYS cc_start: 0.6931 (p) cc_final: 0.6642 (p) REVERT: F 93 SER cc_start: 0.8750 (t) cc_final: 0.8544 (t) REVERT: F 205 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7415 (mtt180) REVERT: F 218 THR cc_start: 0.8458 (m) cc_final: 0.8243 (p) REVERT: F 259 VAL cc_start: 0.8659 (p) cc_final: 0.8411 (m) REVERT: F 376 MET cc_start: 0.7385 (ttp) cc_final: 0.7103 (ttp) REVERT: H 128 VAL cc_start: 0.8414 (m) cc_final: 0.8110 (t) REVERT: H 175 LEU cc_start: 0.8218 (mm) cc_final: 0.7912 (mm) REVERT: H 177 TYR cc_start: 0.8453 (p90) cc_final: 0.8232 (p90) REVERT: H 220 LYS cc_start: 0.8507 (mptt) cc_final: 0.8228 (mptt) REVERT: H 247 LYS cc_start: 0.8570 (mmmm) cc_final: 0.8278 (mmmm) REVERT: I 2 GLU cc_start: 0.8013 (tp30) cc_final: 0.7795 (tp30) REVERT: I 11 VAL cc_start: 0.8749 (t) cc_final: 0.8540 (p) REVERT: I 47 ILE cc_start: 0.8500 (mt) cc_final: 0.8131 (pp) REVERT: I 96 CYS cc_start: 0.8032 (t) cc_final: 0.7648 (m) REVERT: I 101 THR cc_start: 0.8604 (t) cc_final: 0.8396 (p) REVERT: I 137 TYR cc_start: 0.8717 (p90) cc_final: 0.7923 (p90) REVERT: I 247 ASP cc_start: 0.7449 (m-30) cc_final: 0.7136 (m-30) REVERT: I 276 SER cc_start: 0.8539 (p) cc_final: 0.8242 (m) REVERT: I 305 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.7321 (t) REVERT: I 382 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8296 (mtpp) REVERT: I 400 THR cc_start: 0.8604 (m) cc_final: 0.8317 (t) REVERT: J 108 THR cc_start: 0.8369 (p) cc_final: 0.8075 (t) REVERT: J 131 ARG cc_start: 0.8724 (mtt90) cc_final: 0.8492 (mtt90) REVERT: J 152 ARG cc_start: 0.8497 (mtp85) cc_final: 0.8295 (mmm160) REVERT: J 174 ASP cc_start: 0.7802 (t0) cc_final: 0.7577 (t0) REVERT: J 226 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: J 236 ASN cc_start: 0.8359 (t0) cc_final: 0.8129 (t0) REVERT: J 300 ASP cc_start: 0.7835 (t0) cc_final: 0.7476 (t0) REVERT: J 314 VAL cc_start: 0.7901 (t) cc_final: 0.7648 (m) REVERT: J 333 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8164 (mtmm) REVERT: J 344 ASN cc_start: 0.8143 (t0) cc_final: 0.7504 (t0) REVERT: J 346 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7520 (m90) REVERT: J 354 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8131 (p) REVERT: J 398 LYS cc_start: 0.7303 (tmtt) cc_final: 0.6985 (ttpt) REVERT: L 117 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7088 (mmp) REVERT: L 122 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8406 (t) REVERT: L 170 MET cc_start: 0.7825 (pmm) cc_final: 0.7467 (pmm) REVERT: L 194 GLN cc_start: 0.8167 (pt0) cc_final: 0.7872 (pt0) REVERT: M 32 GLN cc_start: 0.8454 (tt0) cc_final: 0.8139 (tt0) REVERT: M 79 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8255 (tp40) REVERT: M 105 GLU cc_start: 0.8123 (pt0) cc_final: 0.7900 (pt0) REVERT: M 112 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7990 (mt-10) REVERT: M 133 VAL cc_start: 0.8225 (m) cc_final: 0.7999 (t) REVERT: M 156 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7991 (tmtm) REVERT: M 203 ASP cc_start: 0.8241 (p0) cc_final: 0.8032 (p0) REVERT: M 229 ILE cc_start: 0.8765 (mm) cc_final: 0.8484 (mt) REVERT: M 299 ASP cc_start: 0.7793 (m-30) cc_final: 0.7549 (m-30) REVERT: M 325 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8351 (ptmm) REVERT: M 367 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8260 (ttmm) REVERT: M 399 PHE cc_start: 0.8025 (t80) cc_final: 0.7451 (t80) REVERT: N 18 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7976 (t0) REVERT: N 24 HIS cc_start: 0.7588 (t-90) cc_final: 0.7343 (t-90) REVERT: N 68 MET cc_start: 0.8002 (mmm) cc_final: 0.7613 (mmm) REVERT: N 186 LYS cc_start: 0.8525 (tptp) cc_final: 0.7966 (tptp) REVERT: N 212 ASP cc_start: 0.7876 (m-30) cc_final: 0.7561 (m-30) REVERT: N 216 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8224 (p) REVERT: N 217 CYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6177 (m) REVERT: N 218 THR cc_start: 0.8214 (p) cc_final: 0.7771 (t) REVERT: N 227 LEU cc_start: 0.8370 (tp) cc_final: 0.8165 (tm) REVERT: N 247 THR cc_start: 0.7470 (OUTLIER) cc_final: 0.6979 (t) REVERT: N 351 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7183 (mm-30) REVERT: N 383 VAL cc_start: 0.8404 (t) cc_final: 0.8161 (t) REVERT: N 415 ILE cc_start: 0.6406 (OUTLIER) cc_final: 0.6198 (mp) REVERT: P 145 ASN cc_start: 0.7891 (t0) cc_final: 0.7437 (t0) REVERT: P 147 GLN cc_start: 0.8166 (mt0) cc_final: 0.7917 (pp30) outliers start: 151 outliers final: 108 residues processed: 1160 average time/residue: 1.3283 time to fit residues: 1853.3000 Evaluate side-chains 1215 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 1088 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 261 TRP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 309 GLU Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 260 CYS Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 306 GLU Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 418 THR Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 439 HIS Chi-restraints excluded: chain N residue 8 GLN Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 217 CYS Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 247 THR Chi-restraints excluded: chain N residue 251 LYS Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 346 HIS Chi-restraints excluded: chain N residue 366 ILE Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain N residue 394 ILE Chi-restraints excluded: chain N residue 415 ILE Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 134 optimal weight: 5.9990 chunk 414 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 361 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 chunk 71 optimal weight: 0.0770 chunk 29 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 380 optimal weight: 20.0000 chunk 300 optimal weight: 0.9990 chunk 360 optimal weight: 0.7980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 343 ASN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 175 HIS B 236 ASN B 302 ASN B 391 ASN E 77 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 HIS F 82 HIS F 118 ASN F 175 HIS I 223 GLN I 439 HIS J 69 ASN J 175 HIS L 197 ASN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 343 ASN M 363 HIS N 69 ASN ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 358 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117189 restraints weight = 52550.717| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.27 r_work: 0.3324 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34076 Z= 0.124 Angle : 0.683 16.026 46512 Z= 0.341 Chirality : 0.047 0.348 5193 Planarity : 0.006 0.078 5965 Dihedral : 5.916 89.943 4799 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 3.84 % Allowed : 34.24 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % 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: -0.66 (0.13), residues: 4224 helix: 1.08 (0.22), residues: 572 sheet: -0.16 (0.15), residues: 1308 loop : -0.97 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 384 HIS 0.006 0.001 HIS B 114 PHE 0.026 0.001 PHE I 95 TYR 0.027 0.001 TYR L 177 ARG 0.011 0.001 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 9) link_NAG-ASN : angle 2.64803 ( 27) hydrogen bonds : bond 0.03182 ( 1153) hydrogen bonds : angle 5.10887 ( 2949) SS BOND : bond 0.00344 ( 61) SS BOND : angle 1.91122 ( 122) covalent geometry : bond 0.00292 (34006) covalent geometry : angle 0.67383 (46363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35951.32 seconds wall clock time: 614 minutes 36.84 seconds (36876.84 seconds total)