Starting phenix.real_space_refine on Tue Aug 26 03:06:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua9_42055/08_2025/8ua9_42055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua9_42055/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ua9_42055/08_2025/8ua9_42055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua9_42055/08_2025/8ua9_42055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ua9_42055/08_2025/8ua9_42055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua9_42055/08_2025/8ua9_42055.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.03, per 1000 atoms: 0.21 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: 2.78 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.70 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: 7.70 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 11036 1.35 - 1.49: 9580 1.49 - 1.63: 13106 1.63 - 1.77: 41 1.77 - 1.91: 243 Bond restraints: 34006 Sorted by residual: bond pdb=" CB CYS M 272 " pdb=" SG CYS M 272 " ideal model delta sigma weight residual 1.808 1.648 0.160 3.30e-02 9.18e+02 2.36e+01 bond pdb=" CB CYS E 371 " pdb=" SG CYS E 371 " ideal model delta sigma weight residual 1.808 1.668 0.140 3.30e-02 9.18e+02 1.80e+01 bond pdb=" CB CYS A 329 " pdb=" SG CYS A 329 " ideal model delta sigma weight residual 1.808 1.678 0.130 3.30e-02 9.18e+02 1.55e+01 bond pdb=" CB CYS A 371 " pdb=" SG CYS A 371 " ideal model delta sigma weight residual 1.808 1.685 0.123 3.30e-02 9.18e+02 1.38e+01 bond pdb=" CB CYS I 329 " pdb=" SG CYS I 329 " ideal model delta sigma weight residual 1.808 1.686 0.122 3.30e-02 9.18e+02 1.36e+01 ... (remaining 34001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 44519 2.97 - 5.94: 1657 5.94 - 8.91: 161 8.91 - 11.88: 21 11.88 - 14.85: 5 Bond angle restraints: 46363 Sorted by residual: angle pdb=" CA PRO L 255 " pdb=" N PRO L 255 " pdb=" CD PRO L 255 " ideal model delta sigma weight residual 112.00 97.15 14.85 1.40e+00 5.10e-01 1.12e+02 angle pdb=" CA PRO B 401 " pdb=" N PRO B 401 " pdb=" CD PRO B 401 " ideal model delta sigma weight residual 112.00 100.38 11.62 1.40e+00 5.10e-01 6.89e+01 angle pdb=" CA PRO D 182 " pdb=" N PRO D 182 " pdb=" CD PRO D 182 " ideal model delta sigma weight residual 112.00 102.39 9.61 1.40e+00 5.10e-01 4.71e+01 angle pdb=" CA CYS M 260 " pdb=" CB CYS M 260 " pdb=" SG CYS M 260 " ideal model delta sigma weight residual 114.40 129.25 -14.85 2.30e+00 1.89e-01 4.17e+01 angle pdb=" CA TYR L 163 " pdb=" CB TYR L 163 " pdb=" CG TYR L 163 " ideal model delta sigma weight residual 113.90 102.55 11.35 1.80e+00 3.09e-01 3.98e+01 ... (remaining 46358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 17175 17.90 - 35.79: 2520 35.79 - 53.69: 697 53.69 - 71.58: 109 71.58 - 89.48: 31 Dihedral angle restraints: 20532 sinusoidal: 8208 harmonic: 12324 Sorted by residual: dihedral pdb=" CA GLU E 265 " pdb=" C GLU E 265 " pdb=" N PRO E 266 " pdb=" CA PRO E 266 " ideal model delta harmonic sigma weight residual -180.00 -95.14 -84.86 0 5.00e+00 4.00e-02 2.88e+02 dihedral pdb=" CA CYS B 201 " pdb=" C CYS B 201 " pdb=" N PRO B 202 " pdb=" CA PRO B 202 " ideal model delta harmonic sigma weight residual -180.00 -119.68 -60.32 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CB CYS M 329 " pdb=" SG CYS M 329 " pdb=" SG CYS M 371 " pdb=" CB CYS M 371 " ideal model delta sinusoidal sigma weight residual 93.00 -177.52 -89.48 1 1.00e+01 1.00e-02 9.51e+01 ... (remaining 20529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 4608 0.113 - 0.226: 549 0.226 - 0.339: 25 0.339 - 0.451: 7 0.451 - 0.564: 4 Chirality restraints: 5193 Sorted by residual: chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 134 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.96e+00 chirality pdb=" C1 NAG I 501 " pdb=" ND2 ASN I 134 " pdb=" C2 NAG I 501 " pdb=" O5 NAG I 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 134 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.22e+00 ... (remaining 5190 not shown) Planarity restraints: 5974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 400 " 0.110 5.00e-02 4.00e+02 1.58e-01 4.00e+01 pdb=" N PRO B 401 " -0.273 5.00e-02 4.00e+02 pdb=" CA PRO B 401 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO B 401 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 254 " 0.107 5.00e-02 4.00e+02 1.48e-01 3.49e+01 pdb=" N PRO L 255 " -0.255 5.00e-02 4.00e+02 pdb=" CA PRO L 255 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO L 255 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 181 " -0.087 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO D 182 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO D 182 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 182 " -0.067 5.00e-02 4.00e+02 ... (remaining 5971 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 369 2.57 - 3.15: 26901 3.15 - 3.73: 49813 3.73 - 4.32: 69096 4.32 - 4.90: 119827 Nonbonded interactions: 266006 Sorted by model distance: nonbonded pdb=" O CYS K 25 " pdb=" OG1 THR K 33 " model vdw 1.983 3.040 nonbonded pdb=" O CYS C 25 " pdb=" OG1 THR C 33 " model vdw 1.984 3.040 nonbonded pdb=" O ALA M 402 " pdb=" OH TYR N 356 " model vdw 1.997 3.040 nonbonded pdb=" OE2 GLU I 2 " pdb=" OG SER I 280 " model vdw 2.001 3.040 nonbonded pdb=" O PRO H 182 " pdb=" OH TYR H 186 " model vdw 2.041 3.040 ... (remaining 266001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 4 through 57) selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.340 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.540 ------------------------------------------------------------------------------- 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 : 7.03 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (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 ARG 0.025 0.001 ARG D 199 TYR 0.085 0.004 TYR F 163 PHE 0.054 0.004 PHE J 6 TRP 0.034 0.004 TRP B 384 HIS 0.025 0.003 HIS J 126 Details of bonding type rmsd covalent geometry : bond 0.01397 (34006) covalent geometry : angle 1.25965 (46363) SS BOND : bond 0.34444 ( 61) SS BOND : angle 8.39793 ( 122) hydrogen bonds : bond 0.12744 ( 1153) hydrogen bonds : angle 7.35734 ( 2949) link_NAG-ASN : bond 0.00627 ( 9) link_NAG-ASN : angle 2.64710 ( 27) *********************** 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 : 1.176 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: 0.6975 time to fit residues: 978.7043 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 : 1.294 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 222 GLN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 95 HIS N 213 HIS 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114081 restraints weight = 52447.346| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.27 r_work: 0.3312 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34076 Z= 0.165 Angle : 0.732 12.821 46512 Z= 0.377 Chirality : 0.050 0.394 5193 Planarity : 0.007 0.111 5965 Dihedral : 7.722 75.979 4937 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 5.87 % Allowed : 27.28 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.13), residues: 4224 helix: 0.74 (0.21), residues: 556 sheet: -0.54 (0.14), residues: 1324 loop : -1.03 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 199 TYR 0.024 0.002 TYR L 177 PHE 0.019 0.002 PHE L 134 TRP 0.025 0.002 TRP D 188 HIS 0.010 0.001 HIS J 126 Details of bonding type rmsd covalent geometry : bond 0.00378 (34006) covalent geometry : angle 0.72053 (46363) SS BOND : bond 0.00452 ( 61) SS BOND : angle 2.30059 ( 122) hydrogen bonds : bond 0.04172 ( 1153) hydrogen bonds : angle 5.97438 ( 2949) link_NAG-ASN : bond 0.00586 ( 9) link_NAG-ASN : angle 2.80920 ( 27) *********************** 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 1323 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 1109 time to evaluate : 1.385 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 4 THR cc_start: 0.8652 (p) cc_final: 0.8400 (m) REVERT: A 30 GLN cc_start: 0.8459 (tt0) cc_final: 0.8258 (tt0) REVERT: A 37 ARG cc_start: 0.8960 (mpp80) cc_final: 0.8622 (mtm180) REVERT: A 54 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8178 (ttpp) REVERT: A 88 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7574 (ptp) REVERT: A 109 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 211 SER cc_start: 0.8139 (m) cc_final: 0.7659 (p) REVERT: A 245 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8378 (mtmt) REVERT: A 279 ILE cc_start: 0.8699 (pt) cc_final: 0.8496 (pt) REVERT: B 6 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7035 (t80) REVERT: B 62 LEU cc_start: 0.8534 (mt) cc_final: 0.8265 (mt) REVERT: B 200 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7886 (tmtt) REVERT: B 210 SER cc_start: 0.8334 (t) cc_final: 0.7966 (p) REVERT: B 274 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 300 ASP cc_start: 0.7964 (t0) cc_final: 0.7742 (t0) REVERT: B 376 MET cc_start: 0.7215 (tpp) cc_final: 0.7008 (tpp) REVERT: B 399 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7711 (mm) REVERT: D 117 MET cc_start: 0.6260 (tmm) cc_final: 0.5911 (tmm) REVERT: D 206 VAL cc_start: 0.6969 (OUTLIER) cc_final: 0.6761 (t) REVERT: E 16 LYS cc_start: 0.8921 (mttt) cc_final: 0.8695 (mttt) REVERT: E 54 LYS cc_start: 0.8698 (tttt) cc_final: 0.8348 (tttt) REVERT: E 113 GLU cc_start: 0.7654 (mp0) cc_final: 0.7241 (mp0) REVERT: E 156 LYS cc_start: 0.8645 (tppt) cc_final: 0.8294 (tppt) REVERT: E 305 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8225 (p) REVERT: F 136 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7236 (mt-10) REVERT: F 175 HIS cc_start: 0.8305 (p-80) cc_final: 0.8088 (p90) REVERT: F 178 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8007 (mm) REVERT: F 217 CYS cc_start: 0.7495 (m) cc_final: 0.7165 (m) REVERT: F 259 VAL cc_start: 0.8694 (p) cc_final: 0.8398 (m) REVERT: F 370 THR cc_start: 0.8109 (t) cc_final: 0.7835 (p) REVERT: F 402 ASN cc_start: 0.7769 (m110) cc_final: 0.7566 (p0) REVERT: G 22 MET cc_start: 0.7243 (mmp) cc_final: 0.6929 (mmp) REVERT: G 48 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7614 (mm-40) REVERT: H 129 VAL cc_start: 0.8325 (t) cc_final: 0.8029 (p) REVERT: H 132 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6491 (mtt90) REVERT: I 30 GLN cc_start: 0.8739 (mt0) cc_final: 0.8479 (mt0) REVERT: I 69 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8095 (p) REVERT: I 96 CYS cc_start: 0.7988 (t) cc_final: 0.7675 (t) REVERT: I 130 GLN cc_start: 0.8773 (mt0) cc_final: 0.8523 (mt0) REVERT: I 137 TYR cc_start: 0.8727 (p90) cc_final: 0.8165 (p90) REVERT: I 212 ASN cc_start: 0.8800 (m-40) cc_final: 0.8595 (m-40) REVERT: I 296 THR cc_start: 0.8785 (p) cc_final: 0.8563 (t) REVERT: I 305 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8346 (p) REVERT: I 426 LEU cc_start: 0.8200 (mt) cc_final: 0.7973 (mm) REVERT: J 6 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6791 (t80) REVERT: J 174 ASP cc_start: 0.7848 (t0) cc_final: 0.7642 (t0) REVERT: J 200 LYS cc_start: 0.8070 (tppp) cc_final: 0.7815 (tppp) REVERT: K 22 MET cc_start: 0.6925 (tpp) cc_final: 0.6575 (tpp) REVERT: L 193 VAL cc_start: 0.7796 (t) cc_final: 0.7531 (m) REVERT: M 35 ASN cc_start: 0.8695 (p0) cc_final: 0.8489 (p0) REVERT: M 61 LYS cc_start: 0.8238 (mmmm) cc_final: 0.8001 (tppp) REVERT: M 75 ASP cc_start: 0.8268 (t0) cc_final: 0.8044 (t0) REVERT: M 141 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7805 (p) REVERT: M 150 ASN cc_start: 0.8343 (p0) cc_final: 0.8134 (p0) REVERT: M 175 ASP cc_start: 0.7925 (m-30) cc_final: 0.7559 (m-30) REVERT: M 208 THR cc_start: 0.8273 (m) cc_final: 0.8072 (m) REVERT: M 214 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8210 (tt) REVERT: M 217 ASN cc_start: 0.8614 (t0) cc_final: 0.8343 (t0) REVERT: N 186 LYS cc_start: 0.8552 (tptp) cc_final: 0.8215 (tptp) REVERT: N 295 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8661 (ptt180) REVERT: N 302 ASN cc_start: 0.8457 (t0) cc_final: 0.8154 (t0) REVERT: N 351 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7523 (mm-30) REVERT: N 364 THR cc_start: 0.8723 (t) cc_final: 0.8518 (t) REVERT: O 22 MET cc_start: 0.5964 (tpp) cc_final: 0.5344 (tpp) outliers start: 214 outliers final: 104 residues processed: 1217 average time/residue: 0.6949 time to fit residues: 1014.4971 Evaluate side-chains 1160 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1041 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 F residue 8 GLN Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 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 393 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 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 292 SER 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 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 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 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 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 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 367 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 383 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 32 GLN I 205 GLN I 223 GLN I 439 HIS J 24 HIS J 69 ASN J 402 ASN M 32 GLN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 HIS M 343 ASN M 361 ASN M 363 HIS N 95 HIS N 151 ASN N 222 GLN N 358 ASN ** O 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 ASN P 198 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111659 restraints weight = 52395.021| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.29 r_work: 0.3276 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 34076 Z= 0.244 Angle : 0.729 13.420 46512 Z= 0.372 Chirality : 0.051 0.359 5193 Planarity : 0.006 0.083 5965 Dihedral : 6.921 77.827 4821 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.45 % Favored : 94.44 % Rotamer: Outliers : 7.43 % Allowed : 26.97 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.13), residues: 4224 helix: 0.78 (0.21), residues: 564 sheet: -0.51 (0.14), residues: 1408 loop : -0.99 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 214 TYR 0.023 0.002 TYR E 137 PHE 0.018 0.002 PHE L 134 TRP 0.025 0.002 TRP D 188 HIS 0.008 0.001 HIS J 82 Details of bonding type rmsd covalent geometry : bond 0.00559 (34006) covalent geometry : angle 0.72042 (46363) SS BOND : bond 0.00551 ( 61) SS BOND : angle 1.97978 ( 122) hydrogen bonds : bond 0.04050 ( 1153) hydrogen bonds : angle 5.74085 ( 2949) link_NAG-ASN : bond 0.00556 ( 9) link_NAG-ASN : angle 2.55791 ( 27) *********************** 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 1324 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 1053 time to evaluate : 1.393 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 21 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8452 (ttt180) REVERT: A 30 GLN cc_start: 0.8488 (tt0) cc_final: 0.8286 (tt0) REVERT: A 37 ARG cc_start: 0.8972 (mpp80) cc_final: 0.8674 (mtm180) REVERT: A 54 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8315 (ttmm) REVERT: A 88 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7570 (mtp) REVERT: A 192 GLU cc_start: 0.7171 (tt0) cc_final: 0.6858 (mt-10) REVERT: A 211 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7726 (p) REVERT: A 242 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 245 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8405 (mttt) REVERT: B 6 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6994 (t80) REVERT: B 62 LEU cc_start: 0.8495 (mt) cc_final: 0.8209 (mt) REVERT: B 102 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8063 (mm-40) REVERT: B 172 VAL cc_start: 0.8526 (t) cc_final: 0.8196 (p) REVERT: B 200 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (tmtt) REVERT: B 249 LYS cc_start: 0.8380 (mttm) cc_final: 0.8159 (mttm) REVERT: B 300 ASP cc_start: 0.8048 (t0) cc_final: 0.7790 (t0) REVERT: B 344 ASN cc_start: 0.8137 (t0) cc_final: 0.7915 (t160) REVERT: B 399 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7752 (mm) REVERT: D 193 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8410 (t) REVERT: E 43 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7826 (t0) REVERT: E 54 LYS cc_start: 0.8701 (tttt) cc_final: 0.8203 (tttm) REVERT: E 96 CYS cc_start: 0.8046 (t) cc_final: 0.7056 (m) REVERT: E 113 GLU cc_start: 0.7707 (mp0) cc_final: 0.7238 (mp0) REVERT: E 223 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8220 (mp10) REVERT: E 303 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8178 (ttpp) REVERT: E 382 LYS cc_start: 0.8669 (mttm) cc_final: 0.8409 (mttm) REVERT: F 27 CYS cc_start: 0.7122 (p) cc_final: 0.6901 (p) REVERT: F 73 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: F 74 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8655 (tttp) REVERT: F 259 VAL cc_start: 0.8725 (p) cc_final: 0.8445 (m) REVERT: G 22 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6864 (mmp) REVERT: G 48 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7599 (mm-40) REVERT: H 129 VAL cc_start: 0.8303 (t) cc_final: 0.8043 (p) REVERT: H 132 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6203 (mmm-85) REVERT: H 175 LEU cc_start: 0.8371 (mm) cc_final: 0.8133 (mm) REVERT: H 247 LYS cc_start: 0.8561 (mmmm) cc_final: 0.8339 (mmmm) REVERT: I 96 CYS cc_start: 0.8096 (t) cc_final: 0.7804 (t) REVERT: I 101 THR cc_start: 0.8561 (t) cc_final: 0.8331 (p) REVERT: I 137 TYR cc_start: 0.8772 (p90) cc_final: 0.8053 (p90) REVERT: I 246 LYS cc_start: 0.8430 (pttt) cc_final: 0.8080 (ptmm) REVERT: I 305 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8314 (p) REVERT: I 422 ILE cc_start: 0.8152 (mm) cc_final: 0.7892 (mm) REVERT: J 6 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.6832 (t80) REVERT: J 37 ARG cc_start: 0.8695 (mmp-170) cc_final: 0.8487 (mmt180) REVERT: J 208 ILE cc_start: 0.8676 (mm) cc_final: 0.8321 (tt) REVERT: J 263 CYS cc_start: 0.7083 (m) cc_final: 0.6746 (m) REVERT: J 354 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8222 (p) REVERT: K 22 MET cc_start: 0.7241 (tpp) cc_final: 0.6716 (tpp) REVERT: L 117 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7200 (mmp) REVERT: L 193 VAL cc_start: 0.7932 (t) cc_final: 0.7660 (m) REVERT: L 204 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8093 (mmt-90) REVERT: M 61 LYS cc_start: 0.8406 (mmmm) cc_final: 0.8138 (tppp) REVERT: M 112 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8097 (mt-10) REVERT: M 161 LYS cc_start: 0.8351 (mtpp) cc_final: 0.8049 (ttpp) REVERT: M 175 ASP cc_start: 0.7851 (m-30) cc_final: 0.7554 (m-30) REVERT: M 214 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8274 (tt) REVERT: M 217 ASN cc_start: 0.8745 (t0) cc_final: 0.8427 (t0) REVERT: M 220 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8086 (pp) REVERT: M 300 LEU cc_start: 0.8672 (mt) cc_final: 0.8448 (mt) REVERT: M 400 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8161 (p) REVERT: M 439 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7872 (t-170) REVERT: N 24 HIS cc_start: 0.7548 (t-90) cc_final: 0.7345 (t-90) REVERT: N 65 MET cc_start: 0.7925 (ptt) cc_final: 0.7620 (ptp) REVERT: N 68 MET cc_start: 0.8168 (mmm) cc_final: 0.7641 (mmm) REVERT: N 186 LYS cc_start: 0.8539 (tptp) cc_final: 0.8049 (tptt) REVERT: N 196 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8079 (tttp) REVERT: N 219 ASP cc_start: 0.8405 (t0) cc_final: 0.8126 (t0) REVERT: N 227 LEU cc_start: 0.8418 (tt) cc_final: 0.8181 (tm) REVERT: N 260 LYS cc_start: 0.8871 (tptp) cc_final: 0.8615 (tptp) REVERT: N 295 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8619 (ptt180) REVERT: N 314 VAL cc_start: 0.8794 (t) cc_final: 0.8466 (m) REVERT: N 351 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7409 (mm-30) REVERT: O 22 MET cc_start: 0.5314 (tpp) cc_final: 0.4793 (tpp) outliers start: 271 outliers final: 133 residues processed: 1193 average time/residue: 0.6704 time to fit residues: 963.2110 Evaluate side-chains 1205 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1047 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 88 MET 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 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 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 200 LYS Chi-restraints excluded: chain B residue 203 ASP 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 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain D residue 155 LYS 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 43 ASN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 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 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 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 G residue 22 MET Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 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 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 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 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 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 228 LEU 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 139 SER Chi-restraints excluded: chain M residue 214 LEU 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 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 123 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 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 142 optimal weight: 0.8980 chunk 370 optimal weight: 5.9990 chunk 367 optimal weight: 0.9990 chunk 378 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 312 optimal weight: 10.0000 chunk 374 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 209 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN F 151 ASN F 213 HIS G 40 ASN H 194 GLN ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 ASN I 439 HIS J 24 HIS J 69 ASN J 144 HIS J 402 ASN K 39 GLN M 100 ASN M 343 ASN 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: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112699 restraints weight = 52416.669| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.26 r_work: 0.3293 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34076 Z= 0.174 Angle : 0.683 14.434 46512 Z= 0.346 Chirality : 0.048 0.311 5193 Planarity : 0.006 0.074 5965 Dihedral : 6.583 79.222 4811 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.18 % Rotamer: Outliers : 7.13 % Allowed : 27.71 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.13), residues: 4224 helix: 0.93 (0.21), residues: 564 sheet: -0.48 (0.14), residues: 1376 loop : -0.92 (0.13), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 214 TYR 0.022 0.002 TYR P 195 PHE 0.015 0.001 PHE I 95 TRP 0.022 0.001 TRP D 188 HIS 0.007 0.001 HIS F 126 Details of bonding type rmsd covalent geometry : bond 0.00400 (34006) covalent geometry : angle 0.67389 (46363) SS BOND : bond 0.00502 ( 61) SS BOND : angle 1.94544 ( 122) hydrogen bonds : bond 0.03661 ( 1153) hydrogen bonds : angle 5.52654 ( 2949) link_NAG-ASN : bond 0.00533 ( 9) link_NAG-ASN : angle 2.57611 ( 27) *********************** 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 1346 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 1086 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8412 (ttt180) REVERT: A 30 GLN cc_start: 0.8512 (tt0) cc_final: 0.8306 (tt0) REVERT: A 37 ARG cc_start: 0.8960 (mpp80) cc_final: 0.8681 (mtm180) REVERT: A 50 LYS cc_start: 0.8573 (tttm) cc_final: 0.7966 (tttm) REVERT: A 54 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8214 (ttpp) REVERT: A 192 GLU cc_start: 0.7205 (tt0) cc_final: 0.6876 (mt-10) REVERT: A 211 SER cc_start: 0.8176 (m) cc_final: 0.7704 (p) REVERT: A 235 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8373 (t) REVERT: A 242 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 245 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8428 (mtmt) REVERT: A 255 VAL cc_start: 0.8602 (t) cc_final: 0.8246 (m) REVERT: A 260 CYS cc_start: 0.7646 (m) cc_final: 0.7433 (m) REVERT: B 6 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6961 (t80) REVERT: B 62 LEU cc_start: 0.8549 (mt) cc_final: 0.8243 (mt) REVERT: B 102 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8002 (mm-40) REVERT: B 228 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8098 (pt) REVERT: B 300 ASP cc_start: 0.8052 (t0) cc_final: 0.7770 (t0) REVERT: B 344 ASN cc_start: 0.8081 (t0) cc_final: 0.7829 (t160) REVERT: B 399 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7643 (mm) REVERT: E 54 LYS cc_start: 0.8704 (tttt) cc_final: 0.8368 (tttt) REVERT: E 96 CYS cc_start: 0.8045 (t) cc_final: 0.7107 (m) REVERT: E 103 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8334 (ttm) REVERT: E 113 GLU cc_start: 0.7720 (mp0) cc_final: 0.7245 (mp0) REVERT: E 223 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8238 (mp10) REVERT: E 235 THR cc_start: 0.8608 (t) cc_final: 0.8386 (m) REVERT: E 305 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8174 (p) REVERT: F 27 CYS cc_start: 0.7106 (p) cc_final: 0.6735 (p) REVERT: F 74 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8606 (tttp) REVERT: F 217 CYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7147 (m) REVERT: F 259 VAL cc_start: 0.8691 (p) cc_final: 0.8418 (m) REVERT: F 398 LYS cc_start: 0.8655 (tppp) cc_final: 0.8359 (ttmm) REVERT: H 129 VAL cc_start: 0.8300 (t) cc_final: 0.8039 (p) REVERT: H 132 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6550 (mtt90) REVERT: H 175 LEU cc_start: 0.8327 (mm) cc_final: 0.8066 (mm) REVERT: H 247 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8316 (mmmm) REVERT: I 30 GLN cc_start: 0.8724 (mt0) cc_final: 0.8507 (mt0) REVERT: I 96 CYS cc_start: 0.8039 (t) cc_final: 0.7761 (t) REVERT: I 101 THR cc_start: 0.8566 (t) cc_final: 0.8310 (p) REVERT: I 137 TYR cc_start: 0.8746 (p90) cc_final: 0.8000 (p90) REVERT: I 217 ASN cc_start: 0.8615 (t0) cc_final: 0.8406 (t0) REVERT: I 305 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.7503 (t) REVERT: I 323 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7940 (t) REVERT: I 382 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8160 (mttm) REVERT: I 404 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7754 (p) REVERT: J 6 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.6787 (t80) REVERT: J 108 THR cc_start: 0.8426 (p) cc_final: 0.8138 (t) REVERT: J 174 ASP cc_start: 0.7904 (t0) cc_final: 0.7606 (t0) REVERT: J 263 CYS cc_start: 0.7082 (m) cc_final: 0.6671 (m) REVERT: J 300 ASP cc_start: 0.7784 (t0) cc_final: 0.7408 (t0) REVERT: J 314 VAL cc_start: 0.8072 (t) cc_final: 0.7688 (t) REVERT: J 346 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7731 (m90) REVERT: J 354 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8149 (p) REVERT: L 117 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7175 (mmp) REVERT: L 193 VAL cc_start: 0.7951 (t) cc_final: 0.7683 (m) REVERT: L 204 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8186 (ttm-80) REVERT: M 99 GLU cc_start: 0.7544 (pt0) cc_final: 0.7330 (pt0) REVERT: M 141 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7811 (p) REVERT: M 156 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8035 (tmtm) REVERT: M 175 ASP cc_start: 0.7867 (m-30) cc_final: 0.7613 (m-30) REVERT: M 220 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8023 (pp) REVERT: M 229 ILE cc_start: 0.8717 (mm) cc_final: 0.8444 (mt) REVERT: M 293 GLU cc_start: 0.8166 (tt0) cc_final: 0.7804 (tt0) REVERT: M 342 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: M 400 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8177 (p) REVERT: N 6 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: N 18 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7984 (t0) REVERT: N 24 HIS cc_start: 0.7539 (t-90) cc_final: 0.7299 (t-90) REVERT: N 25 SER cc_start: 0.8285 (t) cc_final: 0.7882 (p) REVERT: N 65 MET cc_start: 0.7953 (ptt) cc_final: 0.7722 (ptp) REVERT: N 168 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8621 (mt0) REVERT: N 186 LYS cc_start: 0.8530 (tptp) cc_final: 0.7954 (tptt) REVERT: N 196 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8077 (tttp) REVERT: N 219 ASP cc_start: 0.8400 (t0) cc_final: 0.8043 (t0) REVERT: N 221 LYS cc_start: 0.8825 (ptpt) cc_final: 0.8613 (ptpt) REVERT: N 295 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8553 (ptt180) REVERT: N 314 VAL cc_start: 0.8831 (t) cc_final: 0.8463 (m) REVERT: N 351 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7285 (mm-30) REVERT: N 399 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8774 (mt) REVERT: O 22 MET cc_start: 0.5385 (tpp) cc_final: 0.4904 (tpp) REVERT: P 129 VAL cc_start: 0.8201 (t) cc_final: 0.7887 (m) outliers start: 260 outliers final: 140 residues processed: 1214 average time/residue: 0.6349 time to fit residues: 924.9661 Evaluate side-chains 1228 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 1057 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 135 ILE 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 337 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 69 ASN 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 259 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 155 LYS 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 243 THR Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 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 74 LYS Chi-restraints excluded: chain F residue 110 THR 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 254 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 272 CYS Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 323 SER Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain 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 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 309 GLU Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 399 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain 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 125 HIS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 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 6 PHE 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 168 GLN 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 213 optimal weight: 2.9990 chunk 353 optimal weight: 0.0070 chunk 79 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 398 optimal weight: 7.9990 chunk 246 optimal weight: 0.9990 chunk 252 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 HIS B 151 ASN B 155 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 ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN I 439 HIS J 24 HIS J 69 ASN M 100 ASN M 343 ASN M 361 ASN M 363 HIS N 151 ASN N 358 ASN P 145 ASN P 198 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112401 restraints weight = 52216.920| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.30 r_work: 0.3293 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34076 Z= 0.167 Angle : 0.679 15.967 46512 Z= 0.342 Chirality : 0.048 0.307 5193 Planarity : 0.006 0.070 5965 Dihedral : 6.460 81.147 4811 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.41 % Rotamer: Outliers : 6.52 % Allowed : 29.19 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.13), residues: 4224 helix: 1.00 (0.21), residues: 564 sheet: -0.36 (0.14), residues: 1340 loop : -0.94 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 152 TYR 0.025 0.002 TYR P 195 PHE 0.019 0.001 PHE I 95 TRP 0.021 0.001 TRP D 188 HIS 0.007 0.001 HIS F 126 Details of bonding type rmsd covalent geometry : bond 0.00383 (34006) covalent geometry : angle 0.67021 (46363) SS BOND : bond 0.00417 ( 61) SS BOND : angle 1.84741 ( 122) hydrogen bonds : bond 0.03524 ( 1153) hydrogen bonds : angle 5.41856 ( 2949) link_NAG-ASN : bond 0.00611 ( 9) link_NAG-ASN : angle 2.63793 ( 27) *********************** 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 1340 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 1102 time to evaluate : 1.292 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: 0.8871 (OUTLIER) cc_final: 0.8438 (ttt180) REVERT: A 30 GLN cc_start: 0.8525 (tt0) cc_final: 0.8310 (tt0) REVERT: A 37 ARG cc_start: 0.8965 (mpp80) cc_final: 0.8428 (mtm180) REVERT: A 48 THR cc_start: 0.8655 (m) cc_final: 0.8375 (t) REVERT: A 50 LYS cc_start: 0.8571 (tttm) cc_final: 0.7941 (tttm) REVERT: A 54 LYS cc_start: 0.8556 (ttpp) cc_final: 0.7915 (ttmm) REVERT: A 88 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7501 (mtp) REVERT: A 95 PHE cc_start: 0.8176 (t80) cc_final: 0.7929 (t80) REVERT: A 109 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 211 SER cc_start: 0.8198 (m) cc_final: 0.7706 (p) REVERT: A 235 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8361 (t) REVERT: A 242 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 245 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8390 (mtmt) REVERT: A 255 VAL cc_start: 0.8619 (t) cc_final: 0.8260 (m) REVERT: A 260 CYS cc_start: 0.7701 (m) cc_final: 0.7474 (m) REVERT: B 6 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6933 (t80) REVERT: B 62 LEU cc_start: 0.8475 (mt) cc_final: 0.8168 (mt) REVERT: B 102 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7976 (mm-40) REVERT: B 228 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8082 (pt) REVERT: B 249 LYS cc_start: 0.8325 (mttm) cc_final: 0.7973 (mttm) REVERT: B 300 ASP cc_start: 0.8092 (t0) cc_final: 0.7802 (t0) REVERT: B 344 ASN cc_start: 0.8071 (t0) cc_final: 0.7822 (t160) REVERT: B 399 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7531 (mm) REVERT: D 117 MET cc_start: 0.6562 (tmm) cc_final: 0.6118 (tmm) REVERT: D 199 ARG cc_start: 0.7646 (tpp80) cc_final: 0.7435 (tpp80) REVERT: D 233 GLU cc_start: 0.4380 (tp30) cc_final: 0.3878 (tm-30) REVERT: E 54 LYS cc_start: 0.8722 (tttt) cc_final: 0.8403 (tttt) REVERT: E 96 CYS cc_start: 0.8032 (t) cc_final: 0.7077 (m) REVERT: E 103 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8339 (ttm) REVERT: E 113 GLU cc_start: 0.7707 (mp0) cc_final: 0.7210 (mp0) REVERT: E 223 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8231 (mp10) REVERT: E 305 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8225 (p) REVERT: F 27 CYS cc_start: 0.7050 (p) cc_final: 0.6662 (p) REVERT: F 74 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8654 (ttmm) REVERT: F 217 CYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7173 (m) REVERT: F 259 VAL cc_start: 0.8679 (p) cc_final: 0.8429 (m) REVERT: F 376 MET cc_start: 0.7413 (ttp) cc_final: 0.7124 (ttp) REVERT: F 398 LYS cc_start: 0.8643 (tppp) cc_final: 0.8423 (ttmm) REVERT: G 48 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7561 (mm-40) REVERT: H 129 VAL cc_start: 0.8307 (t) cc_final: 0.8069 (p) REVERT: H 132 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6417 (mmm-85) REVERT: H 175 LEU cc_start: 0.8315 (mm) cc_final: 0.8007 (mm) REVERT: H 247 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8266 (mmmm) REVERT: I 96 CYS cc_start: 0.8033 (t) cc_final: 0.7732 (t) REVERT: I 101 THR cc_start: 0.8593 (t) cc_final: 0.8354 (p) REVERT: I 137 TYR cc_start: 0.8747 (p90) cc_final: 0.8000 (p90) REVERT: I 305 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8144 (p) REVERT: I 382 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8174 (mttm) REVERT: I 404 SER cc_start: 0.8053 (OUTLIER) cc_final: 0.7538 (p) REVERT: J 6 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6741 (t80) REVERT: J 108 THR cc_start: 0.8441 (p) cc_final: 0.8153 (t) REVERT: J 131 ARG cc_start: 0.8714 (mtt90) cc_final: 0.8446 (mtt90) REVERT: J 174 ASP cc_start: 0.7853 (t0) cc_final: 0.7562 (t0) REVERT: J 300 ASP cc_start: 0.7805 (t0) cc_final: 0.7421 (t0) REVERT: J 314 VAL cc_start: 0.8011 (t) cc_final: 0.7760 (m) REVERT: J 333 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8188 (mtmm) REVERT: J 344 ASN cc_start: 0.8105 (t0) cc_final: 0.7531 (t0) REVERT: J 346 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7599 (m90) REVERT: J 354 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8164 (p) REVERT: J 380 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7716 (p) REVERT: L 117 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7255 (mmp) REVERT: L 170 MET cc_start: 0.7759 (pmm) cc_final: 0.7359 (pmm) REVERT: L 193 VAL cc_start: 0.7938 (t) cc_final: 0.7699 (m) REVERT: L 204 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.7870 (ttm-80) REVERT: M 32 GLN cc_start: 0.8446 (tt0) cc_final: 0.8073 (tt0) REVERT: M 75 ASP cc_start: 0.8353 (t0) cc_final: 0.8124 (t70) REVERT: M 99 GLU cc_start: 0.7628 (pt0) cc_final: 0.7402 (pt0) REVERT: M 103 MET cc_start: 0.8097 (ttp) cc_final: 0.7839 (tpp) REVERT: M 112 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8003 (mt-10) REVERT: M 141 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7810 (p) REVERT: M 146 ASP cc_start: 0.8015 (t0) cc_final: 0.7808 (t0) REVERT: M 156 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8063 (tmtm) REVERT: M 175 ASP cc_start: 0.7884 (m-30) cc_final: 0.7582 (m-30) REVERT: M 229 ILE cc_start: 0.8708 (mm) cc_final: 0.8419 (mt) REVERT: M 293 GLU cc_start: 0.8198 (tt0) cc_final: 0.7826 (tt0) REVERT: M 342 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: M 400 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8250 (p) REVERT: N 18 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8020 (t0) REVERT: N 24 HIS cc_start: 0.7537 (t-90) cc_final: 0.7287 (t-90) REVERT: N 25 SER cc_start: 0.8351 (t) cc_final: 0.7940 (p) REVERT: N 65 MET cc_start: 0.8012 (ptt) cc_final: 0.7774 (ptp) REVERT: N 68 MET cc_start: 0.8091 (mmm) cc_final: 0.7688 (mmm) REVERT: N 168 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8611 (mt0) REVERT: N 186 LYS cc_start: 0.8510 (tptp) cc_final: 0.8054 (tptp) REVERT: N 196 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8088 (tttp) REVERT: N 219 ASP cc_start: 0.8380 (t0) cc_final: 0.8011 (t0) REVERT: N 221 LYS cc_start: 0.8816 (ptpt) cc_final: 0.8610 (ptpt) REVERT: N 227 LEU cc_start: 0.8404 (tt) cc_final: 0.8155 (tm) REVERT: N 295 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8530 (ptt180) REVERT: N 314 VAL cc_start: 0.8839 (t) cc_final: 0.8445 (m) REVERT: N 319 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8238 (p) REVERT: N 351 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7164 (mm-30) REVERT: O 22 MET cc_start: 0.5307 (tpp) cc_final: 0.4854 (tpp) outliers start: 238 outliers final: 149 residues processed: 1219 average time/residue: 0.6099 time to fit residues: 892.4217 Evaluate side-chains 1238 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1057 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 88 MET Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 MET 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 396 THR 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 6 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 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 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 305 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 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 254 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 392 LEU 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 217 LEU 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 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 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 18 ASP 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 205 ARG Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 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 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 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 226 ILE Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain M residue 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 125 HIS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 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 342 GLU 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 99 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 165 GLU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 36 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 208 optimal weight: 0.4980 chunk 372 optimal weight: 3.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 24 HIS F 82 HIS F 118 ASN ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN J 402 ASN K 40 ASN L 197 ASN M 77 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 343 ASN M 361 ASN M 363 HIS ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 358 ASN P 145 ASN P 198 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.126372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110689 restraints weight = 51513.860| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.27 r_work: 0.3237 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 34076 Z= 0.375 Angle : 0.788 16.103 46512 Z= 0.400 Chirality : 0.054 0.380 5193 Planarity : 0.007 0.080 5965 Dihedral : 6.785 85.226 4809 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.61 % Favored : 93.25 % Rotamer: Outliers : 7.24 % Allowed : 29.14 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.13), residues: 4224 helix: 0.66 (0.21), residues: 564 sheet: -0.43 (0.14), residues: 1316 loop : -1.12 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 152 TYR 0.031 0.003 TYR P 159 PHE 0.024 0.002 PHE N 113 TRP 0.034 0.002 TRP H 188 HIS 0.012 0.002 HIS F 126 Details of bonding type rmsd covalent geometry : bond 0.00851 (34006) covalent geometry : angle 0.77856 (46363) SS BOND : bond 0.00541 ( 61) SS BOND : angle 2.12701 ( 122) hydrogen bonds : bond 0.04217 ( 1153) hydrogen bonds : angle 5.67179 ( 2949) link_NAG-ASN : bond 0.00531 ( 9) link_NAG-ASN : angle 2.71390 ( 27) *********************** 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 1356 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 1092 time to evaluate : 1.193 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: 0.8956 (OUTLIER) cc_final: 0.8468 (ttt90) REVERT: A 30 GLN cc_start: 0.8541 (tt0) cc_final: 0.8310 (tt0) REVERT: A 37 ARG cc_start: 0.9011 (mpp80) cc_final: 0.8699 (mpp-170) REVERT: A 95 PHE cc_start: 0.8257 (t80) cc_final: 0.8011 (t80) REVERT: A 192 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6938 (mt-10) REVERT: A 211 SER cc_start: 0.8287 (OUTLIER) cc_final: 0.7836 (t) REVERT: A 221 LYS cc_start: 0.8401 (ttmt) cc_final: 0.8155 (ttmt) REVERT: A 242 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7879 (mt-10) REVERT: A 245 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8397 (mtmt) REVERT: A 255 VAL cc_start: 0.8718 (t) cc_final: 0.8389 (m) REVERT: A 260 CYS cc_start: 0.7745 (m) cc_final: 0.7498 (m) REVERT: A 300 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7915 (mp) REVERT: A 301 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6786 (tm-30) REVERT: A 341 LYS cc_start: 0.9086 (tttm) cc_final: 0.8686 (tttp) REVERT: B 6 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6922 (t80) REVERT: B 62 LEU cc_start: 0.8684 (mt) cc_final: 0.8299 (mt) REVERT: B 74 LYS cc_start: 0.8771 (tttt) cc_final: 0.8566 (tttm) REVERT: B 102 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8108 (tp40) REVERT: B 121 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8372 (m) REVERT: B 249 LYS cc_start: 0.8427 (mttm) cc_final: 0.8098 (mttm) REVERT: B 263 CYS cc_start: 0.7445 (m) cc_final: 0.7177 (m) REVERT: B 300 ASP cc_start: 0.8158 (t0) cc_final: 0.7841 (t0) REVERT: B 344 ASN cc_start: 0.8207 (t0) cc_final: 0.7963 (t160) REVERT: B 399 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7573 (mm) REVERT: D 133 VAL cc_start: 0.8073 (t) cc_final: 0.7772 (p) REVERT: D 220 LYS cc_start: 0.8146 (mptt) cc_final: 0.7861 (mptt) REVERT: D 233 GLU cc_start: 0.4774 (OUTLIER) cc_final: 0.4223 (tm-30) REVERT: E 54 LYS cc_start: 0.8696 (tttt) cc_final: 0.8353 (tttt) REVERT: E 96 CYS cc_start: 0.8230 (t) cc_final: 0.7291 (m) REVERT: E 113 GLU cc_start: 0.7743 (mp0) cc_final: 0.7191 (mp0) REVERT: E 223 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8078 (mp10) REVERT: E 235 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8174 (t) REVERT: E 299 ASP cc_start: 0.8366 (m-30) cc_final: 0.8140 (m-30) REVERT: F 27 CYS cc_start: 0.7169 (p) cc_final: 0.6770 (p) REVERT: F 74 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8571 (tttp) REVERT: F 200 LYS cc_start: 0.7563 (tptt) cc_final: 0.7148 (tppp) REVERT: F 217 CYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7211 (m) REVERT: F 242 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7667 (ttm110) REVERT: F 259 VAL cc_start: 0.8714 (p) cc_final: 0.8460 (m) REVERT: F 344 ASN cc_start: 0.8531 (t0) cc_final: 0.8312 (t0) REVERT: F 376 MET cc_start: 0.7453 (ttp) cc_final: 0.7174 (ttp) REVERT: F 398 LYS cc_start: 0.8745 (tppp) cc_final: 0.8543 (ttmm) REVERT: H 117 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6343 (mpp) REVERT: H 129 VAL cc_start: 0.8371 (t) cc_final: 0.8146 (p) REVERT: H 132 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6765 (mtt90) REVERT: H 175 LEU cc_start: 0.8380 (mm) cc_final: 0.8061 (mm) REVERT: H 247 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8296 (mmmm) REVERT: I 11 VAL cc_start: 0.8877 (t) cc_final: 0.8622 (p) REVERT: I 96 CYS cc_start: 0.8115 (t) cc_final: 0.7725 (m) REVERT: I 101 THR cc_start: 0.8687 (t) cc_final: 0.8452 (p) REVERT: I 247 ASP cc_start: 0.7390 (m-30) cc_final: 0.7036 (m-30) REVERT: I 276 SER cc_start: 0.8636 (p) cc_final: 0.8325 (m) REVERT: I 305 THR cc_start: 0.8670 (m) cc_final: 0.8300 (p) REVERT: I 382 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8102 (mttm) REVERT: I 400 THR cc_start: 0.8658 (m) cc_final: 0.8409 (t) REVERT: I 404 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7704 (p) REVERT: J 6 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6784 (t80) REVERT: J 174 ASP cc_start: 0.7904 (t0) cc_final: 0.7584 (t0) REVERT: J 300 ASP cc_start: 0.7895 (t0) cc_final: 0.7501 (t0) REVERT: J 314 VAL cc_start: 0.8193 (t) cc_final: 0.7816 (t) REVERT: J 333 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8191 (mtmm) REVERT: J 344 ASN cc_start: 0.8118 (t0) cc_final: 0.7574 (t0) REVERT: J 354 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8196 (p) REVERT: L 117 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7232 (mmp) REVERT: L 193 VAL cc_start: 0.8048 (t) cc_final: 0.7798 (m) REVERT: L 204 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.7961 (ttm-80) REVERT: M 112 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8074 (mt-10) REVERT: M 141 SER cc_start: 0.8077 (OUTLIER) cc_final: 0.7853 (p) REVERT: M 220 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8333 (pp) REVERT: M 350 SER cc_start: 0.8803 (t) cc_final: 0.8474 (p) REVERT: M 400 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8311 (p) REVERT: N 24 HIS cc_start: 0.7684 (t-90) cc_final: 0.7483 (t-90) REVERT: N 65 MET cc_start: 0.8146 (ptt) cc_final: 0.7896 (ptp) REVERT: N 68 MET cc_start: 0.8156 (mmm) cc_final: 0.7754 (mmm) REVERT: N 79 ASP cc_start: 0.8026 (t0) cc_final: 0.7786 (t0) REVERT: N 168 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8630 (mt0) REVERT: N 186 LYS cc_start: 0.8495 (tptp) cc_final: 0.7861 (tptt) REVERT: N 196 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8079 (tttp) REVERT: N 197 TYR cc_start: 0.7615 (p90) cc_final: 0.7156 (p90) REVERT: N 227 LEU cc_start: 0.8438 (tt) cc_final: 0.8161 (tm) REVERT: N 319 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8308 (p) REVERT: N 351 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7240 (mm-30) REVERT: O 22 MET cc_start: 0.5400 (tpp) cc_final: 0.4960 (tpp) REVERT: P 190 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.7844 (m90) REVERT: P 222 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7311 (ptm-80) outliers start: 264 outliers final: 160 residues processed: 1224 average time/residue: 0.5914 time to fit residues: 873.4930 Evaluate side-chains 1271 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 1083 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 47 ILE Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 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 376 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 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 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 204 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 364 THR 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 D residue 122 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 261 TRP Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 SER 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 35 GLU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR 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 43 SER Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 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 100 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 249 LYS Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 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 K residue 36 MET Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 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 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 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 223 GLN Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 260 CYS Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 319 VAL Chi-restraints excluded: chain M residue 397 GLU Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 418 THR Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 439 HIS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 168 GLN Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 346 HIS Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain N residue 394 ILE Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 190 HIS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 222 ARG 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 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 348 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN B 151 ASN B 236 ASN B 302 ASN B 402 ASN E 226 GLN E 343 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 HIS F 82 HIS H 189 HIS ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN J 24 HIS J 69 ASN J 175 HIS J 402 ASN M 100 ASN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111718 restraints weight = 52063.565| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.31 r_work: 0.3285 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34076 Z= 0.152 Angle : 0.687 15.489 46512 Z= 0.347 Chirality : 0.048 0.302 5193 Planarity : 0.006 0.068 5965 Dihedral : 6.492 85.513 4808 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 6.22 % Allowed : 30.56 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.13), residues: 4224 helix: 0.90 (0.21), residues: 568 sheet: -0.41 (0.14), residues: 1364 loop : -1.02 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 310 TYR 0.036 0.002 TYR H 163 PHE 0.023 0.001 PHE I 95 TRP 0.033 0.001 TRP H 188 HIS 0.008 0.001 HIS F 126 Details of bonding type rmsd covalent geometry : bond 0.00355 (34006) covalent geometry : angle 0.67767 (46363) SS BOND : bond 0.00390 ( 61) SS BOND : angle 1.96480 ( 122) hydrogen bonds : bond 0.03505 ( 1153) hydrogen bonds : angle 5.40369 ( 2949) link_NAG-ASN : bond 0.00482 ( 9) link_NAG-ASN : angle 2.60478 ( 27) *********************** 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 1329 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1102 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8563 (ttt180) REVERT: A 37 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8702 (mpp-170) REVERT: A 48 THR cc_start: 0.8625 (m) cc_final: 0.8357 (t) REVERT: A 192 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6963 (mt-10) REVERT: A 211 SER cc_start: 0.8253 (m) cc_final: 0.7788 (t) REVERT: A 221 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8151 (ttmt) REVERT: A 235 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8370 (t) REVERT: A 242 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7983 (mt-10) REVERT: A 255 VAL cc_start: 0.8624 (t) cc_final: 0.8281 (m) REVERT: A 260 CYS cc_start: 0.7768 (m) cc_final: 0.7506 (m) REVERT: A 279 ILE cc_start: 0.8669 (pt) cc_final: 0.8465 (pt) REVERT: A 297 VAL cc_start: 0.9106 (p) cc_final: 0.8894 (m) REVERT: A 301 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6656 (tm-30) REVERT: A 341 LYS cc_start: 0.9042 (tttm) cc_final: 0.8710 (tttp) REVERT: A 418 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7748 (p) REVERT: B 6 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6835 (t80) REVERT: B 62 LEU cc_start: 0.8461 (mt) cc_final: 0.8131 (mt) REVERT: B 74 LYS cc_start: 0.8795 (tttt) cc_final: 0.8580 (tttm) REVERT: B 102 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8061 (mm-40) REVERT: B 249 LYS cc_start: 0.8385 (mttm) cc_final: 0.7991 (mttm) REVERT: B 263 CYS cc_start: 0.7459 (m) cc_final: 0.7178 (m) REVERT: B 300 ASP cc_start: 0.8104 (t0) cc_final: 0.7791 (t0) REVERT: B 344 ASN cc_start: 0.8099 (t0) cc_final: 0.7845 (t160) REVERT: B 376 MET cc_start: 0.7208 (tpp) cc_final: 0.6990 (tpp) REVERT: B 399 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7425 (mm) REVERT: D 135 LYS cc_start: 0.7746 (ptmm) cc_final: 0.7396 (ptpt) REVERT: D 220 LYS cc_start: 0.8091 (mptt) cc_final: 0.7745 (mptt) REVERT: D 233 GLU cc_start: 0.4416 (tp30) cc_final: 0.4076 (tm-30) REVERT: E 54 LYS cc_start: 0.8687 (tttt) cc_final: 0.8324 (tttt) REVERT: E 96 CYS cc_start: 0.8067 (t) cc_final: 0.7187 (m) REVERT: E 113 GLU cc_start: 0.7707 (mp0) cc_final: 0.7209 (mp0) REVERT: E 223 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8098 (mp10) REVERT: E 235 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8113 (t) REVERT: F 74 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8608 (ttmm) REVERT: F 217 CYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7146 (m) REVERT: F 259 VAL cc_start: 0.8676 (p) cc_final: 0.8443 (m) REVERT: F 376 MET cc_start: 0.7416 (ttp) cc_final: 0.7131 (ttp) REVERT: F 398 LYS cc_start: 0.8624 (tppp) cc_final: 0.8392 (ttmm) REVERT: G 6 MET cc_start: 0.6270 (mmm) cc_final: 0.5982 (mmm) REVERT: G 48 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7529 (mm-40) REVERT: H 175 LEU cc_start: 0.8296 (mm) cc_final: 0.7951 (mm) REVERT: H 220 LYS cc_start: 0.8579 (mptt) cc_final: 0.8236 (mptt) REVERT: H 247 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8253 (mmmm) REVERT: I 2 GLU cc_start: 0.7979 (tp30) cc_final: 0.7688 (tp30) REVERT: I 11 VAL cc_start: 0.8823 (t) cc_final: 0.8553 (p) REVERT: I 47 ILE cc_start: 0.8515 (mt) cc_final: 0.8124 (pp) REVERT: I 96 CYS cc_start: 0.8061 (t) cc_final: 0.7725 (t) REVERT: I 101 THR cc_start: 0.8653 (t) cc_final: 0.8441 (p) REVERT: I 247 ASP cc_start: 0.7389 (m-30) cc_final: 0.7038 (m-30) REVERT: I 276 SER cc_start: 0.8576 (p) cc_final: 0.8279 (m) REVERT: I 305 THR cc_start: 0.8582 (m) cc_final: 0.8115 (p) REVERT: I 382 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8097 (mttm) REVERT: I 404 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7604 (p) REVERT: J 6 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6797 (t80) REVERT: J 93 SER cc_start: 0.8808 (t) cc_final: 0.8585 (p) REVERT: J 174 ASP cc_start: 0.7844 (t0) cc_final: 0.7571 (t0) REVERT: J 226 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: J 300 ASP cc_start: 0.7826 (t0) cc_final: 0.7440 (t0) REVERT: J 314 VAL cc_start: 0.8083 (t) cc_final: 0.7821 (m) REVERT: J 333 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8163 (mtmm) REVERT: J 344 ASN cc_start: 0.8178 (t0) cc_final: 0.7571 (t0) REVERT: J 346 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.7738 (m90) REVERT: J 354 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8169 (p) REVERT: J 392 LEU cc_start: 0.8929 (mm) cc_final: 0.8727 (mm) REVERT: L 117 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.7066 (mmp) REVERT: L 122 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8451 (t) REVERT: L 170 MET cc_start: 0.7752 (pmm) cc_final: 0.7217 (pmm) REVERT: L 193 VAL cc_start: 0.7928 (t) cc_final: 0.7690 (m) REVERT: L 204 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8179 (ttm-80) REVERT: M 32 GLN cc_start: 0.8460 (tt0) cc_final: 0.8139 (tt0) REVERT: M 54 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8219 (mtpp) REVERT: M 75 ASP cc_start: 0.8412 (t70) cc_final: 0.8168 (t70) REVERT: M 105 GLU cc_start: 0.8092 (pt0) cc_final: 0.7870 (pt0) REVERT: M 109 GLU cc_start: 0.8214 (pt0) cc_final: 0.8000 (pt0) REVERT: M 112 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8035 (mt-10) REVERT: M 141 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7820 (p) REVERT: M 146 ASP cc_start: 0.8042 (t0) cc_final: 0.7821 (t0) REVERT: M 156 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8067 (tmtm) REVERT: M 203 ASP cc_start: 0.8283 (p0) cc_final: 0.8071 (p0) REVERT: M 399 PHE cc_start: 0.8093 (t80) cc_final: 0.7551 (t80) REVERT: M 400 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8278 (p) REVERT: N 24 HIS cc_start: 0.7592 (t-90) cc_final: 0.7315 (t-90) REVERT: N 25 SER cc_start: 0.8373 (t) cc_final: 0.7928 (p) REVERT: N 65 MET cc_start: 0.8054 (ptt) cc_final: 0.7852 (ptp) REVERT: N 79 ASP cc_start: 0.7982 (t0) cc_final: 0.7742 (t0) REVERT: N 123 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8219 (m) REVERT: N 186 LYS cc_start: 0.8467 (tptp) cc_final: 0.7794 (tptt) REVERT: N 196 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8076 (tttp) REVERT: N 214 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8322 (m) REVERT: N 227 LEU cc_start: 0.8411 (tt) cc_final: 0.8182 (tm) REVERT: N 319 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8285 (p) REVERT: N 351 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7177 (mm-30) REVERT: N 415 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6512 (mp) REVERT: O 22 MET cc_start: 0.5312 (tpp) cc_final: 0.4881 (tpp) outliers start: 227 outliers final: 142 residues processed: 1218 average time/residue: 0.6254 time to fit residues: 912.7365 Evaluate side-chains 1259 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 1088 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 349 GLU 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 B residue 4 THR Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 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 274 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 351 GLU 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 202 VAL Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 45 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 132 MET Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 354 THR 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 9 TYR 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 220 VAL Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 393 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 228 LEU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 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 100 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 399 LEU Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 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 35 GLU Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 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 180 ASP Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 122 optimal weight: 3.9990 chunk 404 optimal weight: 1.9990 chunk 381 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 335 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 343 ASN B 151 ASN 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 ** 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 175 HIS J 402 ASN L 197 ASN M 77 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 343 ASN M 363 HIS N 69 ASN ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 358 ASN ** O 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111636 restraints weight = 52098.434| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.29 r_work: 0.3283 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34076 Z= 0.178 Angle : 0.690 16.202 46512 Z= 0.348 Chirality : 0.048 0.351 5193 Planarity : 0.006 0.071 5965 Dihedral : 6.389 87.435 4806 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 5.81 % Allowed : 31.39 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.13), residues: 4224 helix: 0.93 (0.21), residues: 568 sheet: -0.34 (0.15), residues: 1336 loop : -1.03 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 310 TYR 0.035 0.002 TYR H 163 PHE 0.023 0.001 PHE I 95 TRP 0.036 0.002 TRP H 188 HIS 0.007 0.001 HIS J 126 Details of bonding type rmsd covalent geometry : bond 0.00411 (34006) covalent geometry : angle 0.68152 (46363) SS BOND : bond 0.00476 ( 61) SS BOND : angle 1.96665 ( 122) hydrogen bonds : bond 0.03509 ( 1153) hydrogen bonds : angle 5.32101 ( 2949) link_NAG-ASN : bond 0.00451 ( 9) link_NAG-ASN : angle 2.42000 ( 27) *********************** 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 1310 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 1098 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8711 (mpp-170) REVERT: A 48 THR cc_start: 0.8652 (m) cc_final: 0.8392 (t) REVERT: A 109 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7864 (mt-10) REVERT: A 192 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 211 SER cc_start: 0.8233 (m) cc_final: 0.7769 (t) REVERT: A 221 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8216 (ttmt) REVERT: A 235 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8358 (t) REVERT: A 242 GLU cc_start: 0.8226 (mt-10) cc_final: 0.8024 (mt-10) REVERT: A 245 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8411 (mtmt) REVERT: A 255 VAL cc_start: 0.8657 (t) cc_final: 0.8309 (m) REVERT: A 279 ILE cc_start: 0.8689 (pt) cc_final: 0.8478 (pt) REVERT: A 297 VAL cc_start: 0.9125 (p) cc_final: 0.8909 (m) REVERT: A 301 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6807 (tm-30) REVERT: A 341 LYS cc_start: 0.9022 (tttm) cc_final: 0.8696 (tttp) REVERT: A 418 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7739 (p) REVERT: B 62 LEU cc_start: 0.8591 (mt) cc_final: 0.8362 (mt) REVERT: B 102 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7968 (mm-40) REVERT: B 155 HIS cc_start: 0.7419 (m170) cc_final: 0.7096 (m170) REVERT: B 249 LYS cc_start: 0.8361 (mttm) cc_final: 0.7950 (mttm) REVERT: B 263 CYS cc_start: 0.7462 (m) cc_final: 0.7161 (m) REVERT: B 300 ASP cc_start: 0.8119 (t0) cc_final: 0.7802 (t0) REVERT: B 344 ASN cc_start: 0.8103 (t0) cc_final: 0.7821 (t160) REVERT: B 376 MET cc_start: 0.7213 (tpp) cc_final: 0.6909 (tpp) REVERT: B 399 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7519 (mm) REVERT: D 133 VAL cc_start: 0.7891 (t) cc_final: 0.7613 (p) REVERT: D 135 LYS cc_start: 0.7753 (ptmm) cc_final: 0.7378 (ptpt) REVERT: D 220 LYS cc_start: 0.8136 (mptt) cc_final: 0.7774 (mptt) REVERT: D 233 GLU cc_start: 0.4773 (tp30) cc_final: 0.4389 (tm-30) REVERT: E 54 LYS cc_start: 0.8713 (tttt) cc_final: 0.8338 (tttt) REVERT: E 96 CYS cc_start: 0.8059 (t) cc_final: 0.7273 (m) REVERT: E 113 GLU cc_start: 0.7753 (mp0) cc_final: 0.7239 (mp0) REVERT: E 135 ILE cc_start: 0.8660 (pt) cc_final: 0.8422 (mt) REVERT: E 186 TYR cc_start: 0.8638 (m-80) cc_final: 0.8360 (m-80) REVERT: E 235 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8214 (t) REVERT: E 246 LYS cc_start: 0.8417 (pttt) cc_final: 0.8101 (ptmm) REVERT: F 217 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7204 (m) REVERT: F 218 THR cc_start: 0.8603 (m) cc_final: 0.8370 (p) REVERT: F 259 VAL cc_start: 0.8696 (p) cc_final: 0.8465 (m) REVERT: F 376 MET cc_start: 0.7404 (ttp) cc_final: 0.7121 (ttp) REVERT: G 6 MET cc_start: 0.6412 (mmm) cc_final: 0.6184 (mmm) REVERT: G 22 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6578 (mmp) REVERT: H 117 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6403 (mpp) REVERT: H 175 LEU cc_start: 0.8330 (mm) cc_final: 0.8011 (mm) REVERT: H 220 LYS cc_start: 0.8527 (mptt) cc_final: 0.8179 (mptt) REVERT: H 247 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8272 (mmmm) REVERT: I 2 GLU cc_start: 0.8014 (tp30) cc_final: 0.7717 (tp30) REVERT: I 11 VAL cc_start: 0.8827 (t) cc_final: 0.8558 (p) REVERT: I 47 ILE cc_start: 0.8490 (mt) cc_final: 0.8103 (pp) REVERT: I 96 CYS cc_start: 0.8025 (t) cc_final: 0.7695 (t) REVERT: I 101 THR cc_start: 0.8662 (t) cc_final: 0.8432 (p) REVERT: I 235 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8420 (m) REVERT: I 247 ASP cc_start: 0.7414 (m-30) cc_final: 0.7069 (m-30) REVERT: I 276 SER cc_start: 0.8566 (p) cc_final: 0.8269 (m) REVERT: I 305 THR cc_start: 0.8590 (m) cc_final: 0.8130 (p) REVERT: I 382 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8150 (mttm) REVERT: I 400 THR cc_start: 0.8727 (m) cc_final: 0.8465 (t) REVERT: I 404 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7633 (p) REVERT: J 6 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6816 (t80) REVERT: J 93 SER cc_start: 0.8796 (t) cc_final: 0.8561 (p) REVERT: J 174 ASP cc_start: 0.7897 (t0) cc_final: 0.7667 (t0) REVERT: J 226 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: J 236 ASN cc_start: 0.8404 (t0) cc_final: 0.8163 (t0) REVERT: J 300 ASP cc_start: 0.7841 (t0) cc_final: 0.7455 (t0) REVERT: J 314 VAL cc_start: 0.8053 (t) cc_final: 0.7796 (m) REVERT: J 333 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8181 (mtmm) REVERT: J 344 ASN cc_start: 0.8202 (t0) cc_final: 0.7615 (t0) REVERT: J 346 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7714 (m90) REVERT: J 354 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8198 (p) REVERT: L 117 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.7002 (mmp) REVERT: L 122 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8445 (t) REVERT: L 193 VAL cc_start: 0.7899 (t) cc_final: 0.7648 (m) REVERT: L 204 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8168 (ttm-80) REVERT: M 32 GLN cc_start: 0.8454 (tt0) cc_final: 0.8138 (tt0) REVERT: M 54 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8235 (mtpp) REVERT: M 75 ASP cc_start: 0.8402 (t0) cc_final: 0.8176 (t70) REVERT: M 79 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8340 (tp40) REVERT: M 105 GLU cc_start: 0.8166 (pt0) cc_final: 0.7961 (pt0) REVERT: M 112 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7995 (mt-10) REVERT: M 141 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7832 (p) REVERT: M 156 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8070 (tmtm) REVERT: M 220 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8158 (pp) REVERT: M 264 LEU cc_start: 0.8204 (mt) cc_final: 0.7954 (mt) REVERT: M 399 PHE cc_start: 0.8037 (t80) cc_final: 0.7506 (t80) REVERT: M 400 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8293 (p) REVERT: N 24 HIS cc_start: 0.7551 (t-90) cc_final: 0.7323 (t-90) REVERT: N 65 MET cc_start: 0.8074 (ptt) cc_final: 0.7865 (ptp) REVERT: N 79 ASP cc_start: 0.7952 (t0) cc_final: 0.7698 (t0) REVERT: N 186 LYS cc_start: 0.8489 (tptp) cc_final: 0.8211 (tptm) REVERT: N 196 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8103 (tttp) REVERT: N 217 CYS cc_start: 0.6637 (OUTLIER) cc_final: 0.6311 (m) REVERT: N 351 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7265 (mm-30) REVERT: N 415 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.6400 (mp) REVERT: O 22 MET cc_start: 0.5265 (tpp) cc_final: 0.4888 (tpp) REVERT: P 129 VAL cc_start: 0.8226 (t) cc_final: 0.7923 (m) REVERT: P 222 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7317 (ptm-80) outliers start: 212 outliers final: 141 residues processed: 1197 average time/residue: 0.6393 time to fit residues: 916.8018 Evaluate side-chains 1252 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 1081 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 75 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 296 THR 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 376 THR 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 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 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 389 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 261 TRP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 101 THR 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 354 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 27 CYS 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 220 VAL Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 50 LYS 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 220 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 399 LEU Chi-restraints excluded: chain K residue 8 VAL 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 122 VAL Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 220 LEU 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 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 35 GLU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 210 SER Chi-restraints excluded: chain N residue 217 CYS 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 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 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 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 277 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 278 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 350 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 377 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 B 151 ASN B 175 HIS B 236 ASN B 302 ASN B 402 ASN E 77 GLN E 223 GLN E 226 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN J 24 HIS J 69 ASN J 175 HIS J 402 ASN M 77 GLN M 100 ASN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 343 ASN M 363 HIS ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 358 ASN ** O 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111812 restraints weight = 51870.111| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.23 r_work: 0.3251 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 34076 Z= 0.307 Angle : 0.760 15.772 46512 Z= 0.384 Chirality : 0.052 0.398 5193 Planarity : 0.006 0.074 5965 Dihedral : 6.579 89.355 4804 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.56 % Favored : 93.32 % Rotamer: Outliers : 5.51 % Allowed : 32.32 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.13), residues: 4224 helix: 0.76 (0.21), residues: 564 sheet: -0.36 (0.15), residues: 1336 loop : -1.13 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 310 TYR 0.030 0.002 TYR A 321 PHE 0.023 0.002 PHE I 95 TRP 0.023 0.002 TRP D 188 HIS 0.010 0.001 HIS F 126 Details of bonding type rmsd covalent geometry : bond 0.00701 (34006) covalent geometry : angle 0.75043 (46363) SS BOND : bond 0.00527 ( 61) SS BOND : angle 2.19097 ( 122) hydrogen bonds : bond 0.03898 ( 1153) hydrogen bonds : angle 5.46310 ( 2949) link_NAG-ASN : bond 0.00382 ( 9) link_NAG-ASN : angle 2.75604 ( 27) *********************** 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 1295 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 1094 time to evaluate : 1.132 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: 0.9002 (OUTLIER) cc_final: 0.8709 (mpp-170) REVERT: A 192 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 211 SER cc_start: 0.8282 (m) cc_final: 0.7842 (t) REVERT: A 221 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8250 (ttmt) REVERT: A 235 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8429 (t) REVERT: A 245 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8437 (mtmt) REVERT: A 255 VAL cc_start: 0.8732 (t) cc_final: 0.8387 (m) REVERT: A 301 GLU cc_start: 0.7574 (tm-30) cc_final: 0.6903 (tm-30) REVERT: A 341 LYS cc_start: 0.9074 (tttm) cc_final: 0.8759 (tttp) REVERT: A 418 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7737 (p) REVERT: B 62 LEU cc_start: 0.8518 (mt) cc_final: 0.8284 (mt) REVERT: B 102 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8085 (mm-40) REVERT: B 121 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8366 (m) REVERT: B 263 CYS cc_start: 0.7418 (m) cc_final: 0.7107 (m) REVERT: B 300 ASP cc_start: 0.8149 (t0) cc_final: 0.7827 (t0) REVERT: B 302 ASN cc_start: 0.8556 (t0) cc_final: 0.8262 (t0) REVERT: B 308 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8479 (mt) REVERT: B 344 ASN cc_start: 0.8181 (t0) cc_final: 0.7921 (t160) REVERT: B 399 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7515 (mm) REVERT: D 133 VAL cc_start: 0.7953 (t) cc_final: 0.7682 (p) REVERT: D 220 LYS cc_start: 0.8201 (mptt) cc_final: 0.7823 (mptt) REVERT: D 233 GLU cc_start: 0.4623 (tp30) cc_final: 0.4099 (tm-30) REVERT: D 245 ASN cc_start: 0.8275 (p0) cc_final: 0.8060 (p0) REVERT: E 54 LYS cc_start: 0.8721 (tttt) cc_final: 0.8355 (tttt) REVERT: E 96 CYS cc_start: 0.8173 (t) cc_final: 0.7362 (m) REVERT: E 113 GLU cc_start: 0.7746 (mp0) cc_final: 0.7208 (mp0) REVERT: E 235 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8227 (t) REVERT: E 299 ASP cc_start: 0.8324 (m-30) cc_final: 0.8097 (m-30) REVERT: F 73 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: F 93 SER cc_start: 0.8821 (t) cc_final: 0.8564 (t) REVERT: F 200 LYS cc_start: 0.7498 (tptt) cc_final: 0.7269 (tppp) REVERT: F 217 CYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7269 (m) REVERT: F 218 THR cc_start: 0.8677 (m) cc_final: 0.8418 (p) REVERT: F 259 VAL cc_start: 0.8694 (p) cc_final: 0.8469 (m) REVERT: F 344 ASN cc_start: 0.8552 (t0) cc_final: 0.8328 (t0) REVERT: F 354 VAL cc_start: 0.8054 (p) cc_final: 0.7843 (p) REVERT: F 376 MET cc_start: 0.7459 (ttp) cc_final: 0.7181 (ttp) REVERT: F 390 ARG cc_start: 0.8328 (ttt90) cc_final: 0.8068 (ttt90) REVERT: H 117 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6392 (mpp) REVERT: H 175 LEU cc_start: 0.8427 (mm) cc_final: 0.8122 (mm) REVERT: H 220 LYS cc_start: 0.8524 (mptt) cc_final: 0.8268 (mptt) REVERT: H 247 LYS cc_start: 0.8538 (mmmm) cc_final: 0.8263 (mmmm) REVERT: I 2 GLU cc_start: 0.7975 (tp30) cc_final: 0.7724 (tp30) REVERT: I 11 VAL cc_start: 0.8879 (t) cc_final: 0.8623 (p) REVERT: I 47 ILE cc_start: 0.8519 (mt) cc_final: 0.8178 (pp) REVERT: I 96 CYS cc_start: 0.8051 (t) cc_final: 0.7761 (t) REVERT: I 101 THR cc_start: 0.8692 (t) cc_final: 0.8467 (p) REVERT: I 154 PRO cc_start: 0.8833 (Cg_endo) cc_final: 0.8632 (Cg_exo) REVERT: I 247 ASP cc_start: 0.7421 (m-30) cc_final: 0.7149 (m-30) REVERT: I 276 SER cc_start: 0.8605 (p) cc_final: 0.8319 (m) REVERT: I 305 THR cc_start: 0.8661 (m) cc_final: 0.8283 (p) REVERT: I 382 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8104 (mttm) REVERT: I 400 THR cc_start: 0.8703 (m) cc_final: 0.8454 (t) REVERT: J 93 SER cc_start: 0.8804 (t) cc_final: 0.8548 (p) REVERT: J 174 ASP cc_start: 0.7898 (t0) cc_final: 0.7639 (t0) REVERT: J 200 LYS cc_start: 0.8088 (tppp) cc_final: 0.7801 (tppp) REVERT: J 226 TYR cc_start: 0.8777 (m-80) cc_final: 0.8160 (m-80) REVERT: J 236 ASN cc_start: 0.8412 (t0) cc_final: 0.8184 (t0) REVERT: J 300 ASP cc_start: 0.7841 (t0) cc_final: 0.7459 (t0) REVERT: J 314 VAL cc_start: 0.8169 (t) cc_final: 0.7798 (t) REVERT: J 333 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8180 (mtmm) REVERT: J 344 ASN cc_start: 0.8180 (t0) cc_final: 0.7630 (t0) REVERT: J 354 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8219 (p) REVERT: J 399 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8241 (mm) REVERT: L 117 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7068 (mmp) REVERT: L 122 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8488 (t) REVERT: L 193 VAL cc_start: 0.7971 (t) cc_final: 0.7158 (p) REVERT: L 204 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8184 (ttm-80) REVERT: M 75 ASP cc_start: 0.8398 (t0) cc_final: 0.8030 (t70) REVERT: M 79 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: M 112 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8037 (mt-10) REVERT: M 141 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7842 (p) REVERT: M 220 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8151 (pt) REVERT: M 229 ILE cc_start: 0.8748 (mm) cc_final: 0.8543 (mp) REVERT: M 399 PHE cc_start: 0.8109 (t80) cc_final: 0.7583 (t80) REVERT: M 400 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8319 (p) REVERT: N 24 HIS cc_start: 0.7677 (t-90) cc_final: 0.7442 (t-90) REVERT: N 65 MET cc_start: 0.8157 (ptt) cc_final: 0.7956 (ptp) REVERT: N 79 ASP cc_start: 0.7955 (t0) cc_final: 0.7710 (t0) REVERT: N 186 LYS cc_start: 0.8548 (tptp) cc_final: 0.7919 (tptp) REVERT: N 196 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7998 (tttp) REVERT: N 197 TYR cc_start: 0.7604 (p90) cc_final: 0.7093 (p90) REVERT: N 212 ASP cc_start: 0.7972 (m-30) cc_final: 0.7603 (m-30) REVERT: N 217 CYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6387 (m) REVERT: N 247 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7185 (t) REVERT: N 351 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7273 (mm-30) REVERT: N 415 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6481 (mp) REVERT: O 22 MET cc_start: 0.5294 (tpp) cc_final: 0.4936 (tpp) REVERT: P 129 VAL cc_start: 0.8235 (t) cc_final: 0.7941 (m) REVERT: P 222 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7334 (ptm-80) outliers start: 201 outliers final: 146 residues processed: 1195 average time/residue: 0.6356 time to fit residues: 911.6709 Evaluate side-chains 1261 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 1088 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 303 LYS 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 376 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 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 308 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 252 LYS Chi-restraints excluded: chain D residue 261 TRP Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 163 ILE 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 27 CYS Chi-restraints excluded: chain F residue 73 GLN 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 220 VAL Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 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 F residue 413 CYS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 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 246 GLN Chi-restraints excluded: chain I residue 16 LYS 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 220 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 297 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 434 LEU Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 302 ASN Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 399 LEU Chi-restraints excluded: chain K residue 8 VAL 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 122 VAL Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 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 101 THR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 223 GLN Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 260 CYS Chi-restraints excluded: chain M residue 280 SER Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 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 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 196 LYS Chi-restraints excluded: chain N residue 217 CYS Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 247 THR Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 346 HIS Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain N residue 394 ILE Chi-restraints excluded: chain N residue 415 ILE Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain P residue 179 SER 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 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 205 optimal weight: 10.0000 chunk 316 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN B 95 HIS B 151 ASN B 236 ASN E 77 GLN E 223 GLN E 226 GLN E 343 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 HIS F 80 ASN F 82 HIS H 190 HIS ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN I 439 HIS J 69 ASN J 175 HIS J 402 ASN M 100 ASN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 363 HIS N 151 ASN N 230 ASN N 358 ASN ** O 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111809 restraints weight = 52554.609| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.27 r_work: 0.3282 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2648 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= 0.169 Angle : 0.706 16.237 46512 Z= 0.355 Chirality : 0.049 0.361 5193 Planarity : 0.006 0.075 5965 Dihedral : 6.360 88.452 4802 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.82 % Favored : 94.11 % Rotamer: Outliers : 5.07 % Allowed : 32.73 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.13), residues: 4224 helix: 0.86 (0.21), residues: 568 sheet: -0.32 (0.15), residues: 1328 loop : -1.09 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 310 TYR 0.028 0.002 TYR H 163 PHE 0.025 0.001 PHE I 95 TRP 0.025 0.002 TRP H 188 HIS 0.008 0.001 HIS N 95 Details of bonding type rmsd covalent geometry : bond 0.00393 (34006) covalent geometry : angle 0.69716 (46363) SS BOND : bond 0.00384 ( 61) SS BOND : angle 1.90310 ( 122) hydrogen bonds : bond 0.03477 ( 1153) hydrogen bonds : angle 5.32282 ( 2949) link_NAG-ASN : bond 0.00441 ( 9) link_NAG-ASN : angle 2.68202 ( 27) ********************** 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 1279 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1094 time to evaluate : 1.156 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: 0.8986 (OUTLIER) cc_final: 0.8709 (mpp-170) REVERT: A 50 LYS cc_start: 0.8406 (tttm) cc_final: 0.8191 (mttm) REVERT: A 109 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7892 (mt-10) REVERT: A 192 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6988 (mt-10) REVERT: A 211 SER cc_start: 0.8264 (m) cc_final: 0.7804 (t) REVERT: A 221 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8190 (ttmt) REVERT: A 235 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8366 (t) REVERT: A 245 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8381 (mtmt) REVERT: A 297 VAL cc_start: 0.9111 (p) cc_final: 0.8908 (m) REVERT: A 301 GLU cc_start: 0.7580 (tm-30) cc_final: 0.6906 (tm-30) REVERT: A 341 LYS cc_start: 0.9037 (tttm) cc_final: 0.8740 (tttp) REVERT: A 418 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7712 (p) REVERT: B 62 LEU cc_start: 0.8472 (mt) cc_final: 0.8258 (mt) REVERT: B 102 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8001 (mm-40) REVERT: B 155 HIS cc_start: 0.7487 (m170) cc_final: 0.7127 (m170) REVERT: B 263 CYS cc_start: 0.7425 (m) cc_final: 0.7115 (m) REVERT: B 300 ASP cc_start: 0.8131 (t0) cc_final: 0.7811 (t0) REVERT: B 344 ASN cc_start: 0.8137 (t0) cc_final: 0.7870 (t160) REVERT: B 376 MET cc_start: 0.7174 (tpp) cc_final: 0.6858 (tpp) REVERT: B 399 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7523 (mm) REVERT: D 133 VAL cc_start: 0.7884 (t) cc_final: 0.7627 (p) REVERT: D 135 LYS cc_start: 0.7766 (ptmm) cc_final: 0.7374 (ptpt) REVERT: D 220 LYS cc_start: 0.8096 (mptt) cc_final: 0.7704 (mptt) REVERT: D 233 GLU cc_start: 0.4830 (tp30) cc_final: 0.4438 (tm-30) REVERT: E 54 LYS cc_start: 0.8729 (tttt) cc_final: 0.8321 (tttt) REVERT: E 75 ASP cc_start: 0.8443 (t0) cc_final: 0.8100 (m-30) REVERT: E 96 CYS cc_start: 0.8072 (t) cc_final: 0.7292 (m) REVERT: E 113 GLU cc_start: 0.7741 (mp0) cc_final: 0.7219 (mp0) REVERT: E 223 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8120 (mp10) REVERT: E 235 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8134 (t) REVERT: E 246 LYS cc_start: 0.8410 (pttt) cc_final: 0.8199 (pttt) REVERT: F 93 SER cc_start: 0.8822 (t) cc_final: 0.8572 (t) REVERT: F 217 CYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7212 (m) REVERT: F 218 THR cc_start: 0.8614 (m) cc_final: 0.8368 (p) REVERT: F 259 VAL cc_start: 0.8689 (p) cc_final: 0.8461 (m) REVERT: F 376 MET cc_start: 0.7416 (ttp) cc_final: 0.7134 (ttp) REVERT: F 394 ILE cc_start: 0.8688 (pp) cc_final: 0.8474 (pt) REVERT: H 117 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6426 (mpp) REVERT: H 175 LEU cc_start: 0.8366 (mm) cc_final: 0.8064 (mm) REVERT: H 220 LYS cc_start: 0.8523 (mptt) cc_final: 0.8261 (mptt) REVERT: H 247 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8260 (mmmm) REVERT: I 2 GLU cc_start: 0.7985 (tp30) cc_final: 0.7688 (tp30) REVERT: I 11 VAL cc_start: 0.8847 (t) cc_final: 0.8583 (p) REVERT: I 47 ILE cc_start: 0.8498 (mt) cc_final: 0.8186 (pp) REVERT: I 96 CYS cc_start: 0.8021 (t) cc_final: 0.7684 (t) REVERT: I 247 ASP cc_start: 0.7418 (m-30) cc_final: 0.7147 (m-30) REVERT: I 276 SER cc_start: 0.8565 (p) cc_final: 0.8275 (m) REVERT: I 305 THR cc_start: 0.8590 (m) cc_final: 0.8127 (p) REVERT: I 382 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8110 (mttm) REVERT: I 400 THR cc_start: 0.8657 (m) cc_final: 0.8413 (t) REVERT: J 93 SER cc_start: 0.8781 (t) cc_final: 0.8570 (p) REVERT: J 131 ARG cc_start: 0.8797 (mtt90) cc_final: 0.8482 (mtt90) REVERT: J 174 ASP cc_start: 0.7871 (t0) cc_final: 0.7645 (t0) REVERT: J 200 LYS cc_start: 0.8056 (tppp) cc_final: 0.7783 (tppp) REVERT: J 226 TYR cc_start: 0.8784 (m-80) cc_final: 0.8152 (m-80) REVERT: J 236 ASN cc_start: 0.8391 (t0) cc_final: 0.8170 (t0) REVERT: J 300 ASP cc_start: 0.7826 (t0) cc_final: 0.7443 (t0) REVERT: J 314 VAL cc_start: 0.8074 (t) cc_final: 0.7823 (m) REVERT: J 333 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8180 (mtmm) REVERT: J 344 ASN cc_start: 0.8282 (t0) cc_final: 0.7631 (t0) REVERT: J 354 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8200 (p) REVERT: L 117 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.7038 (mmp) REVERT: L 122 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8450 (t) REVERT: L 193 VAL cc_start: 0.7840 (t) cc_final: 0.7576 (m) REVERT: L 204 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8106 (ttm-80) REVERT: M 32 GLN cc_start: 0.8465 (tt0) cc_final: 0.8147 (tt0) REVERT: M 54 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8251 (mtpp) REVERT: M 75 ASP cc_start: 0.8421 (t0) cc_final: 0.8091 (t70) REVERT: M 112 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8014 (mt-10) REVERT: M 141 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7847 (p) REVERT: M 229 ILE cc_start: 0.8758 (mm) cc_final: 0.8487 (mt) REVERT: M 264 LEU cc_start: 0.8283 (mt) cc_final: 0.8056 (mt) REVERT: M 399 PHE cc_start: 0.8066 (t80) cc_final: 0.7541 (t80) REVERT: M 400 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8308 (p) REVERT: N 18 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7996 (t0) REVERT: N 24 HIS cc_start: 0.7623 (t-90) cc_final: 0.7341 (t-90) REVERT: N 25 SER cc_start: 0.8355 (t) cc_final: 0.7915 (p) REVERT: N 79 ASP cc_start: 0.7980 (t0) cc_final: 0.7728 (t0) REVERT: N 123 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8212 (m) REVERT: N 186 LYS cc_start: 0.8542 (tptp) cc_final: 0.8174 (tptm) REVERT: N 196 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8084 (tttp) REVERT: N 217 CYS cc_start: 0.6646 (OUTLIER) cc_final: 0.6345 (m) REVERT: N 247 THR cc_start: 0.7585 (OUTLIER) cc_final: 0.7117 (t) REVERT: N 351 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7251 (mm-30) REVERT: N 383 VAL cc_start: 0.8435 (t) cc_final: 0.8186 (t) REVERT: P 222 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7288 (ptm-80) outliers start: 185 outliers final: 136 residues processed: 1185 average time/residue: 0.6403 time to fit residues: 912.9199 Evaluate side-chains 1245 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1086 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 303 LYS 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 376 THR 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 8 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 228 ILE 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 386 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 261 TRP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 421 PHE Chi-restraints excluded: chain F residue 80 ASN 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 231 LYS 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 393 CYS Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 226 ILE 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 128 THR 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 382 LYS Chi-restraints excluded: chain I residue 396 THR Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 434 LEU Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 302 ASN Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 399 LEU Chi-restraints excluded: chain J residue 402 ASN Chi-restraints excluded: chain K residue 8 VAL 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 122 VAL Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 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 397 GLU Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 418 THR Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 439 HIS Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain N residue 217 CYS Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 247 THR Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 346 HIS Chi-restraints excluded: chain N residue 371 CYS Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 393 CYS Chi-restraints excluded: chain N residue 394 ILE Chi-restraints excluded: chain 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 206 VAL 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 237 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 411 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 291 optimal weight: 0.9980 chunk 330 optimal weight: 3.9990 chunk 163 optimal weight: 0.3980 chunk 102 optimal weight: 0.3980 chunk 309 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 226 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 118 ASN H 190 HIS ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN I 439 HIS J 69 ASN J 175 HIS ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN M 100 ASN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 363 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 ASN N 358 ASN ** O 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111564 restraints weight = 52114.714| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.30 r_work: 0.3282 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.295 34076 Z= 0.212 Angle : 0.866 59.182 46512 Z= 0.476 Chirality : 0.051 1.146 5193 Planarity : 0.007 0.165 5965 Dihedral : 6.388 88.455 4802 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.08 % Favored : 93.80 % Rotamer: Outliers : 4.91 % Allowed : 33.25 % Favored : 61.84 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.13), residues: 4224 helix: 0.86 (0.21), residues: 568 sheet: -0.32 (0.15), residues: 1328 loop : -1.09 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG L 236 TYR 0.027 0.002 TYR A 321 PHE 0.024 0.001 PHE I 95 TRP 0.021 0.001 TRP J 384 HIS 0.007 0.001 HIS N 95 Details of bonding type rmsd covalent geometry : bond 0.00480 (34006) covalent geometry : angle 0.84591 (46363) SS BOND : bond 0.00590 ( 61) SS BOND : angle 3.47509 ( 122) hydrogen bonds : bond 0.03466 ( 1153) hydrogen bonds : angle 5.32208 ( 2949) link_NAG-ASN : bond 0.00498 ( 9) link_NAG-ASN : angle 2.88544 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17639.59 seconds wall clock time: 299 minutes 51.97 seconds (17991.97 seconds total)