Starting phenix.real_space_refine on Fri May 30 01:16:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua9_42055/05_2025/8ua9_42055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua9_42055/05_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_42055/05_2025/8ua9_42055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua9_42055/05_2025/8ua9_42055.map" model { file = "/net/cci-nas-00/data/ceres_data/8ua9_42055/05_2025/8ua9_42055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua9_42055/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 18.22, per 1000 atoms: 0.55 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: 7.83 Conformation dependent library (CDL) restraints added in 4.3 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: 5.28 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: 12.77 Time building geometry restraints manager: 9.23 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 70.740 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.170 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.730 ------------------------------------------------------------------------------- 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 : 3.417 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: 1.3292 time to fit residues: 1870.8082 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 : 3.589 ------------------------------------------------------------------------------- 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 = 0.129254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114002 restraints weight = 52198.755| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.26 r_work: 0.3307 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- 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 12.966 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 2.72303 ( 27) hydrogen bonds : bond 0.04169 ( 1153) hydrogen bonds : angle 5.96803 ( 2949) SS BOND : bond 0.00516 ( 61) SS BOND : angle 2.34846 ( 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 : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8389 (m) REVERT: A 30 GLN cc_start: 0.8458 (tt0) cc_final: 0.8254 (tt0) REVERT: A 37 ARG cc_start: 0.8960 (mpp80) cc_final: 0.8622 (mtm180) REVERT: A 50 LYS cc_start: 0.8553 (tttm) cc_final: 0.8097 (tttm) REVERT: A 54 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8138 (ttpp) REVERT: A 75 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: A 88 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7601 (ptp) REVERT: A 109 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 192 GLU cc_start: 0.7085 (tt0) cc_final: 0.6788 (tt0) REVERT: A 211 SER cc_start: 0.8148 (m) cc_final: 0.7678 (p) REVERT: A 242 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7795 (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: 0.7496 (OUTLIER) cc_final: 0.7035 (t80) REVERT: B 62 LEU cc_start: 0.8552 (mt) cc_final: 0.8283 (mt) REVERT: B 172 VAL cc_start: 0.8495 (t) cc_final: 0.8232 (p) REVERT: B 200 LYS cc_start: 0.8185 (tmtt) cc_final: 0.7926 (tmtt) REVERT: B 210 SER cc_start: 0.8330 (t) cc_final: 0.7964 (p) REVERT: B 274 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 300 ASP cc_start: 0.7966 (t0) cc_final: 0.7739 (t0) REVERT: B 376 MET cc_start: 0.7211 (tpp) cc_final: 0.7001 (tpp) REVERT: B 399 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7700 (mm) REVERT: D 117 MET cc_start: 0.6291 (tmm) cc_final: 0.5948 (tmm) REVERT: D 206 VAL cc_start: 0.6999 (OUTLIER) cc_final: 0.6791 (t) REVERT: E 16 LYS cc_start: 0.8927 (mttt) cc_final: 0.8700 (mttt) REVERT: E 54 LYS cc_start: 0.8699 (tttt) cc_final: 0.8351 (tttt) REVERT: E 103 MET cc_start: 0.8545 (ttm) cc_final: 0.8336 (ttm) REVERT: E 113 GLU cc_start: 0.7702 (mp0) cc_final: 0.7274 (mp0) REVERT: E 156 LYS cc_start: 0.8644 (tppt) cc_final: 0.8296 (tppt) REVERT: E 305 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8238 (p) REVERT: F 74 LYS cc_start: 0.8894 (ptmt) cc_final: 0.8692 (tttp) REVERT: F 136 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7271 (mt-10) REVERT: F 175 HIS cc_start: 0.8305 (p-80) cc_final: 0.8094 (p90) REVERT: F 178 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8014 (mm) REVERT: F 217 CYS cc_start: 0.7489 (m) cc_final: 0.7186 (m) REVERT: F 259 VAL cc_start: 0.8697 (p) cc_final: 0.8407 (m) REVERT: F 370 THR cc_start: 0.8110 (t) cc_final: 0.7834 (p) REVERT: G 22 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6905 (mmp) REVERT: G 48 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7605 (mm-40) REVERT: H 129 VAL cc_start: 0.8330 (t) cc_final: 0.8040 (p) REVERT: H 132 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6513 (mtt90) REVERT: I 69 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8095 (p) REVERT: I 96 CYS cc_start: 0.8018 (t) cc_final: 0.7706 (t) REVERT: I 137 TYR cc_start: 0.8729 (p90) cc_final: 0.8173 (p90) REVERT: I 246 LYS cc_start: 0.8545 (pttt) cc_final: 0.8151 (ptmm) REVERT: I 296 THR cc_start: 0.8752 (p) cc_final: 0.8534 (t) REVERT: I 305 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8361 (p) REVERT: I 426 LEU cc_start: 0.8199 (mt) cc_final: 0.7975 (mm) REVERT: J 6 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6783 (t80) REVERT: J 200 LYS cc_start: 0.8085 (tppp) cc_final: 0.7873 (tppp) REVERT: K 22 MET cc_start: 0.6929 (tpp) cc_final: 0.6581 (tpp) REVERT: L 193 VAL cc_start: 0.7854 (t) cc_final: 0.7603 (m) REVERT: M 35 ASN cc_start: 0.8695 (p0) cc_final: 0.8489 (p0) REVERT: M 61 LYS cc_start: 0.8243 (mmmm) cc_final: 0.8006 (tppp) REVERT: M 75 ASP cc_start: 0.8272 (t0) cc_final: 0.7959 (t0) REVERT: M 141 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7812 (p) REVERT: M 150 ASN cc_start: 0.8354 (p0) cc_final: 0.8146 (p0) REVERT: M 175 ASP cc_start: 0.7920 (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: 0.8611 (t0) cc_final: 0.8306 (t0) REVERT: M 426 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7526 (mm) REVERT: N 65 MET cc_start: 0.7838 (ptt) cc_final: 0.7450 (ptp) REVERT: N 186 LYS cc_start: 0.8547 (tptp) cc_final: 0.8214 (tptp) REVERT: N 221 LYS cc_start: 0.8848 (ptpt) cc_final: 0.8629 (ptpt) REVERT: N 295 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8665 (ptt180) REVERT: N 302 ASN cc_start: 0.8457 (t0) cc_final: 0.8175 (t0) REVERT: N 351 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7534 (mm-30) REVERT: N 364 THR cc_start: 0.8721 (t) cc_final: 0.8516 (t) REVERT: O 22 MET cc_start: 0.5952 (tpp) cc_final: 0.5328 (tpp) outliers start: 224 outliers final: 107 residues processed: 1205 average time/residue: 1.2798 time to fit residues: 1858.4881 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 : 3.492 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 302 optimal weight: 0.3980 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 E 441 HIS F 8 GLN F 118 ASN F 151 ASN I 223 GLN I 369 GLN I 439 HIS J 24 HIS J 69 ASN J 402 ASN M 30 GLN M 32 GLN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 HIS M 361 ASN M 363 HIS N 151 ASN N 213 HIS N 222 GLN N 230 ASN N 358 ASN P 145 ASN P 198 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111892 restraints weight = 52416.773| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.29 r_work: 0.3281 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 34076 Z= 0.228 Angle : 0.723 13.420 46512 Z= 0.369 Chirality : 0.050 0.356 5193 Planarity : 0.006 0.078 5965 Dihedral : 6.885 77.408 4819 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.41 % Rotamer: Outliers : 7.13 % Allowed : 27.17 % Favored : 65.71 % 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: -0.90 (0.13), residues: 4224 helix: 0.82 (0.21), residues: 564 sheet: -0.50 (0.14), residues: 1408 loop : -0.98 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 188 HIS 0.009 0.001 HIS J 82 PHE 0.018 0.002 PHE L 134 TYR 0.023 0.002 TYR O 26 ARG 0.009 0.001 ARG H 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 9) link_NAG-ASN : angle 2.57139 ( 27) hydrogen bonds : bond 0.04003 ( 1153) hydrogen bonds : angle 5.74258 ( 2949) SS BOND : bond 0.00555 ( 61) SS BOND : angle 2.01295 ( 122) covalent geometry : bond 0.00524 (34006) covalent geometry : angle 0.71417 (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 1313 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 1053 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8433 (ttt180) REVERT: A 37 ARG cc_start: 0.8969 (mpp80) cc_final: 0.8667 (mtm180) REVERT: A 50 LYS cc_start: 0.8561 (tttm) cc_final: 0.8010 (tttm) REVERT: A 54 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8332 (ttmm) REVERT: A 75 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: A 192 GLU cc_start: 0.7161 (tt0) cc_final: 0.6838 (mt-10) REVERT: A 211 SER cc_start: 0.8186 (m) cc_final: 0.7703 (p) REVERT: A 242 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7836 (mt-10) REVERT: A 245 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8415 (mtmt) REVERT: B 6 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7020 (t80) REVERT: B 62 LEU cc_start: 0.8508 (mt) cc_final: 0.8201 (mt) REVERT: B 102 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8060 (mm-40) REVERT: B 172 VAL cc_start: 0.8509 (t) cc_final: 0.8159 (p) REVERT: B 200 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8005 (tmtt) REVERT: B 249 LYS cc_start: 0.8317 (mttm) cc_final: 0.8009 (mttm) REVERT: B 300 ASP cc_start: 0.8048 (t0) cc_final: 0.7803 (t0) REVERT: B 344 ASN cc_start: 0.8129 (t0) cc_final: 0.7904 (t160) REVERT: B 399 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7722 (mm) REVERT: D 117 MET cc_start: 0.6329 (tmm) cc_final: 0.5865 (tmm) REVERT: D 193 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8402 (t) REVERT: E 54 LYS cc_start: 0.8702 (tttt) cc_final: 0.8373 (tttt) REVERT: E 96 CYS cc_start: 0.8059 (t) cc_final: 0.7078 (m) REVERT: E 223 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8241 (mp10) REVERT: E 303 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8156 (ttpp) REVERT: E 305 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8171 (p) REVERT: E 367 LYS cc_start: 0.8599 (tttt) cc_final: 0.8398 (tttt) REVERT: E 382 LYS cc_start: 0.8662 (mttm) cc_final: 0.8383 (mttm) REVERT: F 73 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: F 74 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8654 (tttp) REVERT: F 217 CYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7180 (m) REVERT: F 259 VAL cc_start: 0.8700 (p) cc_final: 0.8415 (m) REVERT: G 22 MET cc_start: 0.7200 (mmp) cc_final: 0.6769 (mmp) REVERT: G 48 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7604 (mm-40) REVERT: H 129 VAL cc_start: 0.8306 (t) cc_final: 0.8033 (p) REVERT: H 132 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6249 (mmm-85) REVERT: H 175 LEU cc_start: 0.8354 (mm) cc_final: 0.8123 (mm) REVERT: H 247 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8362 (mmmm) REVERT: I 75 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: I 96 CYS cc_start: 0.8098 (t) cc_final: 0.7800 (t) REVERT: I 101 THR cc_start: 0.8488 (t) cc_final: 0.8228 (p) REVERT: I 137 TYR cc_start: 0.8756 (p90) cc_final: 0.8031 (p90) REVERT: I 305 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8316 (p) REVERT: I 382 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8302 (mtpp) REVERT: I 422 ILE cc_start: 0.8137 (mm) cc_final: 0.7899 (mm) REVERT: I 426 LEU cc_start: 0.8218 (mt) cc_final: 0.7994 (mm) REVERT: J 6 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.6786 (t80) REVERT: J 37 ARG cc_start: 0.8737 (mmp-170) cc_final: 0.8529 (mmt180) REVERT: J 200 LYS cc_start: 0.8145 (tppp) cc_final: 0.7924 (tppp) REVERT: J 263 CYS cc_start: 0.7109 (m) cc_final: 0.6769 (m) REVERT: J 354 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8160 (p) REVERT: K 22 MET cc_start: 0.7190 (tpp) cc_final: 0.6699 (tpp) REVERT: L 117 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7176 (mmp) REVERT: L 177 TYR cc_start: 0.7953 (p90) cc_final: 0.7735 (p90) REVERT: L 193 VAL cc_start: 0.7922 (t) cc_final: 0.7631 (m) REVERT: L 204 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.7876 (ttm-80) REVERT: M 141 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7805 (p) REVERT: M 161 LYS cc_start: 0.8351 (mtpp) cc_final: 0.8057 (ttpp) REVERT: M 175 ASP cc_start: 0.7875 (m-30) cc_final: 0.7575 (m-30) REVERT: M 214 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8248 (tt) REVERT: M 217 ASN cc_start: 0.8722 (t0) cc_final: 0.8421 (t0) REVERT: M 220 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8075 (pp) REVERT: M 300 LEU cc_start: 0.8663 (mt) cc_final: 0.8429 (mt) REVERT: M 400 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8152 (p) REVERT: M 439 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7834 (t-170) REVERT: N 65 MET cc_start: 0.7930 (ptt) cc_final: 0.7623 (ptp) REVERT: N 186 LYS cc_start: 0.8534 (tptp) cc_final: 0.7954 (tptt) REVERT: N 196 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8062 (tttp) REVERT: N 260 LYS cc_start: 0.8863 (tptp) cc_final: 0.8598 (tptp) REVERT: N 295 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8631 (ptt180) REVERT: N 314 VAL cc_start: 0.8794 (t) cc_final: 0.8448 (m) REVERT: N 351 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7399 (mm-30) REVERT: O 22 MET cc_start: 0.5285 (tpp) cc_final: 0.4772 (tpp) outliers start: 260 outliers final: 147 residues processed: 1182 average time/residue: 1.2551 time to fit residues: 1793.7477 Evaluate side-chains 1229 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 1055 time to evaluate : 3.465 ------------------------------------------------------------------------------- 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 75 ASP Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 126 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 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 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 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 386 LEU Chi-restraints excluded: chain B residue 388 ARG 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 D residue 188 TRP Chi-restraints excluded: chain D residue 193 VAL 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 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 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 75 ASP 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 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 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 35 GLU Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 100 LEU 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 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 J residue 405 VAL Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 33 THR 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 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 141 SER Chi-restraints excluded: chain M residue 209 SER Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 220 LEU 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 318 THR 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 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 62 LEU Chi-restraints excluded: chain N residue 74 LYS 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 295 ARG Chi-restraints excluded: chain N residue 304 THR 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 399 LEU Chi-restraints excluded: chain P residue 128 VAL 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: 8.9990 chunk 253 optimal weight: 5.9990 chunk 366 optimal weight: 6.9990 chunk 315 optimal weight: 4.9990 chunk 417 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 226 GLN A 343 ASN A 439 HIS 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 F 82 HIS F 151 ASN F 213 HIS G 40 ASN I 223 GLN I 328 ASN I 439 HIS J 24 HIS J 69 ASN K 39 GLN M 30 GLN M 125 HIS M 361 ASN M 363 HIS N 151 ASN N 230 ASN N 358 ASN O 29 ASN P 145 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111433 restraints weight = 52349.474| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.30 r_work: 0.3276 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34076 Z= 0.217 Angle : 0.705 14.436 46512 Z= 0.358 Chirality : 0.049 0.336 5193 Planarity : 0.006 0.074 5965 Dihedral : 6.679 78.999 4813 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.97 % Favored : 93.92 % Rotamer: Outliers : 7.43 % Allowed : 27.03 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 4224 helix: 0.87 (0.21), residues: 564 sheet: -0.49 (0.14), residues: 1340 loop : -0.96 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 188 HIS 0.008 0.001 HIS F 175 PHE 0.017 0.002 PHE L 134 TYR 0.022 0.002 TYR P 195 ARG 0.011 0.001 ARG H 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 9) link_NAG-ASN : angle 2.70556 ( 27) hydrogen bonds : bond 0.03812 ( 1153) hydrogen bonds : angle 5.60339 ( 2949) SS BOND : bond 0.00447 ( 61) SS BOND : angle 2.06224 ( 122) covalent geometry : bond 0.00496 (34006) covalent geometry : angle 0.69539 (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 1367 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 1096 time to evaluate : 3.464 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: 0.8897 (OUTLIER) cc_final: 0.8448 (ttt180) REVERT: A 37 ARG cc_start: 0.8976 (mpp80) cc_final: 0.8651 (mpp-170) REVERT: A 48 THR cc_start: 0.8694 (m) cc_final: 0.8399 (t) REVERT: A 50 LYS cc_start: 0.8578 (tttm) cc_final: 0.8010 (tttm) REVERT: A 54 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8258 (ttmm) REVERT: A 211 SER cc_start: 0.8184 (OUTLIER) cc_final: 0.7707 (p) REVERT: A 235 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8392 (t) REVERT: A 242 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 245 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8415 (mtmt) REVERT: A 255 VAL cc_start: 0.8615 (t) cc_final: 0.8259 (m) REVERT: A 260 CYS cc_start: 0.7654 (m) cc_final: 0.7425 (m) REVERT: B 6 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6983 (t80) REVERT: B 62 LEU cc_start: 0.8591 (mt) cc_final: 0.8269 (mt) REVERT: B 102 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8038 (mm-40) REVERT: B 200 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.8024 (tmtt) REVERT: B 228 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8090 (pt) REVERT: B 300 ASP cc_start: 0.8072 (t0) cc_final: 0.7784 (t0) REVERT: B 344 ASN cc_start: 0.8100 (t0) cc_final: 0.7857 (t160) REVERT: B 399 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7654 (mm) REVERT: D 233 GLU cc_start: 0.4603 (OUTLIER) cc_final: 0.3943 (tp30) REVERT: E 54 LYS cc_start: 0.8702 (tttt) cc_final: 0.8366 (tttt) REVERT: E 89 TRP cc_start: 0.8752 (p-90) cc_final: 0.8427 (p-90) REVERT: E 96 CYS cc_start: 0.8066 (t) cc_final: 0.7094 (m) REVERT: E 103 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8403 (ttm) REVERT: E 113 GLU cc_start: 0.7696 (mp0) cc_final: 0.7226 (mp0) REVERT: E 223 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8238 (mp10) REVERT: E 305 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8265 (p) REVERT: F 73 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: F 74 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8609 (tttp) REVERT: F 217 CYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7187 (m) REVERT: F 259 VAL cc_start: 0.8701 (p) cc_final: 0.8425 (m) REVERT: F 398 LYS cc_start: 0.8680 (tppp) cc_final: 0.8475 (ttmm) REVERT: G 6 MET cc_start: 0.6161 (mmm) cc_final: 0.5934 (mmm) REVERT: H 129 VAL cc_start: 0.8328 (t) cc_final: 0.8080 (p) REVERT: H 132 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6270 (mmm-85) REVERT: H 139 VAL cc_start: 0.8735 (p) cc_final: 0.8535 (m) REVERT: H 175 LEU cc_start: 0.8340 (mm) cc_final: 0.8080 (mm) REVERT: H 247 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8327 (mmmm) REVERT: I 96 CYS cc_start: 0.8078 (t) cc_final: 0.7807 (t) REVERT: I 101 THR cc_start: 0.8550 (t) cc_final: 0.8301 (p) REVERT: I 137 TYR cc_start: 0.8783 (p90) cc_final: 0.8044 (p90) REVERT: I 217 ASN cc_start: 0.8688 (t0) cc_final: 0.8461 (t0) REVERT: I 247 ASP cc_start: 0.7419 (m-30) cc_final: 0.7051 (m-30) REVERT: I 305 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8219 (p) REVERT: I 323 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7997 (t) REVERT: I 382 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8298 (mtpp) REVERT: I 404 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.7792 (p) REVERT: I 422 ILE cc_start: 0.8136 (mm) cc_final: 0.7863 (mm) REVERT: J 6 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6813 (t80) REVERT: J 131 ARG cc_start: 0.8711 (mtt90) cc_final: 0.8466 (mtt90) REVERT: J 168 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8647 (tp40) REVERT: J 174 ASP cc_start: 0.7906 (t0) cc_final: 0.7608 (t0) REVERT: J 200 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7787 (tppp) REVERT: J 263 CYS cc_start: 0.7036 (m) cc_final: 0.6650 (m) REVERT: J 300 ASP cc_start: 0.7817 (t0) cc_final: 0.7442 (t0) REVERT: J 314 VAL cc_start: 0.8094 (t) cc_final: 0.7711 (t) REVERT: J 354 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8152 (p) REVERT: L 117 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7191 (mmp) REVERT: L 204 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8128 (ttm-80) REVERT: M 141 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7810 (p) REVERT: M 175 ASP cc_start: 0.7886 (m-30) cc_final: 0.7617 (m-30) REVERT: M 220 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8054 (pp) REVERT: M 229 ILE cc_start: 0.8718 (mm) cc_final: 0.8449 (mt) REVERT: M 293 GLU cc_start: 0.8144 (tt0) cc_final: 0.7788 (tt0) REVERT: M 300 LEU cc_start: 0.8704 (mt) cc_final: 0.8503 (mt) REVERT: M 342 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: M 400 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8229 (p) REVERT: N 18 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7998 (t0) REVERT: N 65 MET cc_start: 0.7964 (ptt) cc_final: 0.7715 (ptp) REVERT: N 186 LYS cc_start: 0.8560 (tptp) cc_final: 0.8255 (tptp) REVERT: N 196 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8101 (tttp) REVERT: N 227 LEU cc_start: 0.8399 (tt) cc_final: 0.8159 (tm) REVERT: N 295 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8537 (ptt180) REVERT: N 314 VAL cc_start: 0.8849 (t) cc_final: 0.8484 (m) REVERT: N 351 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7333 (mm-30) REVERT: N 399 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8776 (mt) REVERT: O 22 MET cc_start: 0.5459 (tpp) cc_final: 0.4971 (tpp) REVERT: P 129 VAL cc_start: 0.8249 (t) cc_final: 0.7934 (m) outliers start: 271 outliers final: 149 residues processed: 1233 average time/residue: 1.3036 time to fit residues: 1937.8230 Evaluate side-chains 1265 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 1083 time to evaluate : 3.830 ------------------------------------------------------------------------------- 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 82 SER Chi-restraints excluded: chain A residue 124 VAL 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 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 18 ASP 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 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 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 388 ARG 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 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 D residue 233 GLU 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 305 THR Chi-restraints excluded: chain E residue 335 SER 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 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 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 378 SER Chi-restraints excluded: chain F residue 393 CYS 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 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 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 272 CYS 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 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 100 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 168 GLN 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 249 LYS Chi-restraints excluded: chain J residue 257 VAL 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 J residue 405 VAL 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 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 L residue 251 VAL Chi-restraints excluded: chain L residue 254 THR 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 139 SER Chi-restraints excluded: chain M residue 141 SER 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 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 66 SER 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 295 ARG Chi-restraints excluded: chain N residue 304 THR 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 N residue 399 LEU Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 143 ILE 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: 0.9990 chunk 311 optimal weight: 6.9990 chunk 343 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 402 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 415 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 144 HIS B 151 ASN B 155 HIS 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 194 GLN I 32 GLN I 439 HIS J 24 HIS J 69 ASN M 30 GLN M 125 HIS M 361 ASN M 363 HIS N 151 ASN N 230 ASN N 358 ASN P 145 ASN P 198 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111293 restraints weight = 52103.295| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.29 r_work: 0.3273 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2035 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= 0.217 Angle : 0.703 14.823 46512 Z= 0.356 Chirality : 0.049 0.325 5193 Planarity : 0.006 0.072 5965 Dihedral : 6.617 80.541 4811 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.92 % Favored : 93.96 % Rotamer: Outliers : 7.51 % Allowed : 28.37 % Favored : 64.12 % 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: -0.84 (0.13), residues: 4224 helix: 0.88 (0.21), residues: 564 sheet: -0.48 (0.14), residues: 1368 loop : -0.93 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 188 HIS 0.008 0.001 HIS N 126 PHE 0.018 0.002 PHE I 95 TYR 0.023 0.002 TYR P 195 ARG 0.008 0.001 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 9) link_NAG-ASN : angle 2.59915 ( 27) hydrogen bonds : bond 0.03737 ( 1153) hydrogen bonds : angle 5.54906 ( 2949) SS BOND : bond 0.00501 ( 61) SS BOND : angle 1.86319 ( 122) covalent geometry : bond 0.00496 (34006) covalent geometry : angle 0.69436 (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 1368 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 274 poor density : 1094 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8511 (ttt180) REVERT: A 37 ARG cc_start: 0.8989 (mpp80) cc_final: 0.8678 (mpp-170) REVERT: A 48 THR cc_start: 0.8700 (m) cc_final: 0.8415 (t) REVERT: A 50 LYS cc_start: 0.8594 (tttm) cc_final: 0.8013 (tttm) REVERT: A 54 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8225 (ttpp) REVERT: A 211 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7755 (t) REVERT: A 221 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8156 (ttmt) REVERT: A 235 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8381 (t) REVERT: A 242 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7834 (mt-10) REVERT: A 245 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8427 (mtmt) REVERT: A 255 VAL cc_start: 0.8638 (t) cc_final: 0.8285 (m) REVERT: A 260 CYS cc_start: 0.7679 (m) cc_final: 0.7474 (m) REVERT: B 6 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6970 (t80) REVERT: B 62 LEU cc_start: 0.8504 (mt) cc_final: 0.8168 (mt) REVERT: B 102 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8042 (mm-40) REVERT: B 300 ASP cc_start: 0.8098 (t0) cc_final: 0.7821 (t0) REVERT: B 344 ASN cc_start: 0.8108 (t0) cc_final: 0.7865 (t160) REVERT: B 399 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7552 (mm) REVERT: D 220 LYS cc_start: 0.8271 (mptt) cc_final: 0.8066 (mptt) REVERT: D 233 GLU cc_start: 0.4568 (OUTLIER) cc_final: 0.3489 (tp30) REVERT: E 54 LYS cc_start: 0.8715 (tttt) cc_final: 0.8386 (tttt) REVERT: E 96 CYS cc_start: 0.8117 (t) cc_final: 0.7128 (m) REVERT: E 103 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8358 (ttm) REVERT: E 113 GLU cc_start: 0.7723 (mp0) cc_final: 0.7223 (mp0) REVERT: E 223 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8178 (mp10) REVERT: F 74 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8614 (tttp) REVERT: F 217 CYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7173 (m) REVERT: F 259 VAL cc_start: 0.8696 (p) cc_final: 0.8428 (m) REVERT: F 376 MET cc_start: 0.7382 (ttp) cc_final: 0.7107 (ttp) REVERT: F 398 LYS cc_start: 0.8676 (tppp) cc_final: 0.8452 (ttmm) REVERT: G 48 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7570 (mm-40) REVERT: H 129 VAL cc_start: 0.8334 (t) cc_final: 0.8095 (p) REVERT: H 132 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6431 (mmm-85) REVERT: H 139 VAL cc_start: 0.8709 (p) cc_final: 0.8507 (m) REVERT: H 154 LYS cc_start: 0.8529 (tmmt) cc_final: 0.8246 (pttm) REVERT: H 175 LEU cc_start: 0.8332 (mm) cc_final: 0.8028 (mm) REVERT: H 247 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8307 (mmmm) REVERT: I 96 CYS cc_start: 0.8070 (t) cc_final: 0.7743 (t) REVERT: I 101 THR cc_start: 0.8602 (t) cc_final: 0.8330 (p) REVERT: I 103 MET cc_start: 0.8384 (ttp) cc_final: 0.8045 (ttp) REVERT: I 137 TYR cc_start: 0.8784 (p90) cc_final: 0.8036 (p90) REVERT: I 247 ASP cc_start: 0.7420 (m-30) cc_final: 0.7040 (m-30) REVERT: I 305 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8199 (p) REVERT: I 382 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8272 (mtpp) REVERT: I 404 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7672 (p) REVERT: J 6 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6880 (t80) REVERT: J 108 THR cc_start: 0.8479 (p) cc_final: 0.8160 (t) REVERT: J 168 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8651 (tp40) REVERT: J 174 ASP cc_start: 0.7861 (t0) cc_final: 0.7572 (t0) REVERT: J 200 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7675 (tppp) REVERT: J 300 ASP cc_start: 0.7819 (t0) cc_final: 0.7441 (t0) REVERT: J 314 VAL cc_start: 0.8094 (t) cc_final: 0.7718 (t) REVERT: J 333 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8181 (mtmm) REVERT: J 344 ASN cc_start: 0.8133 (t0) cc_final: 0.7586 (t0) REVERT: J 354 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8220 (p) REVERT: K 25 CYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7127 (t) REVERT: L 117 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7253 (mmp) REVERT: L 194 GLN cc_start: 0.8189 (pt0) cc_final: 0.7916 (pm20) REVERT: L 204 ARG cc_start: 0.8507 (ttm-80) cc_final: 0.8268 (ttm-80) REVERT: M 32 GLN cc_start: 0.8473 (tt0) cc_final: 0.8179 (tt0) REVERT: M 99 GLU cc_start: 0.7607 (pt0) cc_final: 0.7384 (pt0) REVERT: M 141 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7817 (p) REVERT: M 146 ASP cc_start: 0.8019 (t0) cc_final: 0.7796 (t0) REVERT: M 175 ASP cc_start: 0.7904 (m-30) cc_final: 0.7626 (m-30) REVERT: M 293 GLU cc_start: 0.8240 (tt0) cc_final: 0.7885 (tt0) REVERT: M 342 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: M 400 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8263 (p) REVERT: N 65 MET cc_start: 0.8067 (ptt) cc_final: 0.7807 (ptp) REVERT: N 168 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: N 186 LYS cc_start: 0.8539 (tptp) cc_final: 0.8219 (tptp) REVERT: N 196 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8092 (tttp) REVERT: N 212 ASP cc_start: 0.8061 (m-30) cc_final: 0.7827 (m-30) REVERT: N 227 LEU cc_start: 0.8416 (tt) cc_final: 0.8181 (tm) REVERT: N 295 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8533 (ptt180) REVERT: N 351 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7209 (mm-30) REVERT: O 22 MET cc_start: 0.5346 (tpp) cc_final: 0.4891 (tpp) REVERT: P 129 VAL cc_start: 0.8262 (t) cc_final: 0.7946 (m) outliers start: 274 outliers final: 183 residues processed: 1223 average time/residue: 1.2877 time to fit residues: 1905.4613 Evaluate side-chains 1286 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 1074 time to evaluate : 3.313 ------------------------------------------------------------------------------- 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 82 SER 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 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 18 ASP 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 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 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 388 ARG 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 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 D residue 233 GLU 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 335 SER Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain F residue 55 LEU 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 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 378 SER Chi-restraints excluded: chain F residue 402 ASN 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 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 50 LYS 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 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 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 165 GLU Chi-restraints excluded: chain J residue 168 GLN 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 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 354 VAL 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 J residue 405 VAL Chi-restraints excluded: chain K residue 25 CYS 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 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 247 LYS Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain L residue 254 THR 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 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 297 VAL Chi-restraints excluded: chain M residue 306 GLU 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 8 GLN 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 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 251 LYS Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 295 ARG Chi-restraints excluded: chain N residue 304 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 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 206 VAL Chi-restraints excluded: chain P residue 222 ARG Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 249 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 80 optimal weight: 9.9990 chunk 300 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 182 optimal weight: 8.9990 chunk 341 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 175 HIS B 236 ASN B 302 ASN B 391 ASN B 402 ASN E 226 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 HIS F 82 HIS F 118 ASN F 151 ASN ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN I 439 HIS J 24 HIS J 69 ASN J 402 ASN ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN M 125 HIS ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 ASN M 363 HIS N 151 ASN N 230 ASN N 358 ASN P 145 ASN P 198 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111634 restraints weight = 52845.978| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.26 r_work: 0.3279 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34076 Z= 0.208 Angle : 0.698 15.699 46512 Z= 0.353 Chirality : 0.049 0.320 5193 Planarity : 0.006 0.071 5965 Dihedral : 6.522 82.442 4810 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 7.62 % Allowed : 28.73 % Favored : 63.65 % 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: -0.86 (0.13), residues: 4224 helix: 0.93 (0.21), residues: 564 sheet: -0.50 (0.14), residues: 1364 loop : -0.95 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 188 HIS 0.007 0.001 HIS N 126 PHE 0.021 0.002 PHE I 95 TYR 0.023 0.002 TYR H 125 ARG 0.009 0.001 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 9) link_NAG-ASN : angle 2.58884 ( 27) hydrogen bonds : bond 0.03671 ( 1153) hydrogen bonds : angle 5.49517 ( 2949) SS BOND : bond 0.00461 ( 61) SS BOND : angle 1.95310 ( 122) covalent geometry : bond 0.00478 (34006) covalent geometry : angle 0.68941 (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 1372 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 1094 time to evaluate : 3.534 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: 0.8919 (OUTLIER) cc_final: 0.8590 (ttt180) REVERT: A 37 ARG cc_start: 0.8998 (mpp80) cc_final: 0.8709 (mpp-170) REVERT: A 48 THR cc_start: 0.8694 (m) cc_final: 0.8424 (t) REVERT: A 50 LYS cc_start: 0.8592 (tttm) cc_final: 0.8011 (tttm) REVERT: A 54 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8208 (ttpp) REVERT: A 95 PHE cc_start: 0.8222 (t80) cc_final: 0.8002 (t80) REVERT: A 156 LYS cc_start: 0.8758 (tppt) cc_final: 0.8516 (mmtm) REVERT: A 211 SER cc_start: 0.8228 (m) cc_final: 0.7764 (t) REVERT: A 221 LYS cc_start: 0.8435 (ttmt) cc_final: 0.7909 (ttmt) REVERT: A 223 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: A 235 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8361 (t) REVERT: A 242 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 245 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8416 (mtmt) REVERT: A 255 VAL cc_start: 0.8635 (t) cc_final: 0.8286 (m) REVERT: A 260 CYS cc_start: 0.7743 (m) cc_final: 0.7503 (m) REVERT: A 301 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6649 (tm-30) REVERT: B 6 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6885 (t80) REVERT: B 62 LEU cc_start: 0.8556 (mt) cc_final: 0.8200 (mt) REVERT: B 74 LYS cc_start: 0.8779 (tttt) cc_final: 0.8559 (tttm) REVERT: B 102 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8010 (mm-40) REVERT: B 300 ASP cc_start: 0.8083 (t0) cc_final: 0.7788 (t0) REVERT: B 344 ASN cc_start: 0.8117 (t0) cc_final: 0.7852 (t160) REVERT: B 399 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7470 (mm) REVERT: D 135 LYS cc_start: 0.7799 (ptmm) cc_final: 0.7403 (ptpt) REVERT: D 199 ARG cc_start: 0.7702 (tpp80) cc_final: 0.7501 (tpp80) REVERT: D 220 LYS cc_start: 0.8164 (mptt) cc_final: 0.7893 (mptt) REVERT: D 233 GLU cc_start: 0.4568 (OUTLIER) cc_final: 0.3971 (tm-30) REVERT: E 54 LYS cc_start: 0.8721 (tttt) cc_final: 0.8351 (tttt) REVERT: E 96 CYS cc_start: 0.8095 (t) cc_final: 0.7126 (m) REVERT: E 103 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8359 (ttm) REVERT: E 113 GLU cc_start: 0.7736 (mp0) cc_final: 0.7229 (mp0) REVERT: F 217 CYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7162 (m) REVERT: F 259 VAL cc_start: 0.8691 (p) cc_final: 0.8423 (m) REVERT: F 376 MET cc_start: 0.7391 (ttp) cc_final: 0.7114 (ttp) REVERT: F 398 LYS cc_start: 0.8673 (tppp) cc_final: 0.8470 (ttmm) REVERT: G 48 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7561 (mm-40) REVERT: H 129 VAL cc_start: 0.8336 (t) cc_final: 0.8117 (p) REVERT: H 132 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6367 (mmm-85) REVERT: H 175 LEU cc_start: 0.8328 (mm) cc_final: 0.7992 (mm) REVERT: H 214 ARG cc_start: 0.8202 (mmt180) cc_final: 0.7884 (mmm-85) REVERT: H 247 LYS cc_start: 0.8534 (mmmm) cc_final: 0.8250 (mmmm) REVERT: I 47 ILE cc_start: 0.8514 (mt) cc_final: 0.8142 (pp) REVERT: I 75 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: I 96 CYS cc_start: 0.8047 (t) cc_final: 0.7675 (m) REVERT: I 101 THR cc_start: 0.8646 (t) cc_final: 0.8402 (p) REVERT: I 103 MET cc_start: 0.8190 (ttp) cc_final: 0.7897 (ttp) REVERT: I 247 ASP cc_start: 0.7407 (m-30) cc_final: 0.7039 (m-30) REVERT: I 276 SER cc_start: 0.8568 (p) cc_final: 0.8269 (m) REVERT: I 305 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8207 (p) REVERT: I 323 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7958 (t) REVERT: I 382 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8276 (mtpp) REVERT: J 6 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6785 (t80) REVERT: J 93 SER cc_start: 0.8773 (t) cc_final: 0.8509 (p) REVERT: J 168 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8650 (tp40) REVERT: J 174 ASP cc_start: 0.7887 (t0) cc_final: 0.7596 (t0) REVERT: J 175 HIS cc_start: 0.8098 (p90) cc_final: 0.7875 (p-80) REVERT: J 300 ASP cc_start: 0.7830 (t0) cc_final: 0.7453 (t0) REVERT: J 314 VAL cc_start: 0.8081 (t) cc_final: 0.7707 (t) REVERT: J 333 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8178 (mtmm) REVERT: J 344 ASN cc_start: 0.8152 (t0) cc_final: 0.7588 (t0) REVERT: J 354 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8205 (p) REVERT: K 25 CYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7200 (t) REVERT: L 117 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7223 (mmp) REVERT: L 163 TYR cc_start: 0.5324 (m-80) cc_final: 0.5114 (m-80) REVERT: L 194 GLN cc_start: 0.8207 (pt0) cc_final: 0.7893 (pm20) REVERT: L 204 ARG cc_start: 0.8590 (ttm-80) cc_final: 0.8237 (ttm-80) REVERT: M 30 GLN cc_start: 0.8517 (tt0) cc_final: 0.8197 (tt0) REVERT: M 32 GLN cc_start: 0.8456 (tt0) cc_final: 0.8142 (tt0) REVERT: M 99 GLU cc_start: 0.7754 (pt0) cc_final: 0.7550 (pt0) REVERT: M 105 GLU cc_start: 0.8111 (pt0) cc_final: 0.7870 (pt0) REVERT: M 112 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8003 (mt-10) REVERT: M 156 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8105 (tmtm) REVERT: M 203 ASP cc_start: 0.8300 (p0) cc_final: 0.8092 (p0) REVERT: M 293 GLU cc_start: 0.8352 (tt0) cc_final: 0.7972 (tt0) REVERT: M 378 LYS cc_start: 0.8330 (pttm) cc_final: 0.8095 (pttm) REVERT: M 399 PHE cc_start: 0.8084 (t80) cc_final: 0.7549 (t80) REVERT: M 400 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8285 (p) REVERT: N 18 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8066 (t0) REVERT: N 65 MET cc_start: 0.8017 (ptt) cc_final: 0.7805 (ptp) REVERT: N 79 ASP cc_start: 0.8008 (t0) cc_final: 0.7775 (t0) REVERT: N 168 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8611 (mt0) REVERT: N 186 LYS cc_start: 0.8513 (tptp) cc_final: 0.8168 (tptp) REVERT: N 196 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8085 (tttp) REVERT: N 212 ASP cc_start: 0.8058 (m-30) cc_final: 0.7830 (m-30) REVERT: N 295 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8524 (ptt180) REVERT: N 351 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7223 (mm-30) REVERT: O 22 MET cc_start: 0.5399 (tpp) cc_final: 0.4943 (tpp) outliers start: 278 outliers final: 178 residues processed: 1231 average time/residue: 1.2717 time to fit residues: 1884.5166 Evaluate side-chains 1283 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 1077 time to evaluate : 3.358 ------------------------------------------------------------------------------- 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 82 SER 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 223 GLN 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 376 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 421 PHE 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 18 ASP 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 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 259 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 GLU 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 388 ARG 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 D residue 233 GLU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 261 TRP 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 335 SER Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 55 LEU 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 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 368 LEU 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 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 50 LYS Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 115 SER 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 323 SER Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR 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 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 168 GLN 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 221 LYS 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 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 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 25 CYS 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 177 TYR Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 217 LEU 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 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 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 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 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 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 304 THR 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 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 Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 254 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 258 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 407 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 246 optimal weight: 8.9990 chunk 381 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 236 ASN B 302 ASN B 391 ASN B 402 ASN E 77 GLN E 223 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN F 151 ASN F 175 HIS ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN I 439 HIS J 5 HIS J 24 HIS J 69 ASN J 402 ASN ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN M 125 HIS M 205 GLN M 212 ASN M 343 ASN M 361 ASN M 363 HIS 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113422 restraints weight = 52016.172| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.31 r_work: 0.3308 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34076 Z= 0.130 Angle : 0.673 15.843 46512 Z= 0.339 Chirality : 0.047 0.318 5193 Planarity : 0.006 0.066 5965 Dihedral : 6.308 84.666 4809 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.41 % Rotamer: Outliers : 6.30 % Allowed : 30.21 % Favored : 63.49 % 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: -0.76 (0.13), residues: 4224 helix: 1.11 (0.22), residues: 564 sheet: -0.46 (0.14), residues: 1356 loop : -0.90 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 188 HIS 0.006 0.001 HIS F 126 PHE 0.024 0.001 PHE I 95 TYR 0.030 0.001 TYR H 163 ARG 0.010 0.001 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 9) link_NAG-ASN : angle 2.70375 ( 27) hydrogen bonds : bond 0.03364 ( 1153) hydrogen bonds : angle 5.32921 ( 2949) SS BOND : bond 0.00532 ( 61) SS BOND : angle 1.98484 ( 122) covalent geometry : bond 0.00302 (34006) covalent geometry : angle 0.66326 (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 1332 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 1102 time to evaluate : 3.316 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: 0.8840 (OUTLIER) cc_final: 0.8501 (ttt180) REVERT: A 37 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8736 (mtm180) REVERT: A 48 THR cc_start: 0.8628 (m) cc_final: 0.8389 (t) REVERT: A 50 LYS cc_start: 0.8577 (tttm) cc_final: 0.7983 (tttm) REVERT: A 99 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 109 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7827 (mt-10) REVERT: A 192 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6967 (mt-10) REVERT: A 203 ASP cc_start: 0.7941 (p0) cc_final: 0.7640 (p0) REVERT: A 211 SER cc_start: 0.8207 (m) cc_final: 0.7762 (t) REVERT: A 221 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8140 (ttmt) REVERT: A 235 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8355 (t) REVERT: A 242 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7788 (mt-10) REVERT: A 255 VAL cc_start: 0.8603 (t) cc_final: 0.8257 (m) REVERT: A 382 LYS cc_start: 0.8676 (mtpm) cc_final: 0.8426 (mttp) REVERT: B 6 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6845 (t80) REVERT: B 62 LEU cc_start: 0.8407 (mt) cc_final: 0.8091 (mt) REVERT: B 74 LYS cc_start: 0.8780 (tttt) cc_final: 0.8574 (tttm) REVERT: B 102 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7957 (mm-40) REVERT: B 155 HIS cc_start: 0.7424 (m170) cc_final: 0.7201 (m170) REVERT: B 178 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7746 (mp) REVERT: B 300 ASP cc_start: 0.8062 (t0) cc_final: 0.7768 (t0) REVERT: B 344 ASN cc_start: 0.8071 (t0) cc_final: 0.7823 (t160) REVERT: B 376 MET cc_start: 0.7192 (tpp) cc_final: 0.6924 (tpp) REVERT: B 399 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7496 (mm) REVERT: D 135 LYS cc_start: 0.7708 (ptmm) cc_final: 0.7326 (ptpt) REVERT: D 220 LYS cc_start: 0.8249 (mptt) cc_final: 0.7957 (mptt) REVERT: D 233 GLU cc_start: 0.4870 (tp30) cc_final: 0.4555 (tm-30) REVERT: D 245 ASN cc_start: 0.8175 (p0) cc_final: 0.7973 (p0) REVERT: E 54 LYS cc_start: 0.8700 (tttt) cc_final: 0.8317 (tttt) REVERT: E 96 CYS cc_start: 0.7956 (t) cc_final: 0.7107 (m) REVERT: E 103 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8291 (ttm) REVERT: E 113 GLU cc_start: 0.7737 (mp0) cc_final: 0.7239 (mp0) REVERT: E 135 ILE cc_start: 0.8640 (pt) cc_final: 0.8433 (mm) REVERT: E 186 TYR cc_start: 0.8650 (m-80) cc_final: 0.8296 (m-80) REVERT: E 223 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8200 (mp10) REVERT: E 235 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8089 (t) REVERT: E 246 LYS cc_start: 0.8405 (pttt) cc_final: 0.8096 (ptmm) REVERT: F 217 CYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7106 (m) REVERT: F 259 VAL cc_start: 0.8661 (p) cc_final: 0.8405 (m) REVERT: F 376 MET cc_start: 0.7378 (ttp) cc_final: 0.7102 (ttp) REVERT: F 398 LYS cc_start: 0.8627 (tppp) cc_final: 0.8401 (ttmm) REVERT: G 6 MET cc_start: 0.6298 (mmm) cc_final: 0.5988 (mmm) REVERT: G 48 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7506 (mm-40) REVERT: H 175 LEU cc_start: 0.8293 (mm) cc_final: 0.7973 (mm) REVERT: H 220 LYS cc_start: 0.8565 (mptt) cc_final: 0.8220 (mptt) REVERT: H 247 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8251 (mmmm) REVERT: I 47 ILE cc_start: 0.8495 (mt) cc_final: 0.8105 (pp) REVERT: I 96 CYS cc_start: 0.8000 (t) cc_final: 0.7664 (m) REVERT: I 101 THR cc_start: 0.8646 (t) cc_final: 0.8410 (p) REVERT: I 137 TYR cc_start: 0.8749 (p90) cc_final: 0.8012 (p90) REVERT: I 235 THR cc_start: 0.8579 (t) cc_final: 0.8370 (m) REVERT: I 247 ASP cc_start: 0.7410 (m-30) cc_final: 0.7044 (m-30) REVERT: I 276 SER cc_start: 0.8562 (p) cc_final: 0.8267 (m) REVERT: I 305 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.7364 (t) REVERT: I 323 SER cc_start: 0.8250 (OUTLIER) cc_final: 0.7887 (t) REVERT: I 370 VAL cc_start: 0.8296 (t) cc_final: 0.8010 (p) REVERT: I 382 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8301 (mtpp) REVERT: J 6 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6787 (t80) REVERT: J 93 SER cc_start: 0.8757 (t) cc_final: 0.8552 (p) REVERT: J 108 THR cc_start: 0.8372 (p) cc_final: 0.8096 (t) REVERT: J 174 ASP cc_start: 0.7790 (t0) cc_final: 0.7529 (t0) REVERT: J 251 LYS cc_start: 0.8596 (tttt) cc_final: 0.8339 (tttt) REVERT: J 300 ASP cc_start: 0.7797 (t0) cc_final: 0.7408 (t0) REVERT: J 314 VAL cc_start: 0.7954 (t) cc_final: 0.7696 (m) REVERT: J 333 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8197 (mtmm) REVERT: J 344 ASN cc_start: 0.8127 (t0) cc_final: 0.7496 (t0) REVERT: J 346 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7583 (m90) REVERT: J 354 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8180 (p) REVERT: J 392 LEU cc_start: 0.8878 (mm) cc_final: 0.8666 (mm) REVERT: L 117 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7031 (mmp) REVERT: L 163 TYR cc_start: 0.5159 (m-80) cc_final: 0.4798 (m-80) REVERT: L 170 MET cc_start: 0.7824 (pmm) cc_final: 0.7306 (pmm) REVERT: L 194 GLN cc_start: 0.8187 (pt0) cc_final: 0.7874 (pm20) REVERT: L 204 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8248 (ttm-80) REVERT: M 30 GLN cc_start: 0.8479 (tt0) cc_final: 0.8253 (tt0) REVERT: M 32 GLN cc_start: 0.8453 (tt0) cc_final: 0.8063 (tt0) REVERT: M 105 GLU cc_start: 0.8145 (pt0) cc_final: 0.7903 (pt0) REVERT: M 112 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8024 (mt-10) REVERT: M 156 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8097 (tmtm) REVERT: M 203 ASP cc_start: 0.8300 (p0) cc_final: 0.8093 (p0) REVERT: M 229 ILE cc_start: 0.8607 (mm) cc_final: 0.8317 (mt) REVERT: M 264 LEU cc_start: 0.8094 (mt) cc_final: 0.7863 (mt) REVERT: M 293 GLU cc_start: 0.8343 (tt0) cc_final: 0.7964 (tt0) REVERT: M 378 LYS cc_start: 0.8304 (pttm) cc_final: 0.8074 (pttm) REVERT: M 399 PHE cc_start: 0.8043 (t80) cc_final: 0.7468 (t80) REVERT: N 18 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8035 (t0) REVERT: N 65 MET cc_start: 0.8043 (ptt) cc_final: 0.7841 (ptp) REVERT: N 79 ASP cc_start: 0.7982 (t0) cc_final: 0.7744 (t0) REVERT: N 186 LYS cc_start: 0.8466 (tptp) cc_final: 0.8192 (tptm) REVERT: N 196 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8069 (tttp) REVERT: N 216 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8443 (p) REVERT: N 351 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7149 (mm-30) REVERT: N 415 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6441 (mp) REVERT: O 22 MET cc_start: 0.5368 (tpp) cc_final: 0.4900 (tpp) REVERT: P 159 TYR cc_start: 0.7585 (m-80) cc_final: 0.6949 (m-10) outliers start: 230 outliers final: 152 residues processed: 1215 average time/residue: 1.3072 time to fit residues: 1923.3067 Evaluate side-chains 1260 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 1084 time to evaluate : 3.488 ------------------------------------------------------------------------------- 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 37 ARG 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 120 LYS 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 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 371 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 18 ASP 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 178 LEU 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 274 GLU 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 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 103 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 235 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 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 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 314 VAL 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 402 ASN 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 G residue 48 GLN 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 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 78 CYS Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 115 SER 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 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 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 221 LYS 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 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 394 ILE Chi-restraints excluded: chain J residue 405 VAL 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 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 217 LEU 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 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 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 318 THR Chi-restraints excluded: chain M residue 322 LYS Chi-restraints excluded: chain M residue 345 VAL 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 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 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 179 SER Chi-restraints excluded: chain P residue 180 ASP 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: 3.9990 chunk 419 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 349 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 281 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 175 HIS B 236 ASN B 302 ASN B 402 ASN E 77 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 ASN F 151 ASN F 175 HIS H 189 HIS 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 125 HIS M 205 GLN M 212 ASN M 361 ASN M 363 HIS ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 358 ASN O 29 ASN P 145 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112364 restraints weight = 52155.407| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.31 r_work: 0.3294 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 34076 Z= 0.165 Angle : 0.688 16.127 46512 Z= 0.346 Chirality : 0.048 0.366 5193 Planarity : 0.006 0.066 5965 Dihedral : 6.253 86.502 4805 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.85 % Favored : 94.03 % Rotamer: Outliers : 5.95 % Allowed : 30.76 % Favored : 63.29 % 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: -0.68 (0.13), residues: 4224 helix: 1.10 (0.22), residues: 564 sheet: -0.25 (0.15), residues: 1336 loop : -0.94 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 188 HIS 0.007 0.001 HIS J 126 PHE 0.022 0.001 PHE I 95 TYR 0.040 0.002 TYR H 125 ARG 0.010 0.001 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 9) link_NAG-ASN : angle 2.50857 ( 27) hydrogen bonds : bond 0.03454 ( 1153) hydrogen bonds : angle 5.28845 ( 2949) SS BOND : bond 0.00388 ( 61) SS BOND : angle 2.08961 ( 122) covalent geometry : bond 0.00386 (34006) covalent geometry : angle 0.67845 (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 1317 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 1100 time to evaluate : 3.332 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: 0.8904 (OUTLIER) cc_final: 0.8559 (ttt180) REVERT: A 37 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8483 (mtm180) REVERT: A 48 THR cc_start: 0.8652 (m) cc_final: 0.8420 (t) REVERT: A 50 LYS cc_start: 0.8584 (tttm) cc_final: 0.8019 (tttm) REVERT: A 109 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7838 (mt-10) REVERT: A 156 LYS cc_start: 0.8742 (tppt) cc_final: 0.8502 (mmtm) REVERT: A 203 ASP cc_start: 0.7954 (p0) cc_final: 0.7627 (p0) REVERT: A 211 SER cc_start: 0.8203 (m) cc_final: 0.7766 (t) REVERT: A 221 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8067 (ttmt) REVERT: A 235 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8360 (t) REVERT: A 242 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7827 (mt-10) REVERT: A 255 VAL cc_start: 0.8618 (t) cc_final: 0.8276 (m) REVERT: A 260 CYS cc_start: 0.7776 (m) cc_final: 0.7523 (m) REVERT: A 301 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6627 (tm-30) REVERT: A 382 LYS cc_start: 0.8684 (mtpm) cc_final: 0.8435 (mttp) REVERT: B 74 LYS cc_start: 0.8790 (tttt) cc_final: 0.8588 (tttm) REVERT: B 155 HIS cc_start: 0.7445 (m170) cc_final: 0.7158 (m170) REVERT: B 178 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7766 (mp) REVERT: B 228 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8058 (pt) REVERT: B 300 ASP cc_start: 0.8106 (t0) cc_final: 0.7786 (t0) REVERT: B 344 ASN cc_start: 0.8097 (t0) cc_final: 0.7840 (t160) REVERT: B 376 MET cc_start: 0.7198 (tpp) cc_final: 0.6893 (tpp) REVERT: B 399 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7559 (mm) REVERT: D 135 LYS cc_start: 0.7761 (ptmm) cc_final: 0.7388 (ptpt) REVERT: D 199 ARG cc_start: 0.7584 (tpp80) cc_final: 0.7384 (tpp80) REVERT: D 220 LYS cc_start: 0.8305 (mptt) cc_final: 0.8071 (mptt) REVERT: D 233 GLU cc_start: 0.4956 (tp30) cc_final: 0.4512 (tm-30) REVERT: D 245 ASN cc_start: 0.8206 (p0) cc_final: 0.8003 (p0) REVERT: E 54 LYS cc_start: 0.8719 (tttt) cc_final: 0.8342 (tttt) REVERT: E 96 CYS cc_start: 0.8003 (t) cc_final: 0.7140 (m) REVERT: E 103 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8332 (ttm) REVERT: E 113 GLU cc_start: 0.7742 (mp0) cc_final: 0.7228 (mp0) REVERT: E 186 TYR cc_start: 0.8640 (m-80) cc_final: 0.8384 (m-80) REVERT: E 223 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8206 (mp10) REVERT: E 235 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8109 (t) REVERT: F 217 CYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7097 (m) REVERT: F 259 VAL cc_start: 0.8680 (p) cc_final: 0.8417 (m) REVERT: F 376 MET cc_start: 0.7371 (ttp) cc_final: 0.7093 (ttp) REVERT: G 48 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7490 (mm-40) REVERT: H 175 LEU cc_start: 0.8276 (mm) cc_final: 0.7974 (mm) REVERT: H 220 LYS cc_start: 0.8523 (mptt) cc_final: 0.8174 (mptt) REVERT: H 247 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8267 (mmmm) REVERT: I 2 GLU cc_start: 0.7947 (tp30) cc_final: 0.7744 (tp30) REVERT: I 47 ILE cc_start: 0.8511 (mt) cc_final: 0.8180 (pp) REVERT: I 75 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: I 96 CYS cc_start: 0.8006 (t) cc_final: 0.7694 (m) REVERT: I 137 TYR cc_start: 0.8771 (p90) cc_final: 0.7965 (p90) REVERT: I 235 THR cc_start: 0.8606 (t) cc_final: 0.8393 (m) REVERT: I 247 ASP cc_start: 0.7446 (m-30) cc_final: 0.7101 (m-30) REVERT: I 276 SER cc_start: 0.8575 (p) cc_final: 0.8280 (m) REVERT: I 305 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8125 (p) REVERT: I 323 SER cc_start: 0.8250 (OUTLIER) cc_final: 0.7929 (t) REVERT: I 370 VAL cc_start: 0.8340 (t) cc_final: 0.8053 (p) REVERT: I 382 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8304 (mtpp) REVERT: I 400 THR cc_start: 0.8686 (m) cc_final: 0.8418 (t) REVERT: I 404 SER cc_start: 0.7966 (OUTLIER) cc_final: 0.7554 (p) REVERT: J 6 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6813 (t80) REVERT: J 93 SER cc_start: 0.8802 (t) cc_final: 0.8569 (p) REVERT: J 108 THR cc_start: 0.8437 (p) cc_final: 0.8155 (t) REVERT: J 174 ASP cc_start: 0.7924 (t0) cc_final: 0.7682 (t0) REVERT: J 236 ASN cc_start: 0.8379 (t0) cc_final: 0.8166 (t0) REVERT: J 300 ASP cc_start: 0.7799 (t0) cc_final: 0.7410 (t0) REVERT: J 314 VAL cc_start: 0.7958 (t) cc_final: 0.7694 (m) REVERT: J 333 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8192 (mtmm) REVERT: J 344 ASN cc_start: 0.8150 (t0) cc_final: 0.7504 (t0) REVERT: J 346 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7614 (m90) REVERT: J 354 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8194 (p) REVERT: K 25 CYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7138 (t) REVERT: L 117 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7198 (mmp) REVERT: L 170 MET cc_start: 0.7786 (pmm) cc_final: 0.7267 (pmm) REVERT: L 194 GLN cc_start: 0.8201 (pt0) cc_final: 0.7907 (pm20) REVERT: L 204 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8169 (ttm-80) REVERT: M 32 GLN cc_start: 0.8473 (tt0) cc_final: 0.8158 (tt0) REVERT: M 105 GLU cc_start: 0.8173 (pt0) cc_final: 0.7928 (pt0) REVERT: M 112 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8005 (mt-10) REVERT: M 156 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8034 (tmtm) REVERT: M 229 ILE cc_start: 0.8724 (mm) cc_final: 0.8427 (mt) REVERT: M 264 LEU cc_start: 0.8201 (mt) cc_final: 0.7981 (mt) REVERT: M 378 LYS cc_start: 0.8307 (pttm) cc_final: 0.8080 (pttm) REVERT: M 399 PHE cc_start: 0.8058 (t80) cc_final: 0.7503 (t80) REVERT: M 400 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8296 (p) REVERT: N 18 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8041 (t0) REVERT: N 24 HIS cc_start: 0.7710 (t-90) cc_final: 0.7488 (t-90) REVERT: N 79 ASP cc_start: 0.7963 (t0) cc_final: 0.7730 (t0) REVERT: N 186 LYS cc_start: 0.8512 (tptp) cc_final: 0.7878 (tptp) REVERT: N 196 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8084 (tttp) REVERT: N 216 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8418 (p) REVERT: N 295 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8555 (ptt180) REVERT: N 351 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7210 (mm-30) REVERT: N 415 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6358 (mp) REVERT: O 22 MET cc_start: 0.5436 (tpp) cc_final: 0.4977 (tpp) REVERT: P 159 TYR cc_start: 0.7590 (m-80) cc_final: 0.6906 (m-10) outliers start: 217 outliers final: 149 residues processed: 1206 average time/residue: 1.2631 time to fit residues: 1832.9282 Evaluate side-chains 1248 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 1071 time to evaluate : 3.575 ------------------------------------------------------------------------------- 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 37 ARG 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 135 ILE 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 371 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 35 GLU 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 178 LEU 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 259 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 GLU 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 161 LEU Chi-restraints excluded: chain D residue 188 TRP 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 67 GLN Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 235 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 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 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 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 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 242 VAL 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 75 ASP Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 115 SER 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 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 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 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 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 218 THR Chi-restraints excluded: chain J residue 221 LYS 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 368 LEU Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain K residue 25 CYS 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 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 52 LYS Chi-restraints excluded: chain M residue 69 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 260 CYS Chi-restraints excluded: chain M residue 274 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 306 GLU Chi-restraints excluded: chain M residue 345 VAL 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 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 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 179 SER Chi-restraints excluded: chain P residue 180 ASP 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: 5.9990 chunk 0 optimal weight: 8.9990 chunk 195 optimal weight: 0.0030 chunk 235 optimal weight: 0.0970 chunk 250 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 331 optimal weight: 7.9990 chunk 354 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 chunk 178 optimal weight: 9.9990 overall best weight: 2.0592 ------------------------------------------------------------------------------- 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 151 ASN B 175 HIS B 236 ASN B 302 ASN B 402 ASN E 77 GLN E 226 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 ASN F 151 ASN F 175 HIS 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 77 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 ASN M 363 HIS ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 358 ASN P 145 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114657 restraints weight = 52177.390| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.27 r_work: 0.3299 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34076 Z= 0.170 Angle : 0.697 16.081 46512 Z= 0.350 Chirality : 0.048 0.358 5193 Planarity : 0.006 0.071 5965 Dihedral : 6.175 87.735 4802 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 5.84 % Allowed : 31.85 % Favored : 62.31 % 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: -0.67 (0.13), residues: 4224 helix: 1.11 (0.21), residues: 564 sheet: -0.24 (0.15), residues: 1340 loop : -0.93 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 188 HIS 0.008 0.001 HIS H 189 PHE 0.015 0.001 PHE L 134 TYR 0.030 0.002 TYR L 177 ARG 0.010 0.001 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 9) link_NAG-ASN : angle 2.39486 ( 27) hydrogen bonds : bond 0.03440 ( 1153) hydrogen bonds : angle 5.27231 ( 2949) SS BOND : bond 0.00399 ( 61) SS BOND : angle 2.09657 ( 122) covalent geometry : bond 0.00396 (34006) covalent geometry : angle 0.68737 (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 1297 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 1084 time to evaluate : 3.611 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: 0.8898 (OUTLIER) cc_final: 0.8551 (ttt180) REVERT: A 37 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8737 (mtm180) REVERT: A 48 THR cc_start: 0.8653 (m) cc_final: 0.8432 (t) REVERT: A 50 LYS cc_start: 0.8586 (tttm) cc_final: 0.8123 (tttm) REVERT: A 109 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7848 (mt-10) REVERT: A 156 LYS cc_start: 0.8736 (tppt) cc_final: 0.8525 (mmtm) REVERT: A 203 ASP cc_start: 0.7921 (p0) cc_final: 0.7627 (p0) REVERT: A 211 SER cc_start: 0.8191 (m) cc_final: 0.7756 (t) REVERT: A 221 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8143 (ttmt) REVERT: A 235 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8370 (t) REVERT: A 242 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7812 (mt-10) REVERT: A 255 VAL cc_start: 0.8627 (t) cc_final: 0.8272 (m) REVERT: A 279 ILE cc_start: 0.8668 (pt) cc_final: 0.8467 (pt) REVERT: A 301 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6633 (tm-30) REVERT: A 367 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8566 (ttpm) REVERT: A 382 LYS cc_start: 0.8672 (mtpm) cc_final: 0.8421 (mttp) REVERT: A 418 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7707 (p) REVERT: B 74 LYS cc_start: 0.8780 (tttt) cc_final: 0.8575 (tttm) REVERT: B 102 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8017 (mm-40) REVERT: B 155 HIS cc_start: 0.7477 (m170) cc_final: 0.7129 (m170) REVERT: B 300 ASP cc_start: 0.8101 (t0) cc_final: 0.7782 (t0) REVERT: B 344 ASN cc_start: 0.8086 (t0) cc_final: 0.7821 (t160) REVERT: B 376 MET cc_start: 0.7213 (tpp) cc_final: 0.6904 (tpp) REVERT: B 399 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7534 (mm) REVERT: D 135 LYS cc_start: 0.7752 (ptmm) cc_final: 0.7387 (ptpt) REVERT: D 199 ARG cc_start: 0.7597 (tpp80) cc_final: 0.7349 (tpp80) REVERT: D 220 LYS cc_start: 0.8246 (mptt) cc_final: 0.7927 (mptt) REVERT: D 233 GLU cc_start: 0.4872 (tp30) cc_final: 0.4388 (tm-30) REVERT: D 245 ASN cc_start: 0.8211 (p0) cc_final: 0.8009 (p0) REVERT: E 54 LYS cc_start: 0.8728 (tttt) cc_final: 0.8350 (tttt) REVERT: E 96 CYS cc_start: 0.8006 (t) cc_final: 0.7254 (m) REVERT: E 103 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8332 (ttm) REVERT: E 113 GLU cc_start: 0.7725 (mp0) cc_final: 0.7218 (mp0) REVERT: E 186 TYR cc_start: 0.8627 (m-80) cc_final: 0.8384 (m-80) REVERT: E 223 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8221 (mp10) REVERT: E 235 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8091 (t) REVERT: F 217 CYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7118 (m) REVERT: F 218 THR cc_start: 0.8599 (m) cc_final: 0.8373 (p) REVERT: F 259 VAL cc_start: 0.8710 (p) cc_final: 0.8434 (m) REVERT: F 376 MET cc_start: 0.7388 (ttp) cc_final: 0.7112 (ttp) REVERT: F 402 ASN cc_start: 0.7662 (m-40) cc_final: 0.7388 (p0) REVERT: G 48 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7490 (mm-40) REVERT: H 154 LYS cc_start: 0.8506 (tmmt) cc_final: 0.8207 (pttp) REVERT: H 175 LEU cc_start: 0.8251 (mm) cc_final: 0.7950 (mm) REVERT: H 177 TYR cc_start: 0.8469 (p90) cc_final: 0.8230 (p90) REVERT: H 220 LYS cc_start: 0.8521 (mptt) cc_final: 0.8247 (mptt) REVERT: H 247 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8275 (mmmm) REVERT: I 2 GLU cc_start: 0.7980 (tp30) cc_final: 0.7754 (tp30) REVERT: I 47 ILE cc_start: 0.8510 (mt) cc_final: 0.8138 (pp) REVERT: I 75 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: I 96 CYS cc_start: 0.7971 (t) cc_final: 0.7641 (t) REVERT: I 137 TYR cc_start: 0.8781 (p90) cc_final: 0.7976 (p90) REVERT: I 235 THR cc_start: 0.8611 (t) cc_final: 0.8400 (m) REVERT: I 247 ASP cc_start: 0.7460 (m-30) cc_final: 0.7115 (m-30) REVERT: I 276 SER cc_start: 0.8581 (p) cc_final: 0.8293 (m) REVERT: I 305 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8134 (p) REVERT: I 323 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7946 (t) REVERT: I 370 VAL cc_start: 0.8350 (t) cc_final: 0.8058 (p) REVERT: I 382 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8302 (mtpp) REVERT: I 400 THR cc_start: 0.8695 (m) cc_final: 0.8419 (t) REVERT: J 6 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6903 (t80) REVERT: J 93 SER cc_start: 0.8796 (t) cc_final: 0.8566 (p) REVERT: J 108 THR cc_start: 0.8453 (p) cc_final: 0.8155 (t) REVERT: J 131 ARG cc_start: 0.8781 (mtt90) cc_final: 0.8498 (mtt90) REVERT: J 174 ASP cc_start: 0.7857 (t0) cc_final: 0.7626 (t0) REVERT: J 236 ASN cc_start: 0.8348 (t0) cc_final: 0.8127 (t0) REVERT: J 251 LYS cc_start: 0.8616 (tttt) cc_final: 0.8214 (tttm) REVERT: J 300 ASP cc_start: 0.7804 (t0) cc_final: 0.7417 (t0) REVERT: J 314 VAL cc_start: 0.7969 (t) cc_final: 0.7712 (m) REVERT: J 333 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8189 (mtmm) REVERT: J 344 ASN cc_start: 0.8153 (t0) cc_final: 0.7527 (t0) REVERT: J 346 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7573 (m90) REVERT: J 354 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8208 (p) REVERT: K 25 CYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7158 (t) REVERT: L 117 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7156 (mmp) REVERT: L 170 MET cc_start: 0.7779 (pmm) cc_final: 0.7264 (pmm) REVERT: L 194 GLN cc_start: 0.8210 (pt0) cc_final: 0.7909 (pm20) REVERT: L 204 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8154 (ttm-80) REVERT: M 32 GLN cc_start: 0.8464 (tt0) cc_final: 0.8150 (tt0) REVERT: M 105 GLU cc_start: 0.8165 (pt0) cc_final: 0.7925 (pt0) REVERT: M 112 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7976 (mt-10) REVERT: M 141 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7806 (p) REVERT: M 156 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8058 (tmtm) REVERT: M 229 ILE cc_start: 0.8757 (mm) cc_final: 0.8476 (mt) REVERT: M 264 LEU cc_start: 0.8228 (mt) cc_final: 0.7994 (mt) REVERT: M 299 ASP cc_start: 0.7734 (m-30) cc_final: 0.7515 (m-30) REVERT: M 399 PHE cc_start: 0.8006 (t80) cc_final: 0.7462 (t80) REVERT: M 400 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8299 (p) REVERT: N 18 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.8015 (t0) REVERT: N 24 HIS cc_start: 0.7711 (t-90) cc_final: 0.7505 (t-90) REVERT: N 79 ASP cc_start: 0.7954 (t0) cc_final: 0.7719 (t0) REVERT: N 186 LYS cc_start: 0.8516 (tptp) cc_final: 0.7982 (tptp) REVERT: N 196 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8094 (tttp) REVERT: N 216 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8370 (p) REVERT: N 218 THR cc_start: 0.8202 (p) cc_final: 0.7776 (t) REVERT: N 319 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8251 (p) REVERT: N 351 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7213 (mm-30) REVERT: N 383 VAL cc_start: 0.8413 (t) cc_final: 0.8169 (t) REVERT: N 415 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6341 (mp) REVERT: O 22 MET cc_start: 0.5393 (tpp) cc_final: 0.4995 (tpp) REVERT: P 222 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7305 (ptm-80) outliers start: 213 outliers final: 155 residues processed: 1191 average time/residue: 1.2797 time to fit residues: 1842.8155 Evaluate side-chains 1263 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1078 time to evaluate : 3.834 ------------------------------------------------------------------------------- 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 37 ARG Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 120 LYS 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 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 371 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 18 ASP 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 259 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 GLU 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 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 161 LEU Chi-restraints excluded: chain D residue 188 TRP 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 67 GLN 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 235 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 9 TYR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 133 VAL 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 314 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 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 155 LYS Chi-restraints excluded: chain H residue 170 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 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 75 ASP Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 115 SER 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 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 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 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 218 THR Chi-restraints excluded: chain J residue 221 LYS 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 368 LEU Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain K residue 25 CYS 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 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 141 SER Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 274 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 306 GLU 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 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 171 LEU Chi-restraints excluded: chain N residue 188 THR 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 260 LYS 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 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 179 SER Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 222 ARG Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 254 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 15 optimal weight: 3.9990 chunk 318 optimal weight: 0.8980 chunk 273 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 chunk 394 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 213 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 151 ASN B 236 ASN B 302 ASN E 28 HIS E 77 GLN E 226 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 ASN F 162 HIS F 175 HIS 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 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 363 HIS ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 358 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113633 restraints weight = 52243.336| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.32 r_work: 0.3310 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34076 Z= 0.137 Angle : 0.681 15.969 46512 Z= 0.341 Chirality : 0.048 0.346 5193 Planarity : 0.006 0.075 5965 Dihedral : 6.035 88.552 4802 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 4.99 % Allowed : 32.76 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.67 (0.13), residues: 4224 helix: 1.17 (0.22), residues: 568 sheet: -0.21 (0.15), residues: 1332 loop : -0.98 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 188 HIS 0.007 0.001 HIS N 95 PHE 0.018 0.001 PHE I 95 TYR 0.027 0.001 TYR H 177 ARG 0.011 0.001 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 9) link_NAG-ASN : angle 2.68081 ( 27) hydrogen bonds : bond 0.03282 ( 1153) hydrogen bonds : angle 5.20384 ( 2949) SS BOND : bond 0.00364 ( 61) SS BOND : angle 1.90023 ( 122) covalent geometry : bond 0.00322 (34006) covalent geometry : angle 0.67194 (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 1278 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 1096 time to evaluate : 3.343 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 37 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8700 (mtm180) REVERT: A 48 THR cc_start: 0.8637 (m) cc_final: 0.8428 (t) REVERT: A 50 LYS cc_start: 0.8591 (tttm) cc_final: 0.8128 (tttm) REVERT: A 109 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7870 (mt-10) REVERT: A 156 LYS cc_start: 0.8707 (tppt) cc_final: 0.8506 (mmtm) REVERT: A 203 ASP cc_start: 0.7904 (p0) cc_final: 0.7618 (p0) REVERT: A 211 SER cc_start: 0.8175 (m) cc_final: 0.7757 (t) REVERT: A 221 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8103 (ttmt) REVERT: A 235 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8338 (t) REVERT: A 242 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 279 ILE cc_start: 0.8672 (pt) cc_final: 0.8466 (pt) REVERT: A 301 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6613 (tm-30) REVERT: A 367 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8473 (tttm) REVERT: A 382 LYS cc_start: 0.8665 (mtpm) cc_final: 0.8424 (mttp) REVERT: A 418 THR cc_start: 0.8077 (m) cc_final: 0.7694 (p) REVERT: B 10 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8500 (ptpp) REVERT: B 74 LYS cc_start: 0.8786 (tttt) cc_final: 0.8574 (tttm) REVERT: B 102 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7971 (mm-40) REVERT: B 155 HIS cc_start: 0.7459 (m170) cc_final: 0.7127 (m170) REVERT: B 300 ASP cc_start: 0.8101 (t0) cc_final: 0.7776 (t0) REVERT: B 344 ASN cc_start: 0.8070 (t0) cc_final: 0.7807 (t160) REVERT: B 376 MET cc_start: 0.7203 (tpp) cc_final: 0.6880 (tpp) REVERT: B 399 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7492 (mm) REVERT: D 135 LYS cc_start: 0.7754 (ptmm) cc_final: 0.7396 (ptpt) REVERT: D 199 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7320 (tpp80) REVERT: D 220 LYS cc_start: 0.8222 (mptt) cc_final: 0.7924 (mptt) REVERT: D 233 GLU cc_start: 0.4972 (tp30) cc_final: 0.4534 (tm-30) REVERT: E 1 TYR cc_start: 0.8801 (t80) cc_final: 0.8599 (t80) REVERT: E 54 LYS cc_start: 0.8726 (tttt) cc_final: 0.8337 (tttt) REVERT: E 96 CYS cc_start: 0.8017 (t) cc_final: 0.7301 (m) REVERT: E 103 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8286 (ttm) REVERT: E 113 GLU cc_start: 0.7740 (mp0) cc_final: 0.7240 (mp0) REVERT: E 186 TYR cc_start: 0.8604 (m-80) cc_final: 0.8354 (m-80) REVERT: E 223 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8244 (mp10) REVERT: E 235 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8076 (t) REVERT: E 246 LYS cc_start: 0.8390 (pttt) cc_final: 0.8166 (pttt) REVERT: F 27 CYS cc_start: 0.7168 (p) cc_final: 0.6865 (p) REVERT: F 217 CYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7128 (m) REVERT: F 218 THR cc_start: 0.8545 (m) cc_final: 0.8318 (p) REVERT: F 259 VAL cc_start: 0.8701 (p) cc_final: 0.8430 (m) REVERT: F 376 MET cc_start: 0.7377 (ttp) cc_final: 0.7096 (ttp) REVERT: F 394 ILE cc_start: 0.8663 (pp) cc_final: 0.8442 (pt) REVERT: H 175 LEU cc_start: 0.8298 (mm) cc_final: 0.7990 (mm) REVERT: H 247 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8278 (mmmm) REVERT: I 2 GLU cc_start: 0.7941 (tp30) cc_final: 0.7730 (tp30) REVERT: I 30 GLN cc_start: 0.8734 (mt0) cc_final: 0.8452 (mt0) REVERT: I 47 ILE cc_start: 0.8521 (mt) cc_final: 0.8151 (pp) REVERT: I 75 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: I 96 CYS cc_start: 0.7930 (t) cc_final: 0.7637 (t) REVERT: I 137 TYR cc_start: 0.8753 (p90) cc_final: 0.7950 (p90) REVERT: I 235 THR cc_start: 0.8597 (t) cc_final: 0.8384 (m) REVERT: I 247 ASP cc_start: 0.7476 (m-30) cc_final: 0.7145 (m-30) REVERT: I 276 SER cc_start: 0.8553 (p) cc_final: 0.8275 (m) REVERT: I 305 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8059 (p) REVERT: I 323 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7817 (p) REVERT: I 382 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8304 (mtpp) REVERT: I 400 THR cc_start: 0.8619 (m) cc_final: 0.8329 (t) REVERT: J 6 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6887 (t80) REVERT: J 108 THR cc_start: 0.8371 (p) cc_final: 0.8103 (t) REVERT: J 131 ARG cc_start: 0.8756 (mtt90) cc_final: 0.8459 (mtt90) REVERT: J 174 ASP cc_start: 0.7799 (t0) cc_final: 0.7582 (t0) REVERT: J 236 ASN cc_start: 0.8347 (t0) cc_final: 0.8147 (t0) REVERT: J 300 ASP cc_start: 0.7793 (t0) cc_final: 0.7403 (t0) REVERT: J 314 VAL cc_start: 0.7891 (t) cc_final: 0.7589 (m) REVERT: J 316 PHE cc_start: 0.8274 (m-80) cc_final: 0.8036 (m-80) REVERT: J 333 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8184 (mtmm) REVERT: J 344 ASN cc_start: 0.8105 (t0) cc_final: 0.7472 (t0) REVERT: J 346 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7555 (m90) REVERT: J 354 VAL cc_start: 0.8356 (p) cc_final: 0.8146 (p) REVERT: L 117 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7155 (mmp) REVERT: L 170 MET cc_start: 0.7806 (pmm) cc_final: 0.7265 (pmm) REVERT: L 194 GLN cc_start: 0.8164 (pt0) cc_final: 0.7859 (pt0) REVERT: L 204 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8060 (ttm-80) REVERT: M 32 GLN cc_start: 0.8474 (tt0) cc_final: 0.8142 (tt0) REVERT: M 54 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8325 (mtpp) REVERT: M 105 GLU cc_start: 0.8150 (pt0) cc_final: 0.7899 (pt0) REVERT: M 112 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7968 (mt-10) REVERT: M 133 VAL cc_start: 0.8282 (m) cc_final: 0.8046 (t) REVERT: M 156 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8059 (tmtm) REVERT: M 229 ILE cc_start: 0.8741 (mm) cc_final: 0.8454 (mt) REVERT: M 264 LEU cc_start: 0.8254 (mt) cc_final: 0.8000 (mt) REVERT: M 299 ASP cc_start: 0.7793 (m-30) cc_final: 0.7547 (m-30) REVERT: M 367 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8265 (ttmm) REVERT: M 378 LYS cc_start: 0.8278 (pttm) cc_final: 0.8044 (pttm) REVERT: M 399 PHE cc_start: 0.8020 (t80) cc_final: 0.7445 (t80) REVERT: N 18 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7992 (t0) REVERT: N 24 HIS cc_start: 0.7700 (t-90) cc_final: 0.7492 (t-90) REVERT: N 79 ASP cc_start: 0.7931 (t0) cc_final: 0.7694 (t0) REVERT: N 186 LYS cc_start: 0.8501 (tptp) cc_final: 0.7948 (tptp) REVERT: N 196 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8102 (tttp) REVERT: N 216 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8413 (p) REVERT: N 218 THR cc_start: 0.8186 (p) cc_final: 0.7757 (t) REVERT: N 295 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8547 (ptt180) REVERT: N 319 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8206 (p) REVERT: N 351 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7183 (mm-30) REVERT: N 383 VAL cc_start: 0.8410 (t) cc_final: 0.8174 (t) REVERT: N 415 ILE cc_start: 0.6392 (OUTLIER) cc_final: 0.6183 (mp) REVERT: P 159 TYR cc_start: 0.7496 (m-80) cc_final: 0.6767 (m-10) REVERT: P 222 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7284 (ptm-80) outliers start: 182 outliers final: 137 residues processed: 1179 average time/residue: 1.2468 time to fit residues: 1769.3430 Evaluate side-chains 1237 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1075 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 37 ARG 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 82 SER Chi-restraints excluded: chain A residue 120 LYS 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 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 337 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 18 ASP 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 273 VAL Chi-restraints excluded: chain B residue 274 GLU 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 E residue 2 GLU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 235 THR 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 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 314 VAL 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 178 THR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 242 VAL 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 75 ASP Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 79 GLN 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 292 SER 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 18 ASP Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 221 LYS 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 394 ILE 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 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 156 LYS Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 274 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 306 GLU Chi-restraints excluded: chain M residue 345 VAL 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 171 LEU Chi-restraints excluded: chain N residue 188 THR 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 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 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 179 SER Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 222 ARG 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: 0.0270 chunk 414 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 361 optimal weight: 0.9980 chunk 325 optimal weight: 10.0000 chunk 71 optimal weight: 0.1980 chunk 29 optimal weight: 0.0670 chunk 79 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 300 optimal weight: 7.9990 chunk 360 optimal weight: 0.8980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 151 ASN B 175 HIS B 236 ASN B 302 ASN E 77 GLN E 439 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 ASN F 162 HIS F 175 HIS H 123 ASN I 32 GLN I 205 GLN I 439 HIS J 69 ASN J 175 HIS J 402 ASN K 40 ASN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 363 HIS N 230 ASN N 358 ASN P 145 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115057 restraints weight = 52438.976| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.34 r_work: 0.3337 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 0.046 34076 Z= 0.117 Angle : 0.667 15.761 46512 Z= 0.334 Chirality : 0.047 0.333 5193 Planarity : 0.006 0.077 5965 Dihedral : 5.852 89.068 4800 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 4.33 % Allowed : 33.58 % Favored : 62.09 % 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: -0.62 (0.13), residues: 4224 helix: 1.19 (0.22), residues: 572 sheet: -0.20 (0.15), residues: 1336 loop : -0.93 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 384 HIS 0.006 0.001 HIS H 189 PHE 0.022 0.001 PHE I 95 TYR 0.029 0.001 TYR L 177 ARG 0.010 0.000 ARG N 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 9) link_NAG-ASN : angle 2.71202 ( 27) hydrogen bonds : bond 0.03139 ( 1153) hydrogen bonds : angle 5.12000 ( 2949) SS BOND : bond 0.00329 ( 61) SS BOND : angle 1.66354 ( 122) covalent geometry : bond 0.00275 (34006) covalent geometry : angle 0.65912 (46363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34142.94 seconds wall clock time: 584 minutes 48.13 seconds (35088.13 seconds total)