Starting phenix.real_space_refine on Sun Aug 9 04:39:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yb4_72748/08_2026/9yb4_72748.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yb4_72748/08_2026/9yb4_72748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yb4_72748/08_2026/9yb4_72748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yb4_72748/08_2026/9yb4_72748.map" model { file = "/net/cci-nas-00/data/ceres_data/9yb4_72748/08_2026/9yb4_72748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yb4_72748/08_2026/9yb4_72748.cif" } resolution = 3.1 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= 0.047 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 204 5.16 5 C 20152 2.51 5 N 5530 2.21 5 O 5934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 175 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31820 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "B" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 411} Chain: "C" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 411} Chain: "D" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 411} Chain: "P" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1239 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "Q" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1239 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "R" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1239 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "S" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1239 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "a" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3288 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 385} Chain: "b" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3296 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 386} Chain: "c" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3296 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 386} Chain: "d" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3288 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 385} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "c" 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: "d" 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: 7.70, per 1000 atoms: 0.24 Number of scatterers: 31820 At special positions: 0 Unit cell: (182.21, 182.21, 195.51, 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 204 16.00 O 5934 8.00 N 5530 7.00 C 20152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=58, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.00 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 272 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 377 " distance=2.01 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 371 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.00 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 272 " distance=2.05 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 377 " distance=2.01 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 371 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.01 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.04 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=2.05 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=2.02 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=2.03 Simple disulfide: pdb=" SG CYS a 19 " - pdb=" SG CYS a 122 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 27 " distance=2.04 Simple disulfide: pdb=" SG CYS a 89 " - pdb=" SG CYS a 103 " distance=2.02 Simple disulfide: pdb=" SG CYS a 150 " - pdb=" SG CYS a 263 " distance=2.03 Simple disulfide: pdb=" SG CYS a 199 " - pdb=" SG CYS a 223 " distance=2.02 Simple disulfide: pdb=" SG CYS a 201 " - pdb=" SG CYS a 217 " distance=2.04 Simple disulfide: pdb=" SG CYS a 393 " - pdb=" SG CYS a 413 " distance=2.94 Simple disulfide: pdb=" SG CYS b 19 " - pdb=" SG CYS b 122 " distance=2.03 Simple disulfide: pdb=" SG CYS b 22 " - pdb=" SG CYS b 27 " distance=2.03 Simple disulfide: pdb=" SG CYS b 89 " - pdb=" SG CYS b 103 " distance=2.03 Simple disulfide: pdb=" SG CYS b 150 " - pdb=" SG CYS b 263 " distance=2.03 Simple disulfide: pdb=" SG CYS b 199 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 201 " - pdb=" SG CYS b 217 " distance=2.03 Simple disulfide: pdb=" SG CYS c 19 " - pdb=" SG CYS c 122 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 27 " distance=2.04 Simple disulfide: pdb=" SG CYS c 89 " - pdb=" SG CYS c 103 " distance=2.03 Simple disulfide: pdb=" SG CYS c 150 " - pdb=" SG CYS c 263 " distance=2.03 Simple disulfide: pdb=" SG CYS c 199 " - pdb=" SG CYS c 223 " distance=2.02 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 217 " distance=2.03 Simple disulfide: pdb=" SG CYS c 393 " - pdb=" SG CYS c 413 " distance=2.72 Simple disulfide: pdb=" SG CYS d 19 " - pdb=" SG CYS d 122 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 27 " distance=2.01 Simple disulfide: pdb=" SG CYS d 89 " - pdb=" SG CYS d 103 " distance=2.03 Simple disulfide: pdb=" SG CYS d 150 " - pdb=" SG CYS d 263 " distance=2.03 Simple disulfide: pdb=" SG CYS d 199 " - pdb=" SG CYS d 223 " distance=2.03 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 217 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG F 1 " - " ASN B 134 " " NAG H 1 " - " ASN D 134 " " NAG a 501 " - " ASN a 315 " " NAG b 501 " - " ASN b 315 " " NAG c 501 " - " ASN c 315 " " NAG d 501 " - " ASN d 315 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.7 seconds 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7540 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 85 sheets defined 15.7% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.618A pdb=" N SER A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.963A pdb=" N GLY A 228 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.617A pdb=" N ARG A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.114A pdb=" N GLY A 259 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.512A pdb=" N PHE A 288 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 405 through 436 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 239 through 248 Processing helix chain 'B' and resid 256 through 260 removed outlier: 4.152A pdb=" N GLY B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS B 260 " --> pdb=" O PRO B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 260' Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 406 through 438 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.635A pdb=" N SER C 115 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 248 Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 256 through 260 removed outlier: 4.141A pdb=" N GLY C 259 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 406 through 440 removed outlier: 3.594A pdb=" N ARG C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.600A pdb=" N SER D 115 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 256 through 260 removed outlier: 4.129A pdb=" N GLY D 259 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS D 260 " --> pdb=" O PRO D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 260' Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 406 through 438 removed outlier: 3.558A pdb=" N PHE D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 109 Processing helix chain 'P' and resid 157 through 159 No H-bonds generated for 'chain 'P' and resid 157 through 159' Processing helix chain 'P' and resid 167 through 171 Processing helix chain 'Q' and resid 103 through 110 Processing helix chain 'Q' and resid 145 through 151 removed outlier: 3.838A pdb=" N ILE Q 151 " --> pdb=" O GLN Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 159 No H-bonds generated for 'chain 'Q' and resid 157 through 159' Processing helix chain 'R' and resid 103 through 109 Processing helix chain 'R' and resid 110 through 113 Processing helix chain 'R' and resid 145 through 150 removed outlier: 3.853A pdb=" N ALA R 150 " --> pdb=" O GLU R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 160 Processing helix chain 'R' and resid 167 through 174 removed outlier: 5.585A pdb=" N SER R 172 " --> pdb=" O CYS R 169 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR R 174 " --> pdb=" O LYS R 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 110 Processing helix chain 'S' and resid 157 through 159 No H-bonds generated for 'chain 'S' and resid 157 through 159' Processing helix chain 'S' and resid 167 through 171 removed outlier: 3.985A pdb=" N MET S 170 " --> pdb=" O PRO S 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 8 removed outlier: 3.760A pdb=" N GLN a 8 " --> pdb=" O THR a 4 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 12 Processing helix chain 'a' and resid 180 through 184 removed outlier: 3.658A pdb=" N ALA a 183 " --> pdb=" O ILE a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 223 Processing helix chain 'a' and resid 350 through 360 Processing helix chain 'a' and resid 363 through 400 Proline residue: a 396 - end of helix removed outlier: 3.556A pdb=" N ALA a 400 " --> pdb=" O PRO a 396 " (cutoff:3.500A) Processing helix chain 'a' and resid 406 through 413 Processing helix chain 'b' and resid 3 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 395 removed outlier: 3.927A pdb=" N ILE b 365 " --> pdb=" O PRO b 361 " (cutoff:3.500A) Processing helix chain 'b' and resid 407 through 412 Processing helix chain 'c' and resid 3 through 10 removed outlier: 4.240A pdb=" N TYR c 9 " --> pdb=" O HIS c 5 " (cutoff:3.500A) Processing helix chain 'c' and resid 219 through 221 No H-bonds generated for 'chain 'c' and resid 219 through 221' Processing helix chain 'c' and resid 348 through 360 Processing helix chain 'c' and resid 360 through 400 removed outlier: 3.691A pdb=" N ILE c 365 " --> pdb=" O PRO c 361 " (cutoff:3.500A) Proline residue: c 396 - end of helix Processing helix chain 'c' and resid 406 through 413 Processing helix chain 'd' and resid 3 through 8 removed outlier: 4.600A pdb=" N GLN d 8 " --> pdb=" O THR d 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 12 Processing helix chain 'd' and resid 219 through 221 No H-bonds generated for 'chain 'd' and resid 219 through 221' Processing helix chain 'd' and resid 244 through 248 removed outlier: 3.605A pdb=" N PHE d 248 " --> pdb=" O GLY d 245 " (cutoff:3.500A) Processing helix chain 'd' and resid 348 through 360 Processing helix chain 'd' and resid 360 through 399 Proline residue: d 396 - end of helix Processing helix chain 'd' and resid 406 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.592A pdb=" N MET A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE A 38 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A 128 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR A 46 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 148 current: chain 'A' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 186 current: chain 'A' and resid 269 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 62 removed outlier: 3.690A pdb=" N LYS A 61 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 101 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA7, first strand: chain 'A' and resid 297 through 306 removed outlier: 5.157A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS A 322 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 344 through 347 removed outlier: 3.546A pdb=" N VAL A 345 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 332 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB1, first strand: chain 'B' and resid 2 through 8 removed outlier: 5.454A pdb=" N ILE B 164 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR B 153 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 15 through 19 removed outlier: 3.702A pdb=" N THR B 136 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET B 132 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N THR B 36 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLN B 130 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE B 38 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR B 128 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N TYR B 137 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER B 141 " --> pdb=" O TYR B 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 140 through 148 current: chain 'B' and resid 268 through 270 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 48 removed outlier: 5.968A pdb=" N LEU B 44 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS B 123 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR B 46 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AB5, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AB6, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB7, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AB9, first strand: chain 'B' and resid 298 through 307 removed outlier: 6.298A pdb=" N LEU B 300 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LYS B 322 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N CYS B 302 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA B 320 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ILE B 304 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR B 318 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 344 through 347 Processing sheet with id=AC2, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AC3, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AC4, first strand: chain 'C' and resid 15 through 19 removed outlier: 3.792A pdb=" N VAL C 27 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE C 31 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 136 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU C 33 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN C 134 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR C 126 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN C 43 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU C 45 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 47 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS C 120 " --> pdb=" O ILE C 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 143 through 148 current: chain 'C' and resid 184 through 187 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 184 through 187 current: chain 'C' and resid 268 through 270 Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.676A pdb=" N TYR C 107 " --> pdb=" O LYS C 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AC7, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC8, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AC9, first strand: chain 'C' and resid 221 through 222 Processing sheet with id=AD1, first strand: chain 'C' and resid 297 through 307 removed outlier: 6.424A pdb=" N LEU C 300 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LYS C 322 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N CYS C 302 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALA C 320 " --> pdb=" O CYS C 302 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE C 304 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR C 318 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 344 through 347 removed outlier: 3.892A pdb=" N VAL C 345 " --> pdb=" O CYS C 329 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N CYS C 329 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AD4, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AD5, first strand: chain 'D' and resid 15 through 19 removed outlier: 3.587A pdb=" N VAL D 19 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 27 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE D 38 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR D 128 " --> pdb=" O ILE D 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 143 through 148 current: chain 'D' and resid 269 through 270 Processing sheet with id=AD6, first strand: chain 'D' and resid 42 through 48 removed outlier: 5.700A pdb=" N LEU D 44 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS D 123 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 46 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AD8, first strand: chain 'D' and resid 60 through 61 removed outlier: 3.678A pdb=" N LYS D 61 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR D 101 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.683A pdb=" N MET D 88 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 91 " --> pdb=" O MET D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 204 through 205 Processing sheet with id=AE2, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AE3, first strand: chain 'D' and resid 297 through 307 removed outlier: 6.067A pdb=" N LEU D 300 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LYS D 322 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS D 302 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ALA D 320 " --> pdb=" O CYS D 302 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE D 304 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR D 318 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 344 through 347 removed outlier: 3.517A pdb=" N CYS D 329 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 121 through 125 removed outlier: 5.418A pdb=" N VAL P 122 " --> pdb=" O LEU P 118 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU P 118 " --> pdb=" O VAL P 122 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY P 124 " --> pdb=" O ILE P 116 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 127 through 129 Processing sheet with id=AE7, first strand: chain 'P' and resid 184 through 187 removed outlier: 8.720A 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 199 through 203 current: chain 'P' and resid 223 through 231 removed outlier: 9.456A pdb=" N VAL P 224 " --> pdb=" O TRP P 244 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP P 244 " --> pdb=" O VAL P 224 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER P 240 " --> pdb=" O LEU P 228 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY P 230 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA P 238 " --> pdb=" O GLY P 230 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 142 through 143 removed outlier: 4.305A pdb=" N GLY Q 124 " --> pdb=" O ILE Q 116 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU Q 118 " --> pdb=" O VAL Q 122 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL Q 122 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N TYR Q 125 " --> pdb=" O PRO Q 136 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU Q 161 " --> pdb=" O ALA Q 156 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 184 through 188 removed outlier: 3.577A pdb=" N GLU Q 196 " --> pdb=" O ARG Q 199 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 199 through 202 current: chain 'Q' and resid 223 through 232 removed outlier: 8.829A pdb=" N VAL Q 224 " --> pdb=" O TRP Q 244 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TRP Q 244 " --> pdb=" O VAL Q 224 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER Q 240 " --> pdb=" O LEU Q 228 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY Q 230 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA Q 238 " --> pdb=" O GLY Q 230 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 121 through 125 removed outlier: 4.975A pdb=" N VAL R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU R 118 " --> pdb=" O VAL R 122 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLY R 124 " --> pdb=" O ILE R 116 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 127 through 129 Processing sheet with id=AF3, first strand: chain 'R' and resid 184 through 187 removed outlier: 8.436A pdb=" N ALA R 192 " --> pdb=" O PRO R 203 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 199 through 203 current: chain 'R' and resid 223 through 232 removed outlier: 8.825A pdb=" N VAL R 224 " --> pdb=" O TRP R 244 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TRP R 244 " --> pdb=" O VAL R 224 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER R 240 " --> pdb=" O LEU R 228 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY R 230 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA R 238 " --> pdb=" O GLY R 230 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASN R 232 " --> pdb=" O ARG R 236 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ARG R 236 " --> pdb=" O ASN R 232 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 121 through 125 removed outlier: 3.825A pdb=" N ASN S 123 " --> pdb=" O ILE S 116 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE S 116 " --> pdb=" O ASN S 123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 127 through 129 Processing sheet with id=AF6, first strand: chain 'S' and resid 176 through 177 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 176 through 177 current: chain 'S' and resid 191 through 196 removed outlier: 9.395A pdb=" N ALA S 192 " --> pdb=" O PRO S 203 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 199 through 203 current: chain 'S' and resid 222 through 233 removed outlier: 7.771A pdb=" N ALA S 225 " --> pdb=" O TRP S 244 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TRP S 244 " --> pdb=" O ALA S 225 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL S 227 " --> pdb=" O VAL S 242 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL S 242 " --> pdb=" O VAL S 227 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY S 229 " --> pdb=" O SER S 240 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 17 through 19 Processing sheet with id=AF8, first strand: chain 'a' and resid 34 through 37 removed outlier: 4.460A pdb=" N VAL a 36 " --> pdb=" O ARG a 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG a 46 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR a 98 " --> pdb=" O HIS a 94 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N HIS a 94 " --> pdb=" O TYR a 98 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU a 100 " --> pdb=" O VAL a 92 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 65 through 68 Processing sheet with id=AG1, first strand: chain 'a' and resid 83 through 84 removed outlier: 3.607A pdb=" N THR a 108 " --> pdb=" O HIS a 126 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS a 126 " --> pdb=" O THR a 108 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR a 110 " --> pdb=" O VAL a 124 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL a 124 " --> pdb=" O THR a 110 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 146 through 153 Processing sheet with id=AG3, first strand: chain 'a' and resid 234 through 235 Processing sheet with id=AG4, first strand: chain 'a' and resid 172 through 173 removed outlier: 3.548A pdb=" N VAL a 172 " --> pdb=" O LEU a 227 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 178 through 179 Processing sheet with id=AG6, first strand: chain 'a' and resid 272 through 276 removed outlier: 3.601A pdb=" N GLU a 274 " --> pdb=" O ILE a 281 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 17 through 19 removed outlier: 3.756A pdb=" N ALA b 17 " --> pdb=" O SER b 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER b 29 " --> pdb=" O ALA b 17 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS b 27 " --> pdb=" O CYS b 19 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 33 through 37 removed outlier: 8.474A pdb=" N ILE b 33 " --> pdb=" O SER b 50 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER b 50 " --> pdb=" O ILE b 33 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLU b 35 " --> pdb=" O GLN b 48 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN b 48 " --> pdb=" O GLU b 35 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N SER b 50 " --> pdb=" O MET b 68 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N MET b 68 " --> pdb=" O SER b 50 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR b 64 " --> pdb=" O GLY b 54 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 81 through 84 removed outlier: 3.697A pdb=" N THR b 108 " --> pdb=" O HIS b 126 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS b 126 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR b 110 " --> pdb=" O VAL b 124 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL b 124 " --> pdb=" O THR b 110 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLY b 112 " --> pdb=" O CYS b 122 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N CYS b 122 " --> pdb=" O GLY b 112 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 146 through 153 removed outlier: 3.519A pdb=" N ALA b 265 " --> pdb=" O VAL b 146 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 234 through 235 Processing sheet with id=AH3, first strand: chain 'b' and resid 172 through 173 removed outlier: 3.579A pdb=" N GLY b 207 " --> pdb=" O TYR b 197 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 178 through 181 Processing sheet with id=AH5, first strand: chain 'b' and resid 272 through 276 Processing sheet with id=AH6, first strand: chain 'c' and resid 17 through 19 removed outlier: 3.539A pdb=" N ALA c 17 " --> pdb=" O SER c 29 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS c 27 " --> pdb=" O CYS c 19 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'c' and resid 34 through 37 removed outlier: 4.794A pdb=" N VAL c 36 " --> pdb=" O ARG c 46 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG c 46 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 17.269A pdb=" N GLN c 48 " --> pdb=" O PHE c 67 " (cutoff:3.500A) removed outlier: 13.848A pdb=" N PHE c 67 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 12.373A pdb=" N SER c 50 " --> pdb=" O MET c 65 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N MET c 65 " --> pdb=" O SER c 50 " (cutoff:3.500A) removed outlier: 11.163A pdb=" N MET c 52 " --> pdb=" O ALA c 63 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N ALA c 63 " --> pdb=" O MET c 52 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY c 54 " --> pdb=" O ASP c 61 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'c' and resid 81 through 84 Processing sheet with id=AH9, first strand: chain 'c' and resid 146 through 153 Processing sheet with id=AI1, first strand: chain 'c' and resid 166 through 167 Processing sheet with id=AI2, first strand: chain 'c' and resid 172 through 173 removed outlier: 3.944A pdb=" N VAL c 172 " --> pdb=" O LEU c 227 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'c' and resid 178 through 180 Processing sheet with id=AI4, first strand: chain 'c' and resid 272 through 276 Processing sheet with id=AI5, first strand: chain 'd' and resid 17 through 22 removed outlier: 4.414A pdb=" N ASN d 21 " --> pdb=" O SER d 25 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER d 25 " --> pdb=" O ASN d 21 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'd' and resid 33 through 37 removed outlier: 3.510A pdb=" N GLN d 48 " --> pdb=" O GLU d 34 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL d 36 " --> pdb=" O ARG d 46 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG d 46 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 10.107A pdb=" N SER d 50 " --> pdb=" O MET d 68 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET d 68 " --> pdb=" O SER d 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY d 54 " --> pdb=" O TYR d 64 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR d 64 " --> pdb=" O GLY d 54 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN d 69 " --> pdb=" O THR d 72 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'd' and resid 82 through 84 Processing sheet with id=AI8, first strand: chain 'd' and resid 146 through 153 Processing sheet with id=AI9, first strand: chain 'd' and resid 234 through 235 Processing sheet with id=AJ1, first strand: chain 'd' and resid 172 through 174 removed outlier: 3.721A pdb=" N ASP d 174 " --> pdb=" O ALA d 225 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA d 225 " --> pdb=" O ASP d 174 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'd' and resid 178 through 181 Processing sheet with id=AJ3, first strand: chain 'd' and resid 272 through 276 Processing sheet with id=AJ4, first strand: chain 'd' and resid 304 through 308 1064 hydrogen bonds defined for protein. 2625 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: 7.97 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9847 1.34 - 1.46: 7573 1.46 - 1.59: 15004 1.59 - 1.72: 0 1.72 - 1.85: 256 Bond restraints: 32680 Sorted by residual: bond pdb=" CB THR d 326 " pdb=" OG1 THR d 326 " ideal model delta sigma weight residual 1.433 1.370 0.063 1.60e-02 3.91e+03 1.54e+01 bond pdb=" C LYS A 382 " pdb=" N PRO A 383 " ideal model delta sigma weight residual 1.331 1.364 -0.032 8.70e-03 1.32e+04 1.38e+01 bond pdb=" CZ ARG d 239 " pdb=" NH2 ARG d 239 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.15e-02 7.56e+03 1.31e+01 bond pdb=" N ARG d 135 " pdb=" CA ARG d 135 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.18e-02 7.18e+03 1.28e+01 ... (remaining 32675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 40255 2.55 - 5.11: 3992 5.11 - 7.66: 277 7.66 - 10.22: 14 10.22 - 12.77: 4 Bond angle restraints: 44542 Sorted by residual: angle pdb=" N PHE c 316 " pdb=" CA PHE c 316 " pdb=" CB PHE c 316 " ideal model delta sigma weight residual 110.49 118.87 -8.38 1.69e+00 3.50e-01 2.46e+01 angle pdb=" C VAL c 189 " pdb=" N PRO c 190 " pdb=" CA PRO c 190 " ideal model delta sigma weight residual 119.84 125.87 -6.03 1.25e+00 6.40e-01 2.32e+01 angle pdb=" N SER P 157 " pdb=" CA SER P 157 " pdb=" C SER P 157 " ideal model delta sigma weight residual 111.75 117.90 -6.15 1.28e+00 6.10e-01 2.31e+01 angle pdb=" CB HIS S 190 " pdb=" CG HIS S 190 " pdb=" CD2 HIS S 190 " ideal model delta sigma weight residual 131.20 124.97 6.23 1.30e+00 5.92e-01 2.30e+01 angle pdb=" CB HIS S 189 " pdb=" CG HIS S 189 " pdb=" CD2 HIS S 189 " ideal model delta sigma weight residual 131.20 125.00 6.20 1.30e+00 5.92e-01 2.28e+01 ... (remaining 44537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 17939 21.15 - 42.31: 1521 42.31 - 63.46: 241 63.46 - 84.61: 78 84.61 - 105.77: 29 Dihedral angle restraints: 19808 sinusoidal: 8026 harmonic: 11782 Sorted by residual: dihedral pdb=" CB CYS b 22 " pdb=" SG CYS b 22 " pdb=" SG CYS b 27 " pdb=" CB CYS b 27 " ideal model delta sinusoidal sigma weight residual 93.00 -178.38 -88.62 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS a 19 " pdb=" SG CYS a 19 " pdb=" SG CYS a 122 " pdb=" CB CYS a 122 " ideal model delta sinusoidal sigma weight residual -86.00 -172.08 86.08 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS b 201 " pdb=" SG CYS b 201 " pdb=" SG CYS b 217 " pdb=" CB CYS b 217 " ideal model delta sinusoidal sigma weight residual 93.00 175.00 -82.00 1 1.00e+01 1.00e-02 8.26e+01 ... (remaining 19805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 4399 0.124 - 0.248: 529 0.248 - 0.372: 64 0.372 - 0.496: 7 0.496 - 0.619: 1 Chirality restraints: 5000 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.75e+02 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.12e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.86e+02 ... (remaining 4997 not shown) Planarity restraints: 5726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 134 " -0.078 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" CG ASN B 134 " 0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN B 134 " -0.181 2.00e-02 2.50e+03 pdb=" ND2 ASN B 134 " 0.502 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.330 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 501 " 0.319 2.00e-02 2.50e+03 2.75e-01 9.43e+02 pdb=" C7 NAG c 501 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG c 501 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG c 501 " -0.488 2.00e-02 2.50e+03 pdb=" O7 NAG c 501 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 501 " 0.303 2.00e-02 2.50e+03 2.65e-01 8.75e+02 pdb=" C7 NAG b 501 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG b 501 " 0.048 2.00e-02 2.50e+03 pdb=" N2 NAG b 501 " -0.470 2.00e-02 2.50e+03 pdb=" O7 NAG b 501 " 0.178 2.00e-02 2.50e+03 ... (remaining 5723 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 678 2.69 - 3.24: 30778 3.24 - 3.79: 48792 3.79 - 4.35: 62107 4.35 - 4.90: 103763 Nonbonded interactions: 246118 Sorted by model distance: nonbonded pdb=" NZ LYS b 200 " pdb=" O CYS b 201 " model vdw 2.132 3.120 nonbonded pdb=" OE2 GLU B 184 " pdb=" OH TYR B 186 " model vdw 2.133 3.040 nonbonded pdb=" OD1 ASP B 97 " pdb=" OG1 THR B 98 " model vdw 2.153 3.040 nonbonded pdb=" O SER d 340 " pdb=" OG SER d 340 " model vdw 2.170 3.040 nonbonded pdb=" O SER c 340 " pdb=" OG SER c 340 " model vdw 2.171 3.040 ... (remaining 246113 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'a' selection = (chain 'b' and resid 2 through 501) selection = (chain 'c' and resid 2 through 501) selection = chain 'd' } 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=1.00 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.320 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 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 : 0.011 0.913 32752 Z= 0.653 Angle : 1.534 52.138 44700 Z= 0.975 Chirality : 0.083 0.619 5000 Planarity : 0.018 0.475 5720 Dihedral : 16.290 105.765 12094 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.07 % Favored : 93.54 % Rotamer: Outliers : 4.62 % Allowed : 19.56 % Favored : 75.82 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -1.38 (0.12), residues: 4054 helix: 0.06 (0.24), residues: 450 sheet: 0.03 (0.16), residues: 991 loop : -1.56 (0.11), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 239 TYR 0.160 0.015 TYR D 321 PHE 0.107 0.009 PHE C 95 TRP 0.147 0.014 TRP P 188 HIS 0.025 0.002 HIS d 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00931 / 0.57 (32680) covalent geometry : angle 1.47290 / 0.96 (44542) SS BOND : bond 0.15010 / 8.00 ( 58) SS BOND : angle 7.79550 / 5.10 ( 116) hydrogen bonds : bond 0.20237 / 13.55 ( 1064) hydrogen bonds : angle 8.40941 / 5.76 ( 2625) link_BETA1-4 : bond 0.04642 / 2.45 ( 8) link_BETA1-4 : angle 7.01992 / 4.09 ( 24) link_NAG-ASN : bond 0.00451 / 0.23 ( 6) link_NAG-ASN : angle 4.32107 / 2.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1395 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7987 (ptpt) cc_final: 0.7749 (ptpp) REVERT: A 137 TYR cc_start: 0.6770 (p90) cc_final: 0.6505 (p90) REVERT: A 349 GLU cc_start: 0.7898 (tp30) cc_final: 0.7696 (tp30) REVERT: A 389 VAL cc_start: 0.7543 (m) cc_final: 0.7154 (m) REVERT: A 437 PHE cc_start: 0.6342 (OUTLIER) cc_final: 0.6027 (t80) REVERT: B 52 LYS cc_start: 0.7038 (tttp) cc_final: 0.6795 (tptt) REVERT: B 89 TRP cc_start: 0.8410 (p-90) cc_final: 0.8039 (p-90) REVERT: B 124 VAL cc_start: 0.8182 (t) cc_final: 0.7955 (t) REVERT: B 386 ASP cc_start: 0.7196 (m-30) cc_final: 0.6938 (m-30) REVERT: C 13 ILE cc_start: 0.8197 (pt) cc_final: 0.7949 (pt) REVERT: C 254 ASP cc_start: 0.8058 (m-30) cc_final: 0.7785 (m-30) REVERT: C 284 PRO cc_start: 0.8041 (Cg_endo) cc_final: 0.6991 (Cg_exo) REVERT: C 311 SER cc_start: 0.6817 (m) cc_final: 0.6241 (m) REVERT: C 312 ASP cc_start: 0.6491 (p0) cc_final: 0.5642 (p0) REVERT: C 385 LYS cc_start: 0.3321 (OUTLIER) cc_final: 0.2010 (mttm) REVERT: C 406 THR cc_start: 0.6741 (m) cc_final: 0.6506 (m) REVERT: C 438 PHE cc_start: 0.6090 (t80) cc_final: 0.5856 (t80) REVERT: D 11 VAL cc_start: 0.7763 (p) cc_final: 0.7274 (t) REVERT: D 35 ASN cc_start: 0.6872 (m-40) cc_final: 0.6284 (m-40) REVERT: D 57 SER cc_start: 0.8174 (p) cc_final: 0.7969 (t) REVERT: D 137 TYR cc_start: 0.6963 (p90) cc_final: 0.6465 (p90) REVERT: D 219 ASN cc_start: 0.7497 (t0) cc_final: 0.6874 (t0) REVERT: P 127 CYS cc_start: 0.6855 (t) cc_final: 0.6418 (t) REVERT: P 163 TYR cc_start: 0.7625 (p90) cc_final: 0.6445 (p90) REVERT: Q 104 MET cc_start: 0.3803 (OUTLIER) cc_final: 0.3517 (ptt) REVERT: Q 129 VAL cc_start: 0.7733 (p) cc_final: 0.7319 (t) REVERT: Q 163 TYR cc_start: 0.6558 (p90) cc_final: 0.6131 (p90) REVERT: R 232 ASN cc_start: 0.8393 (t0) cc_final: 0.7977 (t0) REVERT: R 239 LEU cc_start: 0.8782 (mt) cc_final: 0.8458 (mp) REVERT: R 245 ASN cc_start: 0.7747 (p0) cc_final: 0.7304 (p0) REVERT: S 104 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6264 (mtt) REVERT: S 194 GLN cc_start: 0.6208 (tm-30) cc_final: 0.4751 (tp40) REVERT: a 16 ILE cc_start: 0.7713 (pt) cc_final: 0.7235 (mt) REVERT: a 100 LEU cc_start: 0.5220 (tp) cc_final: 0.4367 (tt) REVERT: a 147 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7115 (mm-30) REVERT: a 291 LEU cc_start: 0.7008 (tp) cc_final: 0.6299 (tt) REVERT: a 340 SER cc_start: 0.7926 (t) cc_final: 0.7702 (p) REVERT: a 364 THR cc_start: 0.7691 (m) cc_final: 0.7489 (p) REVERT: a 385 LEU cc_start: 0.8581 (tp) cc_final: 0.8346 (tp) REVERT: b 4 THR cc_start: 0.8890 (m) cc_final: 0.8665 (t) REVERT: b 36 VAL cc_start: 0.6588 (p) cc_final: 0.5817 (p) REVERT: b 146 VAL cc_start: 0.6523 (m) cc_final: 0.4993 (t) REVERT: b 252 LEU cc_start: 0.5712 (OUTLIER) cc_final: 0.4089 (pp) REVERT: c 6 PHE cc_start: 0.7845 (m-80) cc_final: 0.7611 (p90) REVERT: c 31 ILE cc_start: 0.8335 (tt) cc_final: 0.7537 (tt) REVERT: c 72 THR cc_start: 0.7450 (p) cc_final: 0.6697 (p) REVERT: c 253 HIS cc_start: 0.5163 (OUTLIER) cc_final: 0.4430 (m170) REVERT: c 362 LEU cc_start: 0.9040 (tp) cc_final: 0.8617 (pt) REVERT: d 67 PHE cc_start: 0.6170 (p90) cc_final: 0.5204 (p90) REVERT: d 68 MET cc_start: 0.5178 (mmm) cc_final: 0.4508 (mmm) REVERT: d 76 ILE cc_start: 0.6389 (mm) cc_final: 0.6151 (mm) REVERT: d 133 VAL cc_start: 0.8517 (p) cc_final: 0.8181 (p) REVERT: d 165 GLU cc_start: 0.6957 (pm20) cc_final: 0.6570 (tt0) REVERT: d 237 SER cc_start: 0.6033 (p) cc_final: 0.5832 (p) REVERT: d 252 LEU cc_start: 0.7577 (pp) cc_final: 0.7320 (pp) REVERT: d 318 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.6691 (p) REVERT: d 374 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6702 (mm) REVERT: d 378 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7313 (p) outliers start: 161 outliers final: 38 residues processed: 1494 average time/residue: 0.2025 time to fit residues: 480.0721 Evaluate side-chains 932 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 885 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 256 GLU Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 239 LEU Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain b residue 263 CYS Chi-restraints excluded: chain b residue 287 ASP Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 363 THR Chi-restraints excluded: chain c residue 204 VAL Chi-restraints excluded: chain c residue 253 HIS Chi-restraints excluded: chain c residue 415 ILE Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 257 VAL Chi-restraints excluded: chain d residue 318 VAL Chi-restraints excluded: chain d residue 374 ILE Chi-restraints excluded: chain d residue 378 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 226 GLN ** B 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS C 369 GLN C 387 HIS C 394 GLN D 361 ASN R 189 HIS a 114 HIS a 346 HIS ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 GLN c 69 ASN c 73 GLN c 126 HIS c 329 ASN d 48 GLN d 73 GLN d 346 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.101483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076319 restraints weight = 84432.216| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.92 r_work: 0.3062 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 32752 Z= 0.244 Angle : 0.933 14.519 44700 Z= 0.481 Chirality : 0.055 0.477 5000 Planarity : 0.007 0.089 5720 Dihedral : 9.240 83.795 4836 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 8.04 % Allowed : 21.91 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.29 (0.12), residues: 4054 helix: 0.25 (0.24), residues: 455 sheet: -0.19 (0.16), residues: 1045 loop : -1.41 (0.11), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG a 119 TYR 0.025 0.003 TYR A 391 PHE 0.029 0.003 PHE C 366 TRP 0.037 0.003 TRP P 188 HIS 0.020 0.002 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (32680) covalent geometry : angle 0.92215 / 0.48 (44542) SS BOND : bond 0.01494 / 0.93 ( 58) SS BOND : angle 1.63188 / 1.10 ( 116) hydrogen bonds : bond 0.04628 / 3.02 ( 1064) hydrogen bonds : angle 6.65277 / 4.52 ( 2625) link_BETA1-4 : bond 0.01264 / 0.61 ( 8) link_BETA1-4 : angle 3.95858 / 2.22 ( 24) link_NAG-ASN : bond 0.00635 / 0.39 ( 6) link_NAG-ASN : angle 4.37821 / 2.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 954 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.6737 (t70) REVERT: A 120 LYS cc_start: 0.8645 (ptpt) cc_final: 0.8315 (ptpp) REVERT: A 236 GLN cc_start: 0.8060 (pt0) cc_final: 0.7672 (pt0) REVERT: A 290 ARG cc_start: 0.9043 (mmm-85) cc_final: 0.8479 (mmm-85) REVERT: A 306 GLU cc_start: 0.8076 (tp30) cc_final: 0.7432 (tm-30) REVERT: A 328 ASN cc_start: 0.9007 (m-40) cc_final: 0.8613 (t0) REVERT: A 332 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.7423 (p-80) REVERT: A 437 PHE cc_start: 0.7233 (t80) cc_final: 0.6925 (t80) REVERT: A 440 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8252 (tpp80) REVERT: B 109 GLU cc_start: 0.8096 (pm20) cc_final: 0.7746 (pm20) REVERT: B 221 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8118 (mtpp) REVERT: B 242 GLU cc_start: 0.8079 (mp0) cc_final: 0.7828 (mp0) REVERT: B 301 GLU cc_start: 0.9039 (tp30) cc_final: 0.8804 (tp30) REVERT: B 305 THR cc_start: 0.8529 (m) cc_final: 0.8215 (p) REVERT: B 306 GLU cc_start: 0.8395 (tp30) cc_final: 0.8193 (tp30) REVERT: B 394 GLN cc_start: 0.9041 (mm110) cc_final: 0.8668 (mm-40) REVERT: B 421 PHE cc_start: 0.8889 (t80) cc_final: 0.8546 (t80) REVERT: C 10 LYS cc_start: 0.9409 (mtmt) cc_final: 0.9177 (mtmt) REVERT: C 75 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6453 (t0) REVERT: C 242 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7707 (tm-30) REVERT: C 301 GLU cc_start: 0.8483 (tp30) cc_final: 0.7745 (pm20) REVERT: C 304 ILE cc_start: 0.7101 (mp) cc_final: 0.6689 (mt) REVERT: C 306 GLU cc_start: 0.6972 (tt0) cc_final: 0.6518 (tp30) REVERT: C 354 THR cc_start: 0.8481 (m) cc_final: 0.8205 (t) REVERT: C 385 LYS cc_start: 0.4047 (OUTLIER) cc_final: 0.2718 (mttm) REVERT: D 9 ASN cc_start: 0.7927 (t0) cc_final: 0.7345 (t0) REVERT: D 33 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7502 (mt) REVERT: D 97 ASP cc_start: 0.8770 (t0) cc_final: 0.8544 (t0) REVERT: D 130 GLN cc_start: 0.7068 (pt0) cc_final: 0.6809 (mt0) REVERT: D 161 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7682 (mmtt) REVERT: D 242 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8769 (tm-30) REVERT: D 246 ARG cc_start: 0.8615 (mtm110) cc_final: 0.8242 (mtm110) REVERT: D 262 ILE cc_start: 0.7980 (mm) cc_final: 0.7174 (mm) REVERT: D 267 LEU cc_start: 0.8779 (tp) cc_final: 0.8319 (tt) REVERT: P 118 LEU cc_start: 0.9679 (tt) cc_final: 0.9272 (tt) REVERT: P 127 CYS cc_start: 0.7832 (t) cc_final: 0.6869 (t) REVERT: P 132 ARG cc_start: 0.9014 (ttm-80) cc_final: 0.8511 (ttm-80) REVERT: P 144 ASP cc_start: 0.9370 (p0) cc_final: 0.9160 (p0) REVERT: P 151 ILE cc_start: 0.7902 (pt) cc_final: 0.7450 (mp) REVERT: P 154 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8639 (ptpp) REVERT: P 176 GLN cc_start: 0.8722 (mp10) cc_final: 0.8504 (tm-30) REVERT: P 218 ASP cc_start: 0.9136 (t0) cc_final: 0.8560 (t0) REVERT: P 249 VAL cc_start: 0.8035 (t) cc_final: 0.7647 (t) REVERT: Q 104 MET cc_start: 0.3980 (OUTLIER) cc_final: 0.3513 (ptt) REVERT: Q 135 LYS cc_start: 0.6848 (ttpp) cc_final: 0.6224 (ttpp) REVERT: Q 174 THR cc_start: 0.6887 (m) cc_final: 0.6631 (p) REVERT: Q 175 LEU cc_start: 0.8212 (tp) cc_final: 0.7849 (tt) REVERT: Q 217 LEU cc_start: 0.8026 (pp) cc_final: 0.7824 (pp) REVERT: Q 219 ASN cc_start: 0.9395 (p0) cc_final: 0.8940 (p0) REVERT: R 159 TYR cc_start: 0.8256 (m-80) cc_final: 0.7948 (m-80) REVERT: R 168 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6821 (tm-30) REVERT: R 171 LYS cc_start: 0.9465 (mttp) cc_final: 0.9251 (mtmm) REVERT: R 176 GLN cc_start: 0.8589 (pm20) cc_final: 0.8285 (pm20) REVERT: R 204 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7799 (ptm-80) REVERT: R 232 ASN cc_start: 0.9083 (t0) cc_final: 0.8690 (t0) REVERT: R 252 LYS cc_start: 0.9039 (tttt) cc_final: 0.8716 (tptp) REVERT: R 253 ASP cc_start: 0.6924 (p0) cc_final: 0.6490 (p0) REVERT: S 104 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5513 (mtt) REVERT: S 193 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.9061 (p) REVERT: a 67 PHE cc_start: 0.5682 (p90) cc_final: 0.4791 (p90) REVERT: a 152 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.8222 (mmm-85) REVERT: a 264 ILE cc_start: 0.8770 (mt) cc_final: 0.8564 (tt) REVERT: a 321 GLU cc_start: 0.8788 (mp0) cc_final: 0.8481 (mp0) REVERT: a 340 SER cc_start: 0.8216 (t) cc_final: 0.7973 (p) REVERT: a 385 LEU cc_start: 0.8766 (tp) cc_final: 0.8562 (tp) REVERT: b 4 THR cc_start: 0.9458 (m) cc_final: 0.9248 (t) REVERT: b 52 MET cc_start: 0.8992 (mmt) cc_final: 0.8433 (mmm) REVERT: b 68 MET cc_start: 0.6076 (mmm) cc_final: 0.5713 (mmm) REVERT: b 136 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7623 (mt-10) REVERT: b 152 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7389 (mtp85) REVERT: b 246 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7685 (t0) REVERT: b 272 LEU cc_start: 0.8629 (mm) cc_final: 0.8353 (mm) REVERT: b 336 TRP cc_start: 0.7323 (m-90) cc_final: 0.7019 (m-10) REVERT: c 6 PHE cc_start: 0.8420 (m-80) cc_final: 0.8075 (m-80) REVERT: c 35 GLU cc_start: 0.8222 (tp30) cc_final: 0.7974 (tp30) REVERT: c 67 PHE cc_start: 0.5956 (p90) cc_final: 0.5700 (p90) REVERT: c 264 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8524 (mm) REVERT: c 316 PHE cc_start: 0.8498 (m-10) cc_final: 0.8202 (m-80) REVERT: c 340 SER cc_start: 0.7961 (p) cc_final: 0.7619 (t) REVERT: c 362 LEU cc_start: 0.9382 (tp) cc_final: 0.9072 (pt) REVERT: d 3 ASP cc_start: 0.9192 (p0) cc_final: 0.8954 (p0) REVERT: d 6 PHE cc_start: 0.8043 (m-10) cc_final: 0.7701 (m-10) REVERT: d 52 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6569 (mmp) REVERT: d 53 PHE cc_start: 0.6811 (m-80) cc_final: 0.6357 (m-10) REVERT: d 71 LYS cc_start: 0.8365 (pttp) cc_final: 0.8101 (ptpp) REVERT: d 202 PRO cc_start: 0.9149 (Cg_exo) cc_final: 0.8880 (Cg_endo) REVERT: d 234 VAL cc_start: 0.8323 (t) cc_final: 0.8053 (p) REVERT: d 264 ILE cc_start: 0.8880 (mt) cc_final: 0.8370 (tp) outliers start: 280 outliers final: 142 residues processed: 1147 average time/residue: 0.1954 time to fit residues: 364.8408 Evaluate side-chains 992 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 839 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 187 ASN Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 113 THR Chi-restraints excluded: chain Q residue 123 ASN Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 188 TRP Chi-restraints excluded: chain Q residue 193 VAL Chi-restraints excluded: chain Q residue 194 GLN Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain Q residue 223 VAL Chi-restraints excluded: chain Q residue 227 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 188 TRP Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 193 VAL Chi-restraints excluded: chain S residue 196 GLU Chi-restraints excluded: chain S residue 239 LEU Chi-restraints excluded: chain S residue 251 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 122 CYS Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain a residue 292 LEU Chi-restraints excluded: chain a residue 333 LYS Chi-restraints excluded: chain a residue 389 THR Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 124 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 150 CYS Chi-restraints excluded: chain b residue 155 HIS Chi-restraints excluded: chain b residue 181 HIS Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 246 ASP Chi-restraints excluded: chain b residue 294 THR Chi-restraints excluded: chain b residue 315 ASN Chi-restraints excluded: chain b residue 382 SER Chi-restraints excluded: chain b residue 392 LEU Chi-restraints excluded: chain b residue 398 LYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 47 ILE Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 133 VAL Chi-restraints excluded: chain c residue 151 ASN Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 234 VAL Chi-restraints excluded: chain c residue 253 HIS Chi-restraints excluded: chain c residue 263 CYS Chi-restraints excluded: chain c residue 264 ILE Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 342 GLU Chi-restraints excluded: chain c residue 363 THR Chi-restraints excluded: chain c residue 368 LEU Chi-restraints excluded: chain c residue 392 LEU Chi-restraints excluded: chain c residue 415 ILE Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 52 MET Chi-restraints excluded: chain d residue 73 GLN Chi-restraints excluded: chain d residue 94 HIS Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 257 VAL Chi-restraints excluded: chain d residue 309 GLU Chi-restraints excluded: chain d residue 310 ARG Chi-restraints excluded: chain d residue 335 VAL Chi-restraints excluded: chain d residue 351 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 282 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 329 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 363 HIS ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN C 3 HIS ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 ASN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN S 168 GLN S 190 HIS ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 329 ASN b 8 GLN b 69 ASN ** b 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.108970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.083646 restraints weight = 83012.514| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.86 r_work: 0.3039 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.6496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 32752 Z= 0.213 Angle : 0.811 15.532 44700 Z= 0.420 Chirality : 0.051 0.493 5000 Planarity : 0.006 0.060 5720 Dihedral : 7.611 82.585 4790 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 6.09 % Allowed : 24.61 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 are not related in a simple way. whole: -1.16 (0.12), residues: 4054 helix: 0.50 (0.23), residues: 453 sheet: -0.19 (0.16), residues: 1088 loop : -1.32 (0.11), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 143 TYR 0.044 0.002 TYR R 195 PHE 0.030 0.002 PHE B 241 TRP 0.037 0.002 TRP B 89 HIS 0.038 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (32680) covalent geometry : angle 0.79752 / 0.42 (44542) SS BOND : bond 0.00372 / 0.24 ( 58) SS BOND : angle 1.53877 / 1.16 ( 116) hydrogen bonds : bond 0.04432 / 2.93 ( 1064) hydrogen bonds : angle 6.15605 / 4.19 ( 2625) link_BETA1-4 : bond 0.01112 / 0.60 ( 8) link_BETA1-4 : angle 3.59820 / 2.00 ( 24) link_NAG-ASN : bond 0.00924 / 0.61 ( 6) link_NAG-ASN : angle 5.14388 / 3.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 833 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: A 142 TRP cc_start: 0.7473 (m100) cc_final: 0.7123 (m100) REVERT: A 270 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7663 (mm-30) REVERT: A 306 GLU cc_start: 0.8411 (tp30) cc_final: 0.7759 (tm-30) REVERT: A 380 ASP cc_start: 0.8717 (m-30) cc_final: 0.8431 (m-30) REVERT: A 410 TRP cc_start: 0.8759 (t-100) cc_final: 0.8300 (t-100) REVERT: B 88 MET cc_start: 0.9208 (mmm) cc_final: 0.8994 (mmm) REVERT: B 192 GLU cc_start: 0.5232 (tt0) cc_final: 0.4892 (tt0) REVERT: B 221 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8257 (mtpp) REVERT: B 242 GLU cc_start: 0.8577 (mp0) cc_final: 0.8286 (mp0) REVERT: B 305 THR cc_start: 0.8708 (m) cc_final: 0.8404 (p) REVERT: B 306 GLU cc_start: 0.8704 (tp30) cc_final: 0.8466 (tp30) REVERT: B 328 ASN cc_start: 0.8181 (t0) cc_final: 0.7733 (t0) REVERT: B 366 PHE cc_start: 0.8040 (p90) cc_final: 0.7488 (p90) REVERT: B 394 GLN cc_start: 0.9130 (mm110) cc_final: 0.8815 (mm-40) REVERT: B 421 PHE cc_start: 0.9007 (t80) cc_final: 0.8648 (t80) REVERT: C 18 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8333 (pt) REVERT: C 171 TRP cc_start: 0.8801 (t60) cc_final: 0.8600 (t60) REVERT: C 242 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 306 GLU cc_start: 0.7415 (tt0) cc_final: 0.6912 (tp30) REVERT: C 370 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8375 (m) REVERT: C 385 LYS cc_start: 0.4433 (OUTLIER) cc_final: 0.2166 (mttt) REVERT: C 410 TRP cc_start: 0.8762 (t-100) cc_final: 0.8456 (m-90) REVERT: C 415 VAL cc_start: 0.8701 (p) cc_final: 0.8481 (p) REVERT: D 9 ASN cc_start: 0.8491 (t0) cc_final: 0.8218 (t0) REVERT: D 24 TYR cc_start: 0.9280 (m-10) cc_final: 0.8621 (m-10) REVERT: D 97 ASP cc_start: 0.8838 (t0) cc_final: 0.8595 (t0) REVERT: D 193 TYR cc_start: 0.8159 (t80) cc_final: 0.7868 (t80) REVERT: D 242 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8768 (tm-30) REVERT: D 246 ARG cc_start: 0.8812 (mtm110) cc_final: 0.8427 (mtm110) REVERT: D 262 ILE cc_start: 0.8423 (mm) cc_final: 0.7690 (mm) REVERT: D 293 GLU cc_start: 0.8820 (mp0) cc_final: 0.8332 (mp0) REVERT: D 350 SER cc_start: 0.8706 (m) cc_final: 0.8280 (p) REVERT: D 369 GLN cc_start: 0.8945 (mt0) cc_final: 0.8710 (mt0) REVERT: P 127 CYS cc_start: 0.7914 (t) cc_final: 0.7458 (t) REVERT: P 218 ASP cc_start: 0.9187 (t0) cc_final: 0.8386 (t0) REVERT: P 220 LYS cc_start: 0.9238 (mmtm) cc_final: 0.8991 (mppt) REVERT: Q 104 MET cc_start: 0.3682 (OUTLIER) cc_final: 0.3386 (ptt) REVERT: Q 112 LYS cc_start: 0.8539 (mptt) cc_final: 0.7794 (mttt) REVERT: Q 135 LYS cc_start: 0.7240 (ttpp) cc_final: 0.6704 (ttpp) REVERT: Q 155 LYS cc_start: 0.8814 (mttt) cc_final: 0.8339 (ttpt) REVERT: Q 204 ARG cc_start: 0.8275 (ptm160) cc_final: 0.7420 (mtp-110) REVERT: Q 211 ASP cc_start: 0.8165 (m-30) cc_final: 0.7657 (m-30) REVERT: Q 217 LEU cc_start: 0.8446 (pp) cc_final: 0.8197 (pp) REVERT: Q 219 ASN cc_start: 0.9449 (p0) cc_final: 0.8978 (p0) REVERT: Q 246 GLN cc_start: 0.9470 (mp10) cc_final: 0.9030 (mp10) REVERT: Q 252 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7804 (ttpt) REVERT: R 142 ARG cc_start: 0.8716 (ptm-80) cc_final: 0.8319 (tmm160) REVERT: R 155 LYS cc_start: 0.9241 (mtpp) cc_final: 0.8851 (ttpp) REVERT: R 159 TYR cc_start: 0.8685 (m-80) cc_final: 0.7786 (m-80) REVERT: R 168 GLN cc_start: 0.7187 (tm-30) cc_final: 0.6727 (tm-30) REVERT: R 171 LYS cc_start: 0.9512 (mttp) cc_final: 0.9288 (mtmm) REVERT: R 204 ARG cc_start: 0.8439 (ptm-80) cc_final: 0.8178 (ptm-80) REVERT: R 232 ASN cc_start: 0.9171 (t0) cc_final: 0.8716 (t160) REVERT: R 233 GLU cc_start: 0.3707 (tm-30) cc_final: 0.3467 (tm-30) REVERT: R 252 LYS cc_start: 0.9333 (tttt) cc_final: 0.8988 (tttm) REVERT: S 104 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5397 (mpp) REVERT: S 155 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8368 (mmmm) REVERT: S 163 TYR cc_start: 0.7896 (p90) cc_final: 0.7546 (p90) REVERT: S 194 GLN cc_start: 0.6654 (tm-30) cc_final: 0.6022 (tp40) REVERT: S 217 LEU cc_start: 0.9200 (tp) cc_final: 0.8846 (tp) REVERT: S 223 VAL cc_start: 0.9425 (t) cc_final: 0.8952 (p) REVERT: S 244 TRP cc_start: 0.8095 (m-90) cc_final: 0.7278 (m-90) REVERT: a 264 ILE cc_start: 0.9293 (mt) cc_final: 0.8728 (tt) REVERT: a 300 ASP cc_start: 0.8319 (t0) cc_final: 0.8057 (t70) REVERT: a 317 THR cc_start: 0.7936 (p) cc_final: 0.7732 (t) REVERT: a 335 VAL cc_start: 0.9174 (p) cc_final: 0.8825 (m) REVERT: a 340 SER cc_start: 0.8383 (t) cc_final: 0.8094 (p) REVERT: a 364 THR cc_start: 0.8960 (m) cc_final: 0.8651 (p) REVERT: b 6 PHE cc_start: 0.7756 (t80) cc_final: 0.7545 (t80) REVERT: b 52 MET cc_start: 0.8738 (mmt) cc_final: 0.8331 (mmm) REVERT: b 68 MET cc_start: 0.6957 (mmm) cc_final: 0.6351 (mmm) REVERT: b 246 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7362 (t0) REVERT: b 272 LEU cc_start: 0.8867 (mm) cc_final: 0.8560 (mm) REVERT: b 378 SER cc_start: 0.8732 (t) cc_final: 0.8003 (p) REVERT: c 6 PHE cc_start: 0.8609 (m-80) cc_final: 0.8276 (m-80) REVERT: c 166 MET cc_start: 0.8154 (ptt) cc_final: 0.7700 (ptt) REVERT: c 264 ILE cc_start: 0.9269 (mp) cc_final: 0.8899 (mm) REVERT: c 316 PHE cc_start: 0.8897 (m-10) cc_final: 0.8538 (m-80) REVERT: c 340 SER cc_start: 0.8697 (p) cc_final: 0.8456 (t) REVERT: c 348 TRP cc_start: 0.8272 (m100) cc_final: 0.7617 (m-90) REVERT: c 362 LEU cc_start: 0.9436 (tp) cc_final: 0.9127 (pt) REVERT: d 3 ASP cc_start: 0.9098 (p0) cc_final: 0.8837 (p0) REVERT: d 6 PHE cc_start: 0.8514 (m-10) cc_final: 0.8285 (m-10) REVERT: d 53 PHE cc_start: 0.7738 (m-80) cc_final: 0.6125 (m-80) REVERT: d 62 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7041 (tp) REVERT: d 71 LYS cc_start: 0.8774 (pttp) cc_final: 0.8518 (ptpp) REVERT: d 76 ILE cc_start: 0.8927 (tp) cc_final: 0.8571 (tp) REVERT: d 147 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8432 (mm-30) REVERT: d 221 LYS cc_start: 0.9603 (mmmm) cc_final: 0.9339 (tptp) REVERT: d 333 LYS cc_start: 0.9149 (tttp) cc_final: 0.8816 (ttmm) outliers start: 212 outliers final: 130 residues processed: 968 average time/residue: 0.1842 time to fit residues: 291.2084 Evaluate side-chains 889 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 751 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 408 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 128 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 187 ASN Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 113 THR Chi-restraints excluded: chain Q residue 123 ASN Chi-restraints excluded: chain Q residue 193 VAL Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain Q residue 239 LEU Chi-restraints excluded: chain Q residue 256 GLU Chi-restraints excluded: chain Q residue 259 GLU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 222 ARG Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 239 LEU Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 5 HIS Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 122 CYS Chi-restraints excluded: chain a residue 259 VAL Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 365 ILE Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 124 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 151 ASN Chi-restraints excluded: chain b residue 181 HIS Chi-restraints excluded: chain b residue 233 TRP Chi-restraints excluded: chain b residue 246 ASP Chi-restraints excluded: chain b residue 315 ASN Chi-restraints excluded: chain b residue 398 LYS Chi-restraints excluded: chain b residue 408 LEU Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain c residue 47 ILE Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 133 VAL Chi-restraints excluded: chain c residue 204 VAL Chi-restraints excluded: chain c residue 205 ARG Chi-restraints excluded: chain c residue 234 VAL Chi-restraints excluded: chain c residue 253 HIS Chi-restraints excluded: chain c residue 318 VAL Chi-restraints excluded: chain c residue 363 THR Chi-restraints excluded: chain c residue 368 LEU Chi-restraints excluded: chain c residue 392 LEU Chi-restraints excluded: chain c residue 415 ILE Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 252 LEU Chi-restraints excluded: chain d residue 284 LEU Chi-restraints excluded: chain d residue 310 ARG Chi-restraints excluded: chain d residue 335 VAL Chi-restraints excluded: chain d residue 351 GLU Chi-restraints excluded: chain d residue 389 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 39 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 205 optimal weight: 40.0000 chunk 29 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 252 optimal weight: 0.9990 chunk 164 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 77 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS C 30 GLN C 130 GLN ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN D 187 ASN ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 123 ASN ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 338 GLN ** b 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 167 HIS b 338 GLN c 302 ASN c 358 ASN d 120 HIS d 277 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.099099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.072807 restraints weight = 82865.605| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.93 r_work: 0.2946 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.8753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 32752 Z= 0.281 Angle : 0.841 15.467 44700 Z= 0.436 Chirality : 0.053 0.582 5000 Planarity : 0.007 0.081 5720 Dihedral : 7.429 89.096 4785 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 7.61 % Allowed : 23.81 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.28 (0.12), residues: 4054 helix: 0.56 (0.24), residues: 451 sheet: -0.43 (0.15), residues: 1132 loop : -1.36 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG c 152 TYR 0.025 0.002 TYR Q 159 PHE 0.029 0.003 PHE B 241 TRP 0.057 0.003 TRP B 89 HIS 0.013 0.002 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.28 (32680) covalent geometry : angle 0.82891 / 0.43 (44542) SS BOND : bond 0.00945 / 0.58 ( 58) SS BOND : angle 1.75203 / 1.29 ( 116) hydrogen bonds : bond 0.04192 / 2.76 ( 1064) hydrogen bonds : angle 6.09164 / 4.17 ( 2625) link_BETA1-4 : bond 0.01054 / 0.52 ( 8) link_BETA1-4 : angle 3.04405 / 1.74 ( 24) link_NAG-ASN : bond 0.00709 / 0.40 ( 6) link_NAG-ASN : angle 4.75424 / 3.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 760 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9239 (OUTLIER) cc_final: 0.8663 (t) REVERT: A 80 VAL cc_start: 0.9544 (OUTLIER) cc_final: 0.9343 (t) REVERT: A 103 MET cc_start: 0.6926 (tpp) cc_final: 0.6647 (tpp) REVERT: A 113 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8307 (pm20) REVERT: A 132 MET cc_start: 0.8965 (tpp) cc_final: 0.8689 (tpp) REVERT: A 142 TRP cc_start: 0.7895 (m-10) cc_final: 0.7456 (m100) REVERT: A 247 ASP cc_start: 0.8913 (t0) cc_final: 0.8703 (m-30) REVERT: A 305 THR cc_start: 0.9339 (m) cc_final: 0.8928 (p) REVERT: A 328 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7235 (m-40) REVERT: A 344 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7384 (t0) REVERT: A 367 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8527 (tppt) REVERT: A 380 ASP cc_start: 0.9005 (m-30) cc_final: 0.8638 (m-30) REVERT: A 382 LYS cc_start: 0.8921 (mppt) cc_final: 0.8517 (mppt) REVERT: B 75 ASP cc_start: 0.9319 (OUTLIER) cc_final: 0.8872 (m-30) REVERT: B 88 MET cc_start: 0.9461 (mmm) cc_final: 0.9204 (mmm) REVERT: B 189 ASP cc_start: 0.9234 (t0) cc_final: 0.9017 (t0) REVERT: B 192 GLU cc_start: 0.5663 (tt0) cc_final: 0.4455 (mt-10) REVERT: B 200 SER cc_start: 0.8982 (t) cc_final: 0.8689 (p) REVERT: B 221 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8587 (mtpp) REVERT: B 301 GLU cc_start: 0.9168 (tp30) cc_final: 0.8915 (tp30) REVERT: B 305 THR cc_start: 0.9080 (m) cc_final: 0.8811 (p) REVERT: B 328 ASN cc_start: 0.8359 (t0) cc_final: 0.8104 (t0) REVERT: B 344 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8161 (t0) REVERT: B 366 PHE cc_start: 0.8424 (p90) cc_final: 0.7970 (p90) REVERT: B 368 LEU cc_start: 0.9384 (tt) cc_final: 0.8698 (tt) REVERT: B 378 LYS cc_start: 0.7975 (tppp) cc_final: 0.7674 (tppp) REVERT: B 388 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8672 (mm) REVERT: B 421 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8790 (t80) REVERT: C 116 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9111 (tp) REVERT: C 132 MET cc_start: 0.8459 (tpt) cc_final: 0.8169 (tpp) REVERT: C 242 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8462 (tm-30) REVERT: C 282 ASP cc_start: 0.8802 (t0) cc_final: 0.8492 (t0) REVERT: C 301 GLU cc_start: 0.8825 (tp30) cc_final: 0.8503 (tp30) REVERT: C 306 GLU cc_start: 0.8010 (tt0) cc_final: 0.7683 (tm-30) REVERT: C 385 LYS cc_start: 0.4089 (OUTLIER) cc_final: 0.1797 (mttt) REVERT: C 386 ASP cc_start: 0.9040 (m-30) cc_final: 0.8748 (m-30) REVERT: C 387 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.8867 (m-70) REVERT: C 410 TRP cc_start: 0.8982 (t-100) cc_final: 0.8475 (m-90) REVERT: C 423 VAL cc_start: 0.9370 (p) cc_final: 0.9130 (p) REVERT: C 427 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9023 (mp) REVERT: D 67 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8741 (tp-100) REVERT: D 152 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8752 (mp0) REVERT: D 293 GLU cc_start: 0.9091 (mp0) cc_final: 0.8660 (mp0) REVERT: D 369 GLN cc_start: 0.9309 (mt0) cc_final: 0.8969 (mt0) REVERT: D 421 PHE cc_start: 0.9000 (t80) cc_final: 0.8732 (t80) REVERT: P 104 MET cc_start: 0.5579 (pmm) cc_final: 0.5375 (pmm) REVERT: P 114 PHE cc_start: 0.8893 (m-80) cc_final: 0.8685 (m-80) REVERT: P 127 CYS cc_start: 0.8379 (t) cc_final: 0.8139 (t) REVERT: P 135 LYS cc_start: 0.8732 (tttm) cc_final: 0.8416 (tttm) REVERT: P 155 LYS cc_start: 0.9116 (mtmm) cc_final: 0.8860 (ttmm) REVERT: P 196 GLU cc_start: 0.8926 (mp0) cc_final: 0.8683 (mp0) REVERT: Q 112 LYS cc_start: 0.8955 (mptt) cc_final: 0.8255 (mttt) REVERT: Q 135 LYS cc_start: 0.7825 (ttpp) cc_final: 0.6993 (ttpp) REVERT: Q 153 LEU cc_start: 0.9490 (mm) cc_final: 0.9079 (mp) REVERT: Q 155 LYS cc_start: 0.9449 (mttt) cc_final: 0.9187 (tttt) REVERT: Q 161 LEU cc_start: 0.8944 (mt) cc_final: 0.8689 (tp) REVERT: Q 162 GLU cc_start: 0.8578 (pt0) cc_final: 0.8212 (pm20) REVERT: Q 199 ARG cc_start: 0.9120 (ttm-80) cc_final: 0.8585 (tpt170) REVERT: Q 204 ARG cc_start: 0.8513 (ptm160) cc_final: 0.7616 (mtp-110) REVERT: Q 211 ASP cc_start: 0.8680 (m-30) cc_final: 0.8299 (m-30) REVERT: Q 217 LEU cc_start: 0.8524 (pp) cc_final: 0.8181 (pp) REVERT: Q 219 ASN cc_start: 0.9539 (p0) cc_final: 0.8968 (p0) REVERT: Q 244 TRP cc_start: 0.8865 (m-90) cc_final: 0.8067 (m-90) REVERT: R 135 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7967 (tttp) REVERT: R 176 GLN cc_start: 0.8902 (pm20) cc_final: 0.8600 (pm20) REVERT: R 204 ARG cc_start: 0.8946 (ptm-80) cc_final: 0.8714 (ptm-80) REVERT: R 211 ASP cc_start: 0.8837 (m-30) cc_final: 0.8532 (m-30) REVERT: S 104 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.4990 (mpp) REVERT: S 133 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.8894 (p) REVERT: S 155 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8731 (mtpp) REVERT: S 163 TYR cc_start: 0.8642 (p90) cc_final: 0.8250 (p90) REVERT: S 217 LEU cc_start: 0.9276 (tp) cc_final: 0.9023 (tp) REVERT: S 244 TRP cc_start: 0.8497 (m-90) cc_final: 0.7871 (m-90) REVERT: S 247 LYS cc_start: 0.8838 (mttt) cc_final: 0.8458 (mmmt) REVERT: S 252 LYS cc_start: 0.9220 (ttmt) cc_final: 0.8759 (ttmt) REVERT: a 18 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8188 (t0) REVERT: a 34 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7335 (mp0) REVERT: a 48 GLN cc_start: 0.8754 (mt0) cc_final: 0.7636 (tt0) REVERT: a 52 MET cc_start: 0.8353 (mmm) cc_final: 0.8106 (mmm) REVERT: a 64 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7080 (m-80) REVERT: a 165 GLU cc_start: 0.8398 (pp20) cc_final: 0.8136 (pp20) REVERT: a 172 VAL cc_start: 0.9353 (t) cc_final: 0.9088 (p) REVERT: a 264 ILE cc_start: 0.9398 (mt) cc_final: 0.9178 (mm) REVERT: a 335 VAL cc_start: 0.9564 (OUTLIER) cc_final: 0.9321 (m) REVERT: a 340 SER cc_start: 0.8849 (t) cc_final: 0.8542 (p) REVERT: a 348 TRP cc_start: 0.9194 (m100) cc_final: 0.8967 (m-90) REVERT: a 364 THR cc_start: 0.8915 (m) cc_final: 0.8564 (p) REVERT: a 371 CYS cc_start: 0.9425 (t) cc_final: 0.9098 (t) REVERT: a 378 SER cc_start: 0.8839 (t) cc_final: 0.8625 (p) REVERT: b 6 PHE cc_start: 0.7879 (t80) cc_final: 0.7604 (t80) REVERT: b 52 MET cc_start: 0.8780 (mmt) cc_final: 0.8517 (mmt) REVERT: b 246 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7252 (t0) REVERT: b 335 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.9012 (m) REVERT: c 6 PHE cc_start: 0.8896 (m-80) cc_final: 0.8616 (m-80) REVERT: c 35 GLU cc_start: 0.8805 (tp30) cc_final: 0.8401 (tp30) REVERT: c 68 MET cc_start: 0.5700 (mmm) cc_final: 0.5252 (mmm) REVERT: c 248 PHE cc_start: 0.8027 (t80) cc_final: 0.7824 (m-80) REVERT: c 348 TRP cc_start: 0.8451 (m100) cc_final: 0.7970 (m-90) REVERT: c 362 LEU cc_start: 0.9562 (tp) cc_final: 0.9309 (pt) REVERT: d 3 ASP cc_start: 0.9245 (p0) cc_final: 0.8971 (p0) REVERT: d 6 PHE cc_start: 0.8976 (m-10) cc_final: 0.8385 (m-10) REVERT: d 35 GLU cc_start: 0.8521 (pp20) cc_final: 0.8166 (pp20) REVERT: d 52 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7530 (mpp) REVERT: d 194 GLN cc_start: 0.8545 (tt0) cc_final: 0.8276 (tp40) REVERT: d 316 PHE cc_start: 0.9088 (m-80) cc_final: 0.8826 (m-80) REVERT: d 342 GLU cc_start: 0.9125 (tp30) cc_final: 0.8874 (tp30) REVERT: d 404 GLN cc_start: 0.7112 (mm-40) cc_final: 0.6886 (tp-100) REVERT: d 407 ILE cc_start: 0.8968 (mm) cc_final: 0.8667 (mm) outliers start: 265 outliers final: 158 residues processed: 944 average time/residue: 0.1873 time to fit residues: 287.0506 Evaluate side-chains 854 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 674 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 408 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain P residue 128 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain P residue 187 ASN Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain Q residue 123 ASN Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 174 THR Chi-restraints excluded: chain Q residue 193 VAL Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain Q residue 223 VAL Chi-restraints excluded: chain Q residue 227 VAL Chi-restraints excluded: chain Q residue 239 LEU Chi-restraints excluded: chain Q residue 241 VAL Chi-restraints excluded: chain Q residue 253 ASP Chi-restraints excluded: chain Q residue 259 GLU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 239 LEU Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 5 HIS Chi-restraints excluded: chain a residue 18 ASP Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 122 CYS Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 175 HIS Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 203 ASP Chi-restraints excluded: chain a residue 272 LEU Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 333 LYS Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 399 LEU Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 124 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 151 ASN Chi-restraints excluded: chain b residue 181 HIS Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 246 ASP Chi-restraints excluded: chain b residue 254 VAL Chi-restraints excluded: chain b residue 315 ASN Chi-restraints excluded: chain b residue 335 VAL Chi-restraints excluded: chain b residue 379 CYS Chi-restraints excluded: chain b residue 386 LEU Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 398 LYS Chi-restraints excluded: chain b residue 408 LEU Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 47 ILE Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 133 VAL Chi-restraints excluded: chain c residue 151 ASN Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 203 ASP Chi-restraints excluded: chain c residue 204 VAL Chi-restraints excluded: chain c residue 205 ARG Chi-restraints excluded: chain c residue 215 THR Chi-restraints excluded: chain c residue 253 HIS Chi-restraints excluded: chain c residue 318 VAL Chi-restraints excluded: chain c residue 342 GLU Chi-restraints excluded: chain c residue 363 THR Chi-restraints excluded: chain c residue 368 LEU Chi-restraints excluded: chain c residue 374 ILE Chi-restraints excluded: chain c residue 379 CYS Chi-restraints excluded: chain c residue 386 LEU Chi-restraints excluded: chain c residue 415 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 52 MET Chi-restraints excluded: chain d residue 64 TYR Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 234 VAL Chi-restraints excluded: chain d residue 310 ARG Chi-restraints excluded: chain d residue 335 VAL Chi-restraints excluded: chain d residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 54 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 324 optimal weight: 4.9990 chunk 331 optimal weight: 0.9990 chunk 297 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 175 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 162 HIS ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 73 GLN ** b 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 275 HIS c 69 ASN c 168 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.072239 restraints weight = 82499.625| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.85 r_work: 0.2922 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.9375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32752 Z= 0.202 Angle : 0.770 16.154 44700 Z= 0.391 Chirality : 0.050 0.533 5000 Planarity : 0.005 0.063 5720 Dihedral : 7.214 82.030 4777 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.32 % Allowed : 26.05 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.13 (0.13), residues: 4054 helix: 0.85 (0.24), residues: 450 sheet: -0.33 (0.16), residues: 1099 loop : -1.29 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 142 TYR 0.023 0.002 TYR D 321 PHE 0.027 0.002 PHE B 241 TRP 0.029 0.002 TRP P 188 HIS 0.009 0.001 HIS P 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (32680) covalent geometry : angle 0.75816 / 0.39 (44542) SS BOND : bond 0.00552 / 0.40 ( 58) SS BOND : angle 1.55874 / 1.15 ( 116) hydrogen bonds : bond 0.03826 / 2.52 ( 1064) hydrogen bonds : angle 5.88624 / 4.03 ( 2625) link_BETA1-4 : bond 0.00853 / 0.43 ( 8) link_BETA1-4 : angle 3.04803 / 1.71 ( 24) link_NAG-ASN : bond 0.01247 / 0.88 ( 6) link_NAG-ASN : angle 4.61685 / 2.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 725 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8614 (tm-30) REVERT: A 10 LYS cc_start: 0.9112 (mmtp) cc_final: 0.8805 (mmtm) REVERT: A 113 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8514 (pm20) REVERT: A 132 MET cc_start: 0.9039 (tpp) cc_final: 0.8673 (tpp) REVERT: A 142 TRP cc_start: 0.8043 (m-10) cc_final: 0.7707 (m100) REVERT: A 303 LYS cc_start: 0.9076 (mtpp) cc_final: 0.8685 (ptmm) REVERT: A 367 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8448 (tppt) REVERT: A 380 ASP cc_start: 0.9011 (m-30) cc_final: 0.8621 (m-30) REVERT: A 382 LYS cc_start: 0.8977 (mppt) cc_final: 0.8549 (mppt) REVERT: A 421 PHE cc_start: 0.9233 (t80) cc_final: 0.9017 (t80) REVERT: B 50 LYS cc_start: 0.8505 (tttt) cc_final: 0.8155 (tttp) REVERT: B 79 GLN cc_start: 0.9081 (tt0) cc_final: 0.8507 (tm-30) REVERT: B 88 MET cc_start: 0.9486 (mmm) cc_final: 0.9227 (mmm) REVERT: B 189 ASP cc_start: 0.9260 (t0) cc_final: 0.9045 (t0) REVERT: B 192 GLU cc_start: 0.5715 (tt0) cc_final: 0.4536 (mt-10) REVERT: B 197 LYS cc_start: 0.9190 (mmtm) cc_final: 0.8915 (tppt) REVERT: B 221 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8629 (mtpp) REVERT: B 305 THR cc_start: 0.9136 (m) cc_final: 0.8757 (p) REVERT: B 366 PHE cc_start: 0.8519 (p90) cc_final: 0.8116 (p90) REVERT: B 388 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8916 (mm) REVERT: B 421 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8798 (t80) REVERT: C 242 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8274 (tm-30) REVERT: C 282 ASP cc_start: 0.8870 (t0) cc_final: 0.8621 (t0) REVERT: C 301 GLU cc_start: 0.8836 (tp30) cc_final: 0.8506 (tp30) REVERT: C 306 GLU cc_start: 0.8207 (tt0) cc_final: 0.7976 (tm-30) REVERT: C 385 LYS cc_start: 0.4016 (OUTLIER) cc_final: 0.1580 (mtmm) REVERT: C 386 ASP cc_start: 0.9056 (m-30) cc_final: 0.8780 (m-30) REVERT: C 410 TRP cc_start: 0.8970 (t-100) cc_final: 0.8377 (m-90) REVERT: C 423 VAL cc_start: 0.9379 (p) cc_final: 0.9095 (p) REVERT: C 427 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8917 (mp) REVERT: D 152 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8851 (mp0) REVERT: D 156 LYS cc_start: 0.9198 (tppt) cc_final: 0.8935 (tppt) REVERT: D 189 ASP cc_start: 0.9255 (m-30) cc_final: 0.9049 (t0) REVERT: D 197 LYS cc_start: 0.9090 (tppp) cc_final: 0.8883 (tppt) REVERT: D 367 LYS cc_start: 0.8967 (ttmm) cc_final: 0.8721 (ttpp) REVERT: D 369 GLN cc_start: 0.9324 (mt0) cc_final: 0.8988 (mt0) REVERT: D 421 PHE cc_start: 0.9060 (t80) cc_final: 0.8806 (t80) REVERT: P 118 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9216 (mt) REVERT: P 127 CYS cc_start: 0.8414 (t) cc_final: 0.8157 (t) REVERT: P 170 MET cc_start: 0.9054 (mmm) cc_final: 0.8841 (mmm) REVERT: P 204 ARG cc_start: 0.8879 (ttm110) cc_final: 0.8555 (ttm110) REVERT: Q 112 LYS cc_start: 0.8916 (mptt) cc_final: 0.8193 (mttt) REVERT: Q 135 LYS cc_start: 0.7911 (ttpp) cc_final: 0.6757 (ttpp) REVERT: Q 153 LEU cc_start: 0.9524 (mm) cc_final: 0.9030 (mp) REVERT: Q 159 TYR cc_start: 0.9080 (m-80) cc_final: 0.8742 (m-80) REVERT: Q 161 LEU cc_start: 0.8884 (mt) cc_final: 0.8563 (tt) REVERT: Q 162 GLU cc_start: 0.8635 (pt0) cc_final: 0.8335 (pm20) REVERT: Q 199 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8554 (tpt170) REVERT: Q 204 ARG cc_start: 0.8614 (ptm160) cc_final: 0.7689 (mtp-110) REVERT: Q 211 ASP cc_start: 0.8741 (m-30) cc_final: 0.8326 (m-30) REVERT: Q 217 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8356 (pp) REVERT: Q 220 LYS cc_start: 0.9409 (mmtm) cc_final: 0.9139 (mmtt) REVERT: Q 244 TRP cc_start: 0.8915 (m-90) cc_final: 0.7828 (m-90) REVERT: Q 247 LYS cc_start: 0.9403 (mmtm) cc_final: 0.9158 (mmtm) REVERT: R 135 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7863 (tttp) REVERT: R 170 MET cc_start: 0.9628 (mtm) cc_final: 0.9304 (mtm) REVERT: R 171 LYS cc_start: 0.9507 (mttp) cc_final: 0.9266 (mttm) REVERT: R 176 GLN cc_start: 0.8801 (pm20) cc_final: 0.8500 (pm20) REVERT: R 186 TYR cc_start: 0.8651 (m-80) cc_final: 0.8434 (m-80) REVERT: R 204 ARG cc_start: 0.9054 (ptm-80) cc_final: 0.8811 (ptm-80) REVERT: R 211 ASP cc_start: 0.8872 (m-30) cc_final: 0.8482 (m-30) REVERT: R 251 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8585 (m) REVERT: S 104 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.4747 (mpp) REVERT: S 132 ARG cc_start: 0.9025 (ttm110) cc_final: 0.8586 (ttm110) REVERT: S 133 VAL cc_start: 0.9353 (t) cc_final: 0.9046 (p) REVERT: S 155 LYS cc_start: 0.9187 (mtpp) cc_final: 0.8708 (mtpp) REVERT: S 162 GLU cc_start: 0.8745 (tt0) cc_final: 0.8498 (tt0) REVERT: S 194 GLN cc_start: 0.7919 (tp40) cc_final: 0.7547 (tp40) REVERT: S 244 TRP cc_start: 0.8388 (m-90) cc_final: 0.7843 (m-90) REVERT: S 247 LYS cc_start: 0.8869 (mttt) cc_final: 0.8503 (mmmt) REVERT: S 252 LYS cc_start: 0.9213 (ttmt) cc_final: 0.8803 (ttmt) REVERT: a 48 GLN cc_start: 0.8665 (mt0) cc_final: 0.8199 (tt0) REVERT: a 52 MET cc_start: 0.8418 (mmm) cc_final: 0.8204 (mmm) REVERT: a 165 GLU cc_start: 0.8344 (pp20) cc_final: 0.8051 (pp20) REVERT: a 166 MET cc_start: 0.7384 (mpp) cc_final: 0.7127 (mpp) REVERT: a 172 VAL cc_start: 0.9292 (t) cc_final: 0.9018 (p) REVERT: a 242 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8354 (tmm-80) REVERT: a 300 ASP cc_start: 0.9052 (t70) cc_final: 0.8619 (t70) REVERT: a 340 SER cc_start: 0.8733 (t) cc_final: 0.8481 (p) REVERT: a 364 THR cc_start: 0.9136 (m) cc_final: 0.8784 (p) REVERT: a 371 CYS cc_start: 0.9393 (t) cc_final: 0.9134 (t) REVERT: b 6 PHE cc_start: 0.7909 (t80) cc_final: 0.7481 (t80) REVERT: b 52 MET cc_start: 0.8748 (mmt) cc_final: 0.8295 (mmm) REVERT: b 68 MET cc_start: 0.7720 (mmm) cc_final: 0.7490 (mmm) REVERT: b 246 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.6981 (t0) REVERT: b 335 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9059 (m) REVERT: c 34 GLU cc_start: 0.8169 (tp30) cc_final: 0.7910 (tt0) REVERT: c 35 GLU cc_start: 0.8749 (tp30) cc_final: 0.7959 (tp30) REVERT: c 52 MET cc_start: 0.8949 (mmt) cc_final: 0.8579 (mmt) REVERT: c 68 MET cc_start: 0.7052 (mmm) cc_final: 0.6589 (mmm) REVERT: c 310 ARG cc_start: 0.9297 (ptp-110) cc_final: 0.9009 (ptp-110) REVERT: c 339 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8190 (mm-30) REVERT: c 348 TRP cc_start: 0.8565 (m100) cc_final: 0.8128 (m-90) REVERT: c 362 LEU cc_start: 0.9579 (tp) cc_final: 0.9378 (pt) REVERT: c 389 THR cc_start: 0.9350 (m) cc_final: 0.9143 (m) REVERT: d 3 ASP cc_start: 0.9318 (p0) cc_final: 0.9032 (p0) REVERT: d 6 PHE cc_start: 0.9021 (m-10) cc_final: 0.8565 (m-10) REVERT: d 52 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.7734 (mpp) REVERT: d 316 PHE cc_start: 0.9063 (m-80) cc_final: 0.8840 (m-80) REVERT: d 342 GLU cc_start: 0.9216 (tp30) cc_final: 0.8897 (tp30) REVERT: d 407 ILE cc_start: 0.8923 (mm) cc_final: 0.8717 (mm) outliers start: 220 outliers final: 147 residues processed: 881 average time/residue: 0.1901 time to fit residues: 271.9800 Evaluate side-chains 847 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 686 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 408 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 119 ASN Chi-restraints excluded: chain P residue 128 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 187 ASN Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 209 LYS Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 193 VAL Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain Q residue 223 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 239 LEU Chi-restraints excluded: chain Q residue 253 ASP Chi-restraints excluded: chain Q residue 259 GLU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 106 MET Chi-restraints excluded: chain S residue 107 LYS Chi-restraints excluded: chain S residue 222 ARG Chi-restraints excluded: chain S residue 239 LEU Chi-restraints excluded: chain S residue 242 VAL Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 5 HIS Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 122 CYS Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 242 ARG Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 369 CYS Chi-restraints excluded: chain a residue 389 THR Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 124 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 133 VAL Chi-restraints excluded: chain b residue 151 ASN Chi-restraints excluded: chain b residue 181 HIS Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 246 ASP Chi-restraints excluded: chain b residue 254 VAL Chi-restraints excluded: chain b residue 335 VAL Chi-restraints excluded: chain b residue 398 LYS Chi-restraints excluded: chain b residue 408 LEU Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 47 ILE Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 133 VAL Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 203 ASP Chi-restraints excluded: chain c residue 204 VAL Chi-restraints excluded: chain c residue 205 ARG Chi-restraints excluded: chain c residue 215 THR Chi-restraints excluded: chain c residue 234 VAL Chi-restraints excluded: chain c residue 253 HIS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 318 VAL Chi-restraints excluded: chain c residue 363 THR Chi-restraints excluded: chain c residue 368 LEU Chi-restraints excluded: chain c residue 369 CYS Chi-restraints excluded: chain c residue 379 CYS Chi-restraints excluded: chain c residue 385 LEU Chi-restraints excluded: chain c residue 393 CYS Chi-restraints excluded: chain c residue 411 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 52 MET Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 310 ARG Chi-restraints excluded: chain d residue 326 THR Chi-restraints excluded: chain d residue 335 VAL Chi-restraints excluded: chain d residue 351 GLU Chi-restraints excluded: chain d residue 368 LEU Chi-restraints excluded: chain d residue 387 CYS Chi-restraints excluded: chain d residue 389 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 149 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 276 optimal weight: 9.9990 chunk 117 optimal weight: 0.1980 chunk 49 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 402 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 213 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 HIS ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 HIS ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.069031 restraints weight = 83242.589| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.77 r_work: 0.2896 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.9962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32752 Z= 0.196 Angle : 0.753 17.318 44700 Z= 0.380 Chirality : 0.050 0.535 5000 Planarity : 0.006 0.066 5720 Dihedral : 6.949 74.175 4775 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 6.72 % Allowed : 25.82 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.05 (0.13), residues: 4054 helix: 0.88 (0.24), residues: 452 sheet: -0.32 (0.16), residues: 1038 loop : -1.19 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 204 TYR 0.028 0.002 TYR a 64 PHE 0.021 0.002 PHE B 241 TRP 0.046 0.002 TRP C 89 HIS 0.009 0.001 HIS P 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (32680) covalent geometry : angle 0.74065 / 0.38 (44542) SS BOND : bond 0.00399 / 0.26 ( 58) SS BOND : angle 1.54188 / 1.11 ( 116) hydrogen bonds : bond 0.03579 / 2.36 ( 1064) hydrogen bonds : angle 5.78026 / 3.96 ( 2625) link_BETA1-4 : bond 0.00848 / 0.42 ( 8) link_BETA1-4 : angle 2.85155 / 1.61 ( 24) link_NAG-ASN : bond 0.00820 / 0.51 ( 6) link_NAG-ASN : angle 4.83169 / 3.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 713 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8677 (tm-30) REVERT: A 132 MET cc_start: 0.9003 (tpp) cc_final: 0.8568 (tpp) REVERT: A 136 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8615 (m) REVERT: A 142 TRP cc_start: 0.8155 (m-10) cc_final: 0.7854 (m100) REVERT: A 303 LYS cc_start: 0.9119 (mtpp) cc_final: 0.8756 (ptmm) REVERT: A 306 GLU cc_start: 0.8582 (tp30) cc_final: 0.8375 (tp30) REVERT: A 367 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8467 (tppt) REVERT: A 380 ASP cc_start: 0.8990 (m-30) cc_final: 0.8586 (m-30) REVERT: A 382 LYS cc_start: 0.9011 (mppt) cc_final: 0.8645 (mppt) REVERT: A 421 PHE cc_start: 0.9264 (t80) cc_final: 0.9055 (t80) REVERT: B 50 LYS cc_start: 0.8792 (tttt) cc_final: 0.8401 (tttp) REVERT: B 79 GLN cc_start: 0.9194 (tt0) cc_final: 0.8611 (tm-30) REVERT: B 88 MET cc_start: 0.9483 (mmm) cc_final: 0.9159 (mmm) REVERT: B 189 ASP cc_start: 0.9322 (t0) cc_final: 0.9121 (t0) REVERT: B 192 GLU cc_start: 0.5740 (tt0) cc_final: 0.4970 (tt0) REVERT: B 197 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8893 (tppt) REVERT: B 221 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8614 (mtpp) REVERT: B 301 GLU cc_start: 0.9114 (tp30) cc_final: 0.8743 (tp30) REVERT: B 305 THR cc_start: 0.9300 (m) cc_final: 0.8856 (p) REVERT: B 366 PHE cc_start: 0.8630 (p90) cc_final: 0.8399 (p90) REVERT: B 421 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8852 (t80) REVERT: C 242 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8379 (tm-30) REVERT: C 282 ASP cc_start: 0.8865 (t0) cc_final: 0.8640 (t0) REVERT: C 301 GLU cc_start: 0.8789 (tp30) cc_final: 0.8448 (tp30) REVERT: C 385 LYS cc_start: 0.3959 (OUTLIER) cc_final: 0.1537 (mtmm) REVERT: C 386 ASP cc_start: 0.9121 (m-30) cc_final: 0.8848 (m-30) REVERT: C 410 TRP cc_start: 0.8966 (t-100) cc_final: 0.8320 (m-90) REVERT: C 423 VAL cc_start: 0.9400 (p) cc_final: 0.9092 (p) REVERT: C 427 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8925 (mp) REVERT: C 439 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.5877 (t70) REVERT: D 152 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8809 (mp0) REVERT: D 156 LYS cc_start: 0.9153 (tppt) cc_final: 0.8678 (tppt) REVERT: D 197 LYS cc_start: 0.9151 (tppp) cc_final: 0.8911 (tppt) REVERT: D 306 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7935 (tm-30) REVERT: D 369 GLN cc_start: 0.9299 (mt0) cc_final: 0.8954 (mt0) REVERT: D 408 TRP cc_start: 0.8481 (OUTLIER) cc_final: 0.7945 (t60) REVERT: P 117 MET cc_start: 0.8732 (mmm) cc_final: 0.8378 (mmp) REVERT: P 118 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9241 (mt) REVERT: P 127 CYS cc_start: 0.8450 (t) cc_final: 0.8186 (t) REVERT: P 135 LYS cc_start: 0.8660 (tttm) cc_final: 0.8437 (tmtt) REVERT: P 155 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8855 (ttmm) REVERT: P 204 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8684 (ttm110) REVERT: P 211 ASP cc_start: 0.9079 (m-30) cc_final: 0.8778 (m-30) REVERT: Q 135 LYS cc_start: 0.7949 (ttpp) cc_final: 0.7128 (ttpp) REVERT: Q 159 TYR cc_start: 0.9061 (m-80) cc_final: 0.8562 (m-80) REVERT: Q 161 LEU cc_start: 0.8923 (mt) cc_final: 0.8514 (tt) REVERT: Q 162 GLU cc_start: 0.8650 (pt0) cc_final: 0.8357 (pm20) REVERT: Q 181 LYS cc_start: 0.8927 (ptpp) cc_final: 0.8695 (ptpp) REVERT: Q 199 ARG cc_start: 0.9136 (ttm-80) cc_final: 0.8476 (tpt170) REVERT: Q 211 ASP cc_start: 0.8760 (m-30) cc_final: 0.8375 (m-30) REVERT: Q 217 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8291 (pp) REVERT: Q 219 ASN cc_start: 0.9559 (p0) cc_final: 0.8620 (p0) REVERT: Q 220 LYS cc_start: 0.9419 (mmtm) cc_final: 0.9047 (mmtm) REVERT: R 106 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6275 (mmt) REVERT: R 127 CYS cc_start: 0.8507 (t) cc_final: 0.8276 (m) REVERT: R 135 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7851 (tttp) REVERT: R 176 GLN cc_start: 0.8754 (pm20) cc_final: 0.8402 (pm20) REVERT: R 186 TYR cc_start: 0.8775 (m-80) cc_final: 0.8553 (m-80) REVERT: R 204 ARG cc_start: 0.9097 (ptm-80) cc_final: 0.8872 (ptm-80) REVERT: R 211 ASP cc_start: 0.8934 (m-30) cc_final: 0.8390 (m-30) REVERT: R 251 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8475 (m) REVERT: S 104 MET cc_start: 0.5481 (OUTLIER) cc_final: 0.4860 (mpp) REVERT: S 132 ARG cc_start: 0.9026 (ttm110) cc_final: 0.8615 (tpp80) REVERT: S 133 VAL cc_start: 0.9397 (t) cc_final: 0.9061 (p) REVERT: S 135 LYS cc_start: 0.8510 (tttm) cc_final: 0.8198 (tttm) REVERT: S 137 LEU cc_start: 0.9214 (tt) cc_final: 0.8776 (mt) REVERT: S 155 LYS cc_start: 0.9172 (mtpp) cc_final: 0.8882 (mtpp) REVERT: S 162 GLU cc_start: 0.8832 (tt0) cc_final: 0.8538 (tt0) REVERT: S 246 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8681 (tm-30) REVERT: S 247 LYS cc_start: 0.8932 (mttt) cc_final: 0.8449 (mmmt) REVERT: S 252 LYS cc_start: 0.9230 (ttmt) cc_final: 0.8842 (ttmt) REVERT: a 48 GLN cc_start: 0.8793 (mt0) cc_final: 0.8300 (tt0) REVERT: a 52 MET cc_start: 0.8472 (mmm) cc_final: 0.8241 (mmm) REVERT: a 165 GLU cc_start: 0.8489 (pp20) cc_final: 0.8131 (pp20) REVERT: a 166 MET cc_start: 0.6913 (mpp) cc_final: 0.6612 (mpp) REVERT: a 172 VAL cc_start: 0.9420 (t) cc_final: 0.9121 (p) REVERT: a 227 LEU cc_start: 0.9149 (mt) cc_final: 0.8864 (mm) REVERT: a 270 GLU cc_start: 0.9343 (tp30) cc_final: 0.8792 (pm20) REVERT: a 300 ASP cc_start: 0.9132 (t70) cc_final: 0.8745 (t70) REVERT: a 364 THR cc_start: 0.9178 (m) cc_final: 0.8825 (p) REVERT: a 371 CYS cc_start: 0.9402 (t) cc_final: 0.9132 (t) REVERT: b 6 PHE cc_start: 0.8057 (t80) cc_final: 0.7593 (t80) REVERT: b 35 GLU cc_start: 0.8804 (tt0) cc_final: 0.8592 (tm-30) REVERT: b 52 MET cc_start: 0.8824 (mmt) cc_final: 0.8477 (mmm) REVERT: b 152 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8506 (mtm-85) REVERT: b 246 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.6872 (t0) REVERT: c 6 PHE cc_start: 0.8769 (m-80) cc_final: 0.8546 (m-10) REVERT: c 35 GLU cc_start: 0.8768 (tp30) cc_final: 0.8078 (tp30) REVERT: c 52 MET cc_start: 0.9008 (mmt) cc_final: 0.8503 (mmt) REVERT: c 68 MET cc_start: 0.6521 (mmm) cc_final: 0.6057 (mmm) REVERT: c 166 MET cc_start: 0.7427 (ptt) cc_final: 0.7186 (ppp) REVERT: c 310 ARG cc_start: 0.9316 (ptp-110) cc_final: 0.9037 (ptp-110) REVERT: c 348 TRP cc_start: 0.8682 (m100) cc_final: 0.8181 (m-90) REVERT: d 3 ASP cc_start: 0.9297 (p0) cc_final: 0.9011 (p0) REVERT: d 6 PHE cc_start: 0.9108 (m-10) cc_final: 0.8725 (m-10) REVERT: d 52 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.7782 (mpp) REVERT: d 65 MET cc_start: 0.8004 (ttp) cc_final: 0.7778 (ttp) REVERT: d 151 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8786 (p0) REVERT: d 166 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6570 (pmm) REVERT: d 316 PHE cc_start: 0.9149 (m-80) cc_final: 0.8927 (m-80) REVERT: d 342 GLU cc_start: 0.9107 (tp30) cc_final: 0.8674 (tp30) outliers start: 234 outliers final: 161 residues processed: 866 average time/residue: 0.2002 time to fit residues: 279.3781 Evaluate side-chains 845 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 667 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 408 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 439 HIS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 128 VAL Chi-restraints excluded: chain P residue 155 LYS Chi-restraints excluded: chain P residue 187 ASN Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain Q residue 113 THR Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain Q residue 123 ASN Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 193 VAL Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain Q residue 223 VAL Chi-restraints excluded: chain Q residue 239 LEU Chi-restraints excluded: chain Q residue 259 GLU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 107 LYS Chi-restraints excluded: chain S residue 222 ARG Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 239 LEU Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 122 CYS Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 203 ASP Chi-restraints excluded: chain a residue 272 LEU Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain a residue 317 THR Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 369 CYS Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 124 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 151 ASN Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 246 ASP Chi-restraints excluded: chain b residue 254 VAL Chi-restraints excluded: chain b residue 377 VAL Chi-restraints excluded: chain b residue 382 SER Chi-restraints excluded: chain b residue 386 LEU Chi-restraints excluded: chain b residue 398 LYS Chi-restraints excluded: chain b residue 408 LEU Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain c residue 47 ILE Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 133 VAL Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 203 ASP Chi-restraints excluded: chain c residue 205 ARG Chi-restraints excluded: chain c residue 215 THR Chi-restraints excluded: chain c residue 234 VAL Chi-restraints excluded: chain c residue 253 HIS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 318 VAL Chi-restraints excluded: chain c residue 342 GLU Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 368 LEU Chi-restraints excluded: chain c residue 374 ILE Chi-restraints excluded: chain c residue 379 CYS Chi-restraints excluded: chain c residue 398 LYS Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 52 MET Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 166 MET Chi-restraints excluded: chain d residue 270 GLU Chi-restraints excluded: chain d residue 294 THR Chi-restraints excluded: chain d residue 310 ARG Chi-restraints excluded: chain d residue 326 THR Chi-restraints excluded: chain d residue 335 VAL Chi-restraints excluded: chain d residue 351 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 27 optimal weight: 0.8980 chunk 395 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 384 optimal weight: 7.9990 chunk 187 optimal weight: 30.0000 chunk 262 optimal weight: 20.0000 chunk 210 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS A 30 GLN ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 GLN ** a 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 213 HIS ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 ASN ** b 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.066401 restraints weight = 84754.140| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.87 r_work: 0.2845 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 1.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 32752 Z= 0.241 Angle : 0.793 16.627 44700 Z= 0.401 Chirality : 0.050 0.361 5000 Planarity : 0.006 0.073 5720 Dihedral : 6.947 67.840 4773 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 6.81 % Allowed : 26.48 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.15 (0.13), residues: 4054 helix: 0.66 (0.23), residues: 480 sheet: -0.40 (0.16), residues: 1071 loop : -1.25 (0.12), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 199 TYR 0.031 0.002 TYR a 64 PHE 0.020 0.002 PHE c 316 TRP 0.032 0.002 TRP P 188 HIS 0.019 0.001 HIS b 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (32680) covalent geometry : angle 0.77967 / 0.40 (44542) SS BOND : bond 0.00445 / 0.29 ( 58) SS BOND : angle 1.58784 / 1.13 ( 116) hydrogen bonds : bond 0.03746 / 2.47 ( 1064) hydrogen bonds : angle 5.69802 / 3.89 ( 2625) link_BETA1-4 : bond 0.00890 / 0.44 ( 8) link_BETA1-4 : angle 3.14019 / 1.74 ( 24) link_NAG-ASN : bond 0.00437 / 0.28 ( 6) link_NAG-ASN : angle 5.40159 / 3.51 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 696 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8578 (tm-30) REVERT: A 132 MET cc_start: 0.8974 (tpp) cc_final: 0.8514 (tpp) REVERT: A 136 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8730 (m) REVERT: A 142 TRP cc_start: 0.8154 (m-10) cc_final: 0.7886 (m100) REVERT: A 303 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8847 (ptmm) REVERT: A 341 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8961 (ttmm) REVERT: A 344 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7773 (t0) REVERT: A 367 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8551 (tppt) REVERT: A 385 LYS cc_start: 0.9051 (pttt) cc_final: 0.8819 (pptt) REVERT: A 421 PHE cc_start: 0.9228 (t80) cc_final: 0.8855 (t80) REVERT: B 50 LYS cc_start: 0.8993 (tttt) cc_final: 0.8532 (tttt) REVERT: B 88 MET cc_start: 0.9502 (mmm) cc_final: 0.9132 (mmm) REVERT: B 103 MET cc_start: 0.9111 (tpp) cc_final: 0.8906 (tpp) REVERT: B 192 GLU cc_start: 0.5514 (tt0) cc_final: 0.4792 (tt0) REVERT: B 197 LYS cc_start: 0.9166 (mmtm) cc_final: 0.8891 (tppt) REVERT: B 221 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8572 (mtpp) REVERT: B 276 SER cc_start: 0.9438 (p) cc_final: 0.9004 (t) REVERT: B 421 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8816 (t80) REVERT: C 10 LYS cc_start: 0.9492 (mtpt) cc_final: 0.9248 (mtmm) REVERT: C 88 MET cc_start: 0.9430 (mmt) cc_final: 0.9115 (mmm) REVERT: C 132 MET cc_start: 0.8989 (tpt) cc_final: 0.8241 (tpp) REVERT: C 162 LEU cc_start: 0.9435 (tt) cc_final: 0.9042 (tp) REVERT: C 175 ASP cc_start: 0.9336 (OUTLIER) cc_final: 0.9118 (t70) REVERT: C 242 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8428 (tm-30) REVERT: C 301 GLU cc_start: 0.8913 (tp30) cc_final: 0.8549 (tp30) REVERT: C 385 LYS cc_start: 0.4089 (OUTLIER) cc_final: 0.1564 (mtmm) REVERT: C 386 ASP cc_start: 0.9209 (m-30) cc_final: 0.8903 (m-30) REVERT: C 410 TRP cc_start: 0.8854 (m-90) cc_final: 0.8242 (m-90) REVERT: C 423 VAL cc_start: 0.9417 (p) cc_final: 0.9099 (p) REVERT: C 427 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9103 (mp) REVERT: C 439 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6100 (t70) REVERT: D 152 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8804 (mp0) REVERT: D 156 LYS cc_start: 0.9179 (tppt) cc_final: 0.8889 (tppt) REVERT: D 197 LYS cc_start: 0.9156 (tppp) cc_final: 0.8821 (tppt) REVERT: D 213 ASP cc_start: 0.9099 (t0) cc_final: 0.8714 (t0) REVERT: D 290 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8606 (tpp80) REVERT: D 306 GLU cc_start: 0.8260 (tm-30) cc_final: 0.8031 (tm-30) REVERT: D 369 GLN cc_start: 0.9341 (mt0) cc_final: 0.9003 (mt0) REVERT: D 408 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.8325 (t60) REVERT: D 412 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8715 (ptpt) REVERT: P 118 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9107 (mt) REVERT: P 127 CYS cc_start: 0.8475 (t) cc_final: 0.8256 (t) REVERT: P 132 ARG cc_start: 0.8899 (tpp80) cc_final: 0.8668 (tpp80) REVERT: P 204 ARG cc_start: 0.9183 (ttm110) cc_final: 0.8983 (ttm110) REVERT: P 211 ASP cc_start: 0.9068 (m-30) cc_final: 0.8768 (m-30) REVERT: P 212 SER cc_start: 0.9577 (p) cc_final: 0.9147 (m) REVERT: P 222 ARG cc_start: 0.9370 (ptp90) cc_final: 0.9091 (mtm-85) REVERT: P 246 GLN cc_start: 0.9485 (tp40) cc_final: 0.9134 (tm-30) REVERT: P 247 LYS cc_start: 0.9258 (tppt) cc_final: 0.9015 (mmtm) REVERT: Q 117 MET cc_start: 0.9116 (mmm) cc_final: 0.8549 (mmm) REVERT: Q 135 LYS cc_start: 0.7892 (ttpp) cc_final: 0.6984 (ttpp) REVERT: Q 153 LEU cc_start: 0.9462 (mm) cc_final: 0.9187 (mm) REVERT: Q 159 TYR cc_start: 0.9147 (m-80) cc_final: 0.8619 (m-80) REVERT: Q 161 LEU cc_start: 0.9051 (mt) cc_final: 0.8638 (tt) REVERT: Q 162 GLU cc_start: 0.8829 (pt0) cc_final: 0.8429 (pm20) REVERT: Q 163 TYR cc_start: 0.9059 (p90) cc_final: 0.8570 (p90) REVERT: Q 188 TRP cc_start: 0.8099 (t60) cc_final: 0.7628 (t60) REVERT: Q 199 ARG cc_start: 0.9221 (ttm-80) cc_final: 0.8509 (tpt170) REVERT: Q 211 ASP cc_start: 0.8915 (m-30) cc_final: 0.8528 (m-30) REVERT: R 104 MET cc_start: 0.5254 (mmp) cc_final: 0.4989 (mmt) REVERT: R 106 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6668 (mmt) REVERT: R 114 PHE cc_start: 0.8983 (m-80) cc_final: 0.8658 (m-80) REVERT: R 127 CYS cc_start: 0.8721 (t) cc_final: 0.8511 (m) REVERT: R 170 MET cc_start: 0.9622 (mtm) cc_final: 0.9205 (mtm) REVERT: R 176 GLN cc_start: 0.8792 (pm20) cc_final: 0.8420 (pm20) REVERT: R 199 ARG cc_start: 0.9113 (tpp-160) cc_final: 0.8724 (tpt170) REVERT: R 204 ARG cc_start: 0.9135 (ptm-80) cc_final: 0.8889 (ptm-80) REVERT: R 211 ASP cc_start: 0.8973 (m-30) cc_final: 0.8577 (m-30) REVERT: R 251 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8444 (m) REVERT: S 104 MET cc_start: 0.4742 (OUTLIER) cc_final: 0.4174 (mpp) REVERT: S 132 ARG cc_start: 0.8993 (ttm110) cc_final: 0.8587 (tpp80) REVERT: S 133 VAL cc_start: 0.9351 (t) cc_final: 0.9052 (p) REVERT: S 137 LEU cc_start: 0.9318 (tt) cc_final: 0.8747 (mt) REVERT: S 155 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8867 (mtpp) REVERT: S 159 TYR cc_start: 0.7926 (m-80) cc_final: 0.7616 (m-80) REVERT: S 162 GLU cc_start: 0.9018 (tt0) cc_final: 0.8642 (tt0) REVERT: S 214 ARG cc_start: 0.8810 (tpp-160) cc_final: 0.8303 (tpp80) REVERT: S 246 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8818 (tm-30) REVERT: S 247 LYS cc_start: 0.8988 (mttt) cc_final: 0.8704 (mmtp) REVERT: S 252 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8904 (ttpt) REVERT: a 48 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: a 52 MET cc_start: 0.8684 (mmm) cc_final: 0.8424 (mmm) REVERT: a 65 MET cc_start: 0.8968 (tpp) cc_final: 0.8763 (tpp) REVERT: a 165 GLU cc_start: 0.8585 (pp20) cc_final: 0.8201 (tm-30) REVERT: a 166 MET cc_start: 0.6946 (mpp) cc_final: 0.6583 (mpp) REVERT: a 172 VAL cc_start: 0.9414 (t) cc_final: 0.9102 (p) REVERT: a 227 LEU cc_start: 0.9157 (mt) cc_final: 0.8943 (mp) REVERT: a 270 GLU cc_start: 0.9339 (tp30) cc_final: 0.8916 (pm20) REVERT: a 300 ASP cc_start: 0.9219 (t70) cc_final: 0.8848 (t70) REVERT: a 310 ARG cc_start: 0.9293 (mtm110) cc_final: 0.8989 (mmt180) REVERT: b 6 PHE cc_start: 0.8156 (t80) cc_final: 0.7611 (t80) REVERT: b 35 GLU cc_start: 0.8844 (tt0) cc_final: 0.8644 (tm-30) REVERT: b 52 MET cc_start: 0.8708 (mmt) cc_final: 0.8307 (mmm) REVERT: b 152 ARG cc_start: 0.8883 (mtp85) cc_final: 0.8509 (mtm-85) REVERT: b 274 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8999 (mt-10) REVERT: b 376 MET cc_start: 0.9116 (tmm) cc_final: 0.8870 (tmm) REVERT: c 6 PHE cc_start: 0.8985 (m-80) cc_final: 0.8756 (m-10) REVERT: c 35 GLU cc_start: 0.8387 (tp30) cc_final: 0.7869 (tp30) REVERT: c 68 MET cc_start: 0.7543 (mmm) cc_final: 0.6855 (mmm) REVERT: c 160 GLN cc_start: 0.8850 (tp40) cc_final: 0.8473 (tp40) REVERT: c 166 MET cc_start: 0.7682 (ptt) cc_final: 0.7390 (ppp) REVERT: c 339 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8030 (mm-30) REVERT: c 348 TRP cc_start: 0.8712 (m100) cc_final: 0.8248 (m-90) REVERT: d 3 ASP cc_start: 0.9377 (p0) cc_final: 0.9086 (p0) REVERT: d 6 PHE cc_start: 0.9330 (m-10) cc_final: 0.8829 (m-10) REVERT: d 65 MET cc_start: 0.8314 (ttp) cc_final: 0.8078 (ttp) REVERT: d 151 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8694 (p0) REVERT: d 166 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6400 (pmm) REVERT: d 316 PHE cc_start: 0.9215 (m-80) cc_final: 0.8925 (m-80) REVERT: d 342 GLU cc_start: 0.9086 (tp30) cc_final: 0.8668 (tp30) outliers start: 237 outliers final: 168 residues processed: 861 average time/residue: 0.2035 time to fit residues: 283.1431 Evaluate side-chains 845 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 659 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 408 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 439 HIS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 412 LYS Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 128 VAL Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 187 ASN Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain Q residue 113 THR Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 193 VAL Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 259 GLU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 246 GLN Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 107 LYS Chi-restraints excluded: chain S residue 239 LEU Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 242 VAL Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 5 HIS Chi-restraints excluded: chain a residue 48 GLN Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 122 CYS Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 203 ASP Chi-restraints excluded: chain a residue 317 THR Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 324 GLU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 369 CYS Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 124 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 151 ASN Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 254 VAL Chi-restraints excluded: chain b residue 377 VAL Chi-restraints excluded: chain b residue 398 LYS Chi-restraints excluded: chain b residue 408 LEU Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 99 ILE Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 133 VAL Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 203 ASP Chi-restraints excluded: chain c residue 205 ARG Chi-restraints excluded: chain c residue 215 THR Chi-restraints excluded: chain c residue 234 VAL Chi-restraints excluded: chain c residue 253 HIS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 318 VAL Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 368 LEU Chi-restraints excluded: chain c residue 379 CYS Chi-restraints excluded: chain c residue 398 LYS Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 166 MET Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 234 VAL Chi-restraints excluded: chain d residue 270 GLU Chi-restraints excluded: chain d residue 294 THR Chi-restraints excluded: chain d residue 310 ARG Chi-restraints excluded: chain d residue 326 THR Chi-restraints excluded: chain d residue 335 VAL Chi-restraints excluded: chain d residue 351 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 271 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 312 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 GLN ** a 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 155 HIS ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 160 GLN c 277 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.067082 restraints weight = 84051.340| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.85 r_work: 0.2861 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 1.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32752 Z= 0.182 Angle : 0.762 13.380 44700 Z= 0.382 Chirality : 0.049 0.360 5000 Planarity : 0.005 0.066 5720 Dihedral : 6.815 64.214 4772 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.09 % Allowed : 27.66 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.01 (0.13), residues: 4054 helix: 0.88 (0.24), residues: 456 sheet: -0.20 (0.16), residues: 996 loop : -1.19 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 236 TYR 0.032 0.002 TYR R 195 PHE 0.018 0.002 PHE b 316 TRP 0.031 0.002 TRP P 188 HIS 0.008 0.001 HIS P 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (32680) covalent geometry : angle 0.75258 / 0.38 (44542) SS BOND : bond 0.00365 / 0.24 ( 58) SS BOND : angle 1.37571 / 0.96 ( 116) hydrogen bonds : bond 0.03547 / 2.36 ( 1064) hydrogen bonds : angle 5.63842 / 3.84 ( 2625) link_BETA1-4 : bond 0.00902 / 0.45 ( 8) link_BETA1-4 : angle 2.67173 / 1.49 ( 24) link_NAG-ASN : bond 0.00629 / 0.36 ( 6) link_NAG-ASN : angle 4.50027 / 2.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 709 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8553 (tm-30) REVERT: A 132 MET cc_start: 0.8977 (tpp) cc_final: 0.8519 (tpp) REVERT: A 136 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8729 (m) REVERT: A 142 TRP cc_start: 0.8319 (m-10) cc_final: 0.8113 (m100) REVERT: A 303 LYS cc_start: 0.9142 (mtpp) cc_final: 0.8830 (ptmm) REVERT: A 344 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8014 (t0) REVERT: A 367 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8534 (tppt) REVERT: A 385 LYS cc_start: 0.9144 (pttt) cc_final: 0.8885 (pptt) REVERT: A 421 PHE cc_start: 0.9239 (t80) cc_final: 0.8899 (t80) REVERT: B 50 LYS cc_start: 0.9019 (tttt) cc_final: 0.8509 (tttt) REVERT: B 79 GLN cc_start: 0.9213 (tt0) cc_final: 0.8636 (tm-30) REVERT: B 88 MET cc_start: 0.9561 (mmm) cc_final: 0.9081 (mmm) REVERT: B 192 GLU cc_start: 0.5699 (tt0) cc_final: 0.4829 (tt0) REVERT: B 197 LYS cc_start: 0.9102 (mmtm) cc_final: 0.8807 (tppt) REVERT: B 221 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8553 (mtpp) REVERT: B 242 GLU cc_start: 0.8826 (mp0) cc_final: 0.7904 (mp0) REVERT: B 276 SER cc_start: 0.9496 (p) cc_final: 0.9090 (t) REVERT: B 293 GLU cc_start: 0.9516 (mp0) cc_final: 0.9239 (pm20) REVERT: B 421 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8730 (t80) REVERT: C 88 MET cc_start: 0.9452 (mmt) cc_final: 0.9124 (mmm) REVERT: C 132 MET cc_start: 0.8936 (tpt) cc_final: 0.8293 (tpp) REVERT: C 242 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8435 (tm-30) REVERT: C 246 ARG cc_start: 0.8897 (mtm110) cc_final: 0.8690 (mtm110) REVERT: C 299 ASP cc_start: 0.9243 (m-30) cc_final: 0.8990 (m-30) REVERT: C 301 GLU cc_start: 0.8932 (tp30) cc_final: 0.8553 (tp30) REVERT: C 385 LYS cc_start: 0.3985 (OUTLIER) cc_final: 0.1448 (mtmm) REVERT: C 386 ASP cc_start: 0.8952 (m-30) cc_final: 0.8639 (m-30) REVERT: C 410 TRP cc_start: 0.8991 (m-90) cc_final: 0.8301 (m-90) REVERT: C 423 VAL cc_start: 0.9456 (p) cc_final: 0.9131 (p) REVERT: C 427 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9176 (mp) REVERT: C 439 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6223 (t70) REVERT: D 152 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8586 (mp0) REVERT: D 197 LYS cc_start: 0.9137 (tppp) cc_final: 0.8808 (tppt) REVERT: D 213 ASP cc_start: 0.8988 (t0) cc_final: 0.8581 (t0) REVERT: D 290 ARG cc_start: 0.8851 (tpp80) cc_final: 0.8556 (tpp80) REVERT: D 306 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7649 (tm-30) REVERT: D 367 LYS cc_start: 0.9172 (ttpt) cc_final: 0.8926 (ttpp) REVERT: D 369 GLN cc_start: 0.9337 (mt0) cc_final: 0.9007 (mt0) REVERT: D 408 TRP cc_start: 0.8664 (OUTLIER) cc_final: 0.8412 (t60) REVERT: D 412 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8816 (ptmt) REVERT: P 116 ILE cc_start: 0.9717 (mp) cc_final: 0.9471 (pt) REVERT: P 132 ARG cc_start: 0.8965 (tpp80) cc_final: 0.8752 (tpp80) REVERT: P 135 LYS cc_start: 0.8859 (tttm) cc_final: 0.8458 (tmtt) REVERT: P 199 ARG cc_start: 0.8795 (tpp-160) cc_final: 0.8514 (tpp-160) REVERT: P 211 ASP cc_start: 0.9088 (m-30) cc_final: 0.8853 (m-30) REVERT: P 212 SER cc_start: 0.9533 (p) cc_final: 0.9109 (m) REVERT: P 222 ARG cc_start: 0.9423 (ptp90) cc_final: 0.8724 (ptp90) REVERT: P 246 GLN cc_start: 0.9497 (tp40) cc_final: 0.9172 (tm-30) REVERT: P 247 LYS cc_start: 0.9327 (tppt) cc_final: 0.9075 (mmtm) REVERT: Q 135 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7306 (ttpp) REVERT: Q 153 LEU cc_start: 0.9423 (mm) cc_final: 0.9054 (mm) REVERT: Q 154 LYS cc_start: 0.9416 (ptpp) cc_final: 0.8901 (ptpp) REVERT: Q 159 TYR cc_start: 0.9120 (m-80) cc_final: 0.8558 (m-80) REVERT: Q 161 LEU cc_start: 0.9069 (mt) cc_final: 0.8830 (tp) REVERT: Q 162 GLU cc_start: 0.8854 (pt0) cc_final: 0.8461 (pm20) REVERT: Q 176 GLN cc_start: 0.9292 (pp30) cc_final: 0.9050 (pp30) REVERT: Q 188 TRP cc_start: 0.8267 (t60) cc_final: 0.7799 (t60) REVERT: Q 211 ASP cc_start: 0.8895 (m-30) cc_final: 0.8463 (m-30) REVERT: R 104 MET cc_start: 0.5227 (mmp) cc_final: 0.4508 (mmt) REVERT: R 106 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6929 (mmt) REVERT: R 114 PHE cc_start: 0.9025 (m-80) cc_final: 0.8672 (m-80) REVERT: R 127 CYS cc_start: 0.8846 (t) cc_final: 0.8596 (m) REVERT: R 162 GLU cc_start: 0.8511 (mp0) cc_final: 0.8177 (mp0) REVERT: R 170 MET cc_start: 0.9584 (mtm) cc_final: 0.9140 (mtm) REVERT: R 176 GLN cc_start: 0.8809 (pm20) cc_final: 0.8445 (pm20) REVERT: R 186 TYR cc_start: 0.8792 (m-80) cc_final: 0.8523 (m-80) REVERT: R 199 ARG cc_start: 0.9113 (tpp-160) cc_final: 0.8888 (tpp-160) REVERT: R 204 ARG cc_start: 0.9205 (ptm-80) cc_final: 0.8962 (ptm-80) REVERT: R 251 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8371 (m) REVERT: S 104 MET cc_start: 0.4689 (OUTLIER) cc_final: 0.4136 (mpp) REVERT: S 132 ARG cc_start: 0.9146 (ttm110) cc_final: 0.8760 (tpp80) REVERT: S 133 VAL cc_start: 0.9467 (t) cc_final: 0.9211 (p) REVERT: S 135 LYS cc_start: 0.8795 (tttm) cc_final: 0.8316 (ptmm) REVERT: S 137 LEU cc_start: 0.9279 (tt) cc_final: 0.8959 (mt) REVERT: S 159 TYR cc_start: 0.8007 (m-80) cc_final: 0.7706 (m-80) REVERT: S 162 GLU cc_start: 0.8988 (tt0) cc_final: 0.8325 (tt0) REVERT: S 166 VAL cc_start: 0.9301 (OUTLIER) cc_final: 0.8989 (t) REVERT: S 194 GLN cc_start: 0.7927 (tp40) cc_final: 0.7674 (tp40) REVERT: S 214 ARG cc_start: 0.8826 (tpp-160) cc_final: 0.8336 (tpp80) REVERT: S 222 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8796 (mtm-85) REVERT: S 244 TRP cc_start: 0.9038 (m-90) cc_final: 0.8432 (m-90) REVERT: S 246 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8849 (tm-30) REVERT: S 247 LYS cc_start: 0.8946 (mttt) cc_final: 0.8688 (mmtp) REVERT: S 252 LYS cc_start: 0.9174 (ttmt) cc_final: 0.8928 (ttmt) REVERT: a 35 GLU cc_start: 0.7917 (tp30) cc_final: 0.7704 (tp30) REVERT: a 48 GLN cc_start: 0.8952 (mt0) cc_final: 0.8593 (tt0) REVERT: a 52 MET cc_start: 0.8706 (mmm) cc_final: 0.8378 (mmm) REVERT: a 65 MET cc_start: 0.8994 (tpp) cc_final: 0.8737 (tpp) REVERT: a 165 GLU cc_start: 0.8590 (pp20) cc_final: 0.8134 (tm-30) REVERT: a 172 VAL cc_start: 0.9429 (t) cc_final: 0.9137 (p) REVERT: a 227 LEU cc_start: 0.9163 (mt) cc_final: 0.8944 (mp) REVERT: a 270 GLU cc_start: 0.9341 (tp30) cc_final: 0.8954 (pm20) REVERT: a 300 ASP cc_start: 0.9166 (t70) cc_final: 0.8850 (t70) REVERT: a 310 ARG cc_start: 0.9260 (mtm110) cc_final: 0.8997 (mmt180) REVERT: a 409 LEU cc_start: 0.9027 (tt) cc_final: 0.8737 (mm) REVERT: b 6 PHE cc_start: 0.8156 (t80) cc_final: 0.7560 (t80) REVERT: b 52 MET cc_start: 0.8633 (mmt) cc_final: 0.8232 (mmm) REVERT: b 137 LYS cc_start: 0.9558 (mttm) cc_final: 0.9337 (mttp) REVERT: b 152 ARG cc_start: 0.8848 (mtp85) cc_final: 0.8500 (mtm-85) REVERT: b 165 GLU cc_start: 0.8130 (pm20) cc_final: 0.7886 (pm20) REVERT: b 246 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.6707 (t0) REVERT: b 274 GLU cc_start: 0.9207 (mt-10) cc_final: 0.9001 (mt-10) REVERT: b 371 CYS cc_start: 0.9309 (t) cc_final: 0.9025 (m) REVERT: c 35 GLU cc_start: 0.8288 (tp30) cc_final: 0.7860 (tp30) REVERT: c 52 MET cc_start: 0.9140 (mmt) cc_final: 0.8444 (mmt) REVERT: c 68 MET cc_start: 0.7594 (mmm) cc_final: 0.6835 (mmm) REVERT: c 160 GLN cc_start: 0.8840 (tp40) cc_final: 0.8463 (tp40) REVERT: c 166 MET cc_start: 0.7632 (ptt) cc_final: 0.7393 (ppp) REVERT: c 348 TRP cc_start: 0.8698 (m100) cc_final: 0.8287 (m-90) REVERT: d 3 ASP cc_start: 0.9379 (p0) cc_final: 0.9077 (p0) REVERT: d 6 PHE cc_start: 0.9356 (m-10) cc_final: 0.8901 (m-10) REVERT: d 65 MET cc_start: 0.8399 (ttp) cc_final: 0.8137 (ttp) REVERT: d 151 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8678 (p0) REVERT: d 166 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6464 (pmm) REVERT: d 272 LEU cc_start: 0.9245 (tp) cc_final: 0.8771 (mm) REVERT: d 316 PHE cc_start: 0.9233 (m-80) cc_final: 0.8924 (m-80) REVERT: d 342 GLU cc_start: 0.9054 (tp30) cc_final: 0.8655 (tp30) outliers start: 212 outliers final: 149 residues processed: 856 average time/residue: 0.2056 time to fit residues: 282.0164 Evaluate side-chains 839 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 673 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 408 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 439 HIS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 408 TRP Chi-restraints excluded: chain D residue 412 LYS Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain P residue 128 VAL Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 187 ASN Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 113 THR Chi-restraints excluded: chain Q residue 123 ASN Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 193 VAL Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain Q residue 259 GLU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 106 MET Chi-restraints excluded: chain S residue 107 LYS Chi-restraints excluded: chain S residue 154 LYS Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain S residue 222 ARG Chi-restraints excluded: chain S residue 239 LEU Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 122 CYS Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 155 HIS Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 175 HIS Chi-restraints excluded: chain a residue 317 THR Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 324 GLU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 369 CYS Chi-restraints excluded: chain a residue 399 LEU Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 124 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 151 ASN Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 246 ASP Chi-restraints excluded: chain b residue 254 VAL Chi-restraints excluded: chain b residue 318 VAL Chi-restraints excluded: chain b residue 398 LYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 99 ILE Chi-restraints excluded: chain c residue 133 VAL Chi-restraints excluded: chain c residue 203 ASP Chi-restraints excluded: chain c residue 205 ARG Chi-restraints excluded: chain c residue 215 THR Chi-restraints excluded: chain c residue 234 VAL Chi-restraints excluded: chain c residue 253 HIS Chi-restraints excluded: chain c residue 318 VAL Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 368 LEU Chi-restraints excluded: chain c residue 374 ILE Chi-restraints excluded: chain c residue 385 LEU Chi-restraints excluded: chain c residue 398 LYS Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 166 MET Chi-restraints excluded: chain d residue 270 GLU Chi-restraints excluded: chain d residue 326 THR Chi-restraints excluded: chain d residue 335 VAL Chi-restraints excluded: chain d residue 351 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 359 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 314 optimal weight: 0.0050 chunk 375 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 328 optimal weight: 20.0000 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 ASN ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 187 ASN ** a 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 GLN d 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.093465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.066809 restraints weight = 84104.694| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.85 r_work: 0.2851 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 1.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 32752 Z= 0.195 Angle : 0.787 12.156 44700 Z= 0.393 Chirality : 0.049 0.438 5000 Planarity : 0.005 0.068 5720 Dihedral : 6.764 62.321 4772 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.40 % Allowed : 28.32 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -0.98 (0.13), residues: 4054 helix: 0.93 (0.24), residues: 454 sheet: -0.32 (0.16), residues: 1099 loop : -1.13 (0.12), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 204 TYR 0.031 0.002 TYR P 195 PHE 0.025 0.002 PHE C 437 TRP 0.032 0.002 TRP P 188 HIS 0.038 0.001 HIS a 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (32680) covalent geometry : angle 0.77753 / 0.39 (44542) SS BOND : bond 0.00371 / 0.25 ( 58) SS BOND : angle 1.42144 / 0.97 ( 116) hydrogen bonds : bond 0.03566 / 2.38 ( 1064) hydrogen bonds : angle 5.66928 / 3.86 ( 2625) link_BETA1-4 : bond 0.00867 / 0.43 ( 8) link_BETA1-4 : angle 2.64808 / 1.48 ( 24) link_NAG-ASN : bond 0.00452 / 0.26 ( 6) link_NAG-ASN : angle 4.31821 / 2.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 708 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 132 MET cc_start: 0.9000 (tpp) cc_final: 0.8560 (tpp) REVERT: A 136 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8709 (m) REVERT: A 303 LYS cc_start: 0.9177 (mtpp) cc_final: 0.8878 (ptmm) REVERT: A 341 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9021 (ttmm) REVERT: A 367 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8643 (tppt) REVERT: A 385 LYS cc_start: 0.9164 (pttt) cc_final: 0.8929 (pptt) REVERT: A 421 PHE cc_start: 0.9247 (t80) cc_final: 0.8881 (t80) REVERT: B 50 LYS cc_start: 0.9051 (tttt) cc_final: 0.8572 (tttt) REVERT: B 88 MET cc_start: 0.9558 (mmm) cc_final: 0.9067 (mmm) REVERT: B 192 GLU cc_start: 0.5351 (tt0) cc_final: 0.4591 (tt0) REVERT: B 197 LYS cc_start: 0.9029 (mmtm) cc_final: 0.8722 (tppt) REVERT: B 221 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8558 (mtpp) REVERT: B 242 GLU cc_start: 0.8836 (mp0) cc_final: 0.7888 (mp0) REVERT: B 276 SER cc_start: 0.9483 (p) cc_final: 0.9175 (t) REVERT: B 293 GLU cc_start: 0.9499 (mp0) cc_final: 0.9214 (pm20) REVERT: B 421 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8730 (t80) REVERT: C 88 MET cc_start: 0.9456 (mmt) cc_final: 0.9180 (mmm) REVERT: C 132 MET cc_start: 0.8979 (tpt) cc_final: 0.8268 (tpp) REVERT: C 162 LEU cc_start: 0.9488 (tt) cc_final: 0.9083 (tp) REVERT: C 242 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8457 (tm-30) REVERT: C 299 ASP cc_start: 0.9265 (m-30) cc_final: 0.8915 (m-30) REVERT: C 301 GLU cc_start: 0.8932 (tp30) cc_final: 0.8546 (tp30) REVERT: C 385 LYS cc_start: 0.3997 (OUTLIER) cc_final: 0.1514 (mtmm) REVERT: C 386 ASP cc_start: 0.9029 (m-30) cc_final: 0.8772 (m-30) REVERT: C 410 TRP cc_start: 0.9035 (m-90) cc_final: 0.8287 (m-90) REVERT: C 423 VAL cc_start: 0.9469 (p) cc_final: 0.9144 (p) REVERT: C 427 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9208 (mp) REVERT: C 439 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6158 (t-170) REVERT: D 152 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8821 (mp0) REVERT: D 197 LYS cc_start: 0.9142 (tppp) cc_final: 0.8828 (tppt) REVERT: D 213 ASP cc_start: 0.8965 (t0) cc_final: 0.8542 (t0) REVERT: D 290 ARG cc_start: 0.8902 (tpp80) cc_final: 0.8604 (tpp80) REVERT: D 306 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8029 (tm-30) REVERT: D 367 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8972 (ttpp) REVERT: D 412 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8873 (ptmt) REVERT: D 421 PHE cc_start: 0.9136 (t80) cc_final: 0.8906 (t80) REVERT: P 116 ILE cc_start: 0.9591 (mp) cc_final: 0.9364 (pt) REVERT: P 117 MET cc_start: 0.8929 (mmm) cc_final: 0.8687 (tpp) REVERT: P 132 ARG cc_start: 0.9003 (tpp80) cc_final: 0.8380 (tpp80) REVERT: P 135 LYS cc_start: 0.8773 (tttm) cc_final: 0.8474 (tmtt) REVERT: P 187 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.7988 (p0) REVERT: P 199 ARG cc_start: 0.8802 (tpp-160) cc_final: 0.8542 (tpp-160) REVERT: P 200 PHE cc_start: 0.8865 (m-10) cc_final: 0.8408 (m-10) REVERT: P 211 ASP cc_start: 0.9079 (m-30) cc_final: 0.8851 (m-30) REVERT: P 212 SER cc_start: 0.9572 (p) cc_final: 0.9149 (m) REVERT: P 222 ARG cc_start: 0.9460 (ptp90) cc_final: 0.8599 (ptp90) REVERT: P 246 GLN cc_start: 0.9477 (tp40) cc_final: 0.9151 (tm-30) REVERT: P 247 LYS cc_start: 0.9390 (tppt) cc_final: 0.8915 (mmmm) REVERT: Q 117 MET cc_start: 0.9147 (mmm) cc_final: 0.8677 (mmm) REVERT: Q 135 LYS cc_start: 0.8023 (ttpp) cc_final: 0.7310 (ttpp) REVERT: Q 137 LEU cc_start: 0.9388 (mm) cc_final: 0.8769 (mm) REVERT: Q 144 ASP cc_start: 0.7871 (m-30) cc_final: 0.6867 (m-30) REVERT: Q 153 LEU cc_start: 0.9429 (mm) cc_final: 0.9024 (mm) REVERT: Q 154 LYS cc_start: 0.9410 (ptpp) cc_final: 0.8894 (ptpp) REVERT: Q 159 TYR cc_start: 0.9147 (m-80) cc_final: 0.8604 (m-80) REVERT: Q 161 LEU cc_start: 0.9052 (mt) cc_final: 0.8582 (tt) REVERT: Q 162 GLU cc_start: 0.8864 (pt0) cc_final: 0.8353 (pm20) REVERT: Q 170 MET cc_start: 0.9120 (pmm) cc_final: 0.8497 (pmm) REVERT: Q 176 GLN cc_start: 0.9199 (pp30) cc_final: 0.8850 (pp30) REVERT: Q 181 LYS cc_start: 0.9125 (ttmm) cc_final: 0.8906 (ttmm) REVERT: Q 188 TRP cc_start: 0.8201 (t60) cc_final: 0.7756 (t60) REVERT: Q 211 ASP cc_start: 0.9066 (m-30) cc_final: 0.8695 (m-30) REVERT: Q 217 LEU cc_start: 0.8916 (pp) cc_final: 0.8617 (pp) REVERT: R 104 MET cc_start: 0.5018 (mmp) cc_final: 0.4494 (mmt) REVERT: R 106 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7345 (mmt) REVERT: R 114 PHE cc_start: 0.9046 (m-80) cc_final: 0.8735 (m-10) REVERT: R 127 CYS cc_start: 0.8773 (t) cc_final: 0.8501 (m) REVERT: R 144 ASP cc_start: 0.8169 (p0) cc_final: 0.7902 (p0) REVERT: R 162 GLU cc_start: 0.8434 (mp0) cc_final: 0.8219 (mp0) REVERT: R 170 MET cc_start: 0.9587 (mtm) cc_final: 0.9247 (mtm) REVERT: R 176 GLN cc_start: 0.8847 (pm20) cc_final: 0.8431 (pm20) REVERT: R 204 ARG cc_start: 0.9200 (ptm-80) cc_final: 0.8953 (ptm-80) REVERT: R 251 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8413 (m) REVERT: S 104 MET cc_start: 0.4436 (OUTLIER) cc_final: 0.4048 (mpp) REVERT: S 132 ARG cc_start: 0.9070 (ttm110) cc_final: 0.8774 (tpp80) REVERT: S 135 LYS cc_start: 0.8761 (tttm) cc_final: 0.8255 (ptmm) REVERT: S 137 LEU cc_start: 0.9168 (tt) cc_final: 0.8816 (tp) REVERT: S 159 TYR cc_start: 0.7958 (m-80) cc_final: 0.7714 (m-80) REVERT: S 162 GLU cc_start: 0.8947 (tt0) cc_final: 0.8254 (tt0) REVERT: S 166 VAL cc_start: 0.9367 (OUTLIER) cc_final: 0.8875 (t) REVERT: S 214 ARG cc_start: 0.8869 (tpp-160) cc_final: 0.8352 (tpp80) REVERT: S 244 TRP cc_start: 0.9084 (m-90) cc_final: 0.8637 (m-90) REVERT: S 252 LYS cc_start: 0.9149 (ttmt) cc_final: 0.8900 (ttmt) REVERT: a 8 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7576 (pt0) REVERT: a 35 GLU cc_start: 0.7931 (tp30) cc_final: 0.7723 (tp30) REVERT: a 48 GLN cc_start: 0.8795 (mt0) cc_final: 0.8359 (tt0) REVERT: a 52 MET cc_start: 0.8711 (mmm) cc_final: 0.8353 (mmm) REVERT: a 65 MET cc_start: 0.9013 (tpp) cc_final: 0.8741 (tpp) REVERT: a 139 ARG cc_start: 0.8999 (mmt90) cc_final: 0.7264 (mtm110) REVERT: a 165 GLU cc_start: 0.8603 (pp20) cc_final: 0.8066 (tm-30) REVERT: a 166 MET cc_start: 0.8256 (mpp) cc_final: 0.7954 (mtm) REVERT: a 172 VAL cc_start: 0.9496 (t) cc_final: 0.9208 (p) REVERT: a 227 LEU cc_start: 0.9179 (mt) cc_final: 0.8954 (mp) REVERT: a 270 GLU cc_start: 0.9306 (tp30) cc_final: 0.8955 (pm20) REVERT: a 300 ASP cc_start: 0.9225 (t70) cc_final: 0.9014 (t70) REVERT: a 310 ARG cc_start: 0.9276 (mtm110) cc_final: 0.9016 (mmt180) REVERT: a 409 LEU cc_start: 0.9096 (tt) cc_final: 0.8865 (mm) REVERT: b 6 PHE cc_start: 0.8201 (t80) cc_final: 0.7579 (t80) REVERT: b 52 MET cc_start: 0.8635 (mmt) cc_final: 0.8237 (mmm) REVERT: b 152 ARG cc_start: 0.8850 (mtp85) cc_final: 0.8503 (mtm-85) REVERT: b 246 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.6657 (t0) REVERT: c 35 GLU cc_start: 0.8274 (tp30) cc_final: 0.7763 (tp30) REVERT: c 52 MET cc_start: 0.9122 (mmt) cc_final: 0.8336 (mmt) REVERT: c 68 MET cc_start: 0.7887 (mmm) cc_final: 0.6941 (mmm) REVERT: c 160 GLN cc_start: 0.8849 (tp40) cc_final: 0.8482 (tp40) REVERT: c 348 TRP cc_start: 0.8786 (m100) cc_final: 0.8387 (m-90) REVERT: d 3 ASP cc_start: 0.9361 (p0) cc_final: 0.9055 (p0) REVERT: d 6 PHE cc_start: 0.9365 (m-10) cc_final: 0.8850 (m-10) REVERT: d 151 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8783 (p0) REVERT: d 166 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6326 (pmm) REVERT: d 272 LEU cc_start: 0.9249 (tp) cc_final: 0.8746 (mm) REVERT: d 316 PHE cc_start: 0.9213 (m-80) cc_final: 0.8937 (m-80) REVERT: d 324 GLU cc_start: 0.8955 (tt0) cc_final: 0.8638 (tt0) REVERT: d 342 GLU cc_start: 0.9074 (tp30) cc_final: 0.8652 (tp30) REVERT: d 395 THR cc_start: 0.9344 (t) cc_final: 0.9068 (p) outliers start: 188 outliers final: 151 residues processed: 836 average time/residue: 0.2060 time to fit residues: 276.6936 Evaluate side-chains 845 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 678 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 408 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 439 HIS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 412 LYS Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain P residue 128 VAL Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 187 ASN Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 209 LYS Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 113 THR Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 193 VAL Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 106 MET Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain S residue 239 LEU Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 122 CYS Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 317 THR Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 324 GLU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 369 CYS Chi-restraints excluded: chain a residue 399 LEU Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 124 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 151 ASN Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 246 ASP Chi-restraints excluded: chain b residue 254 VAL Chi-restraints excluded: chain b residue 318 VAL Chi-restraints excluded: chain b residue 379 CYS Chi-restraints excluded: chain b residue 386 LEU Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 99 ILE Chi-restraints excluded: chain c residue 133 VAL Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 203 ASP Chi-restraints excluded: chain c residue 205 ARG Chi-restraints excluded: chain c residue 215 THR Chi-restraints excluded: chain c residue 234 VAL Chi-restraints excluded: chain c residue 253 HIS Chi-restraints excluded: chain c residue 318 VAL Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 368 LEU Chi-restraints excluded: chain c residue 374 ILE Chi-restraints excluded: chain c residue 398 LYS Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 166 MET Chi-restraints excluded: chain d residue 270 GLU Chi-restraints excluded: chain d residue 326 THR Chi-restraints excluded: chain d residue 335 VAL Chi-restraints excluded: chain d residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 188 optimal weight: 40.0000 chunk 339 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 367 optimal weight: 3.9990 chunk 311 optimal weight: 30.0000 chunk 281 optimal weight: 8.9990 chunk 346 optimal weight: 5.9990 chunk 321 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 197 ASN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.065419 restraints weight = 84710.063| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.85 r_work: 0.2820 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 1.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 32752 Z= 0.241 Angle : 0.816 14.656 44700 Z= 0.409 Chirality : 0.050 0.319 5000 Planarity : 0.006 0.066 5720 Dihedral : 6.944 62.183 4772 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 5.26 % Allowed : 28.60 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.07 (0.13), residues: 4054 helix: 0.74 (0.24), residues: 474 sheet: -0.45 (0.15), residues: 1118 loop : -1.14 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG P 204 TYR 0.034 0.002 TYR P 195 PHE 0.033 0.002 PHE c 316 TRP 0.034 0.002 TRP P 188 HIS 0.009 0.001 HIS P 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (32680) covalent geometry : angle 0.80779 / 0.41 (44542) SS BOND : bond 0.00437 / 0.30 ( 58) SS BOND : angle 1.55080 / 1.06 ( 116) hydrogen bonds : bond 0.03619 / 2.41 ( 1064) hydrogen bonds : angle 5.73283 / 3.89 ( 2625) link_BETA1-4 : bond 0.00814 / 0.40 ( 8) link_BETA1-4 : angle 2.65195 / 1.50 ( 24) link_NAG-ASN : bond 0.00829 / 0.58 ( 6) link_NAG-ASN : angle 3.89833 / 2.53 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 687 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8959 (tpp) cc_final: 0.8487 (tpp) REVERT: A 209 SER cc_start: 0.9196 (m) cc_final: 0.8773 (t) REVERT: A 223 GLN cc_start: 0.9650 (mm110) cc_final: 0.9345 (mm110) REVERT: A 303 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8891 (ptmm) REVERT: A 367 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8785 (tppt) REVERT: A 385 LYS cc_start: 0.9202 (pttt) cc_final: 0.8997 (pptt) REVERT: A 421 PHE cc_start: 0.9249 (t80) cc_final: 0.8827 (t80) REVERT: B 50 LYS cc_start: 0.9122 (tttt) cc_final: 0.8651 (tttt) REVERT: B 88 MET cc_start: 0.9529 (mmm) cc_final: 0.9229 (mmm) REVERT: B 103 MET cc_start: 0.9171 (tpp) cc_final: 0.8813 (tpt) REVERT: B 192 GLU cc_start: 0.5395 (tt0) cc_final: 0.4605 (tt0) REVERT: B 197 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8821 (tppt) REVERT: B 221 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8567 (mtpp) REVERT: B 242 GLU cc_start: 0.8849 (mp0) cc_final: 0.7932 (mp0) REVERT: B 276 SER cc_start: 0.9482 (p) cc_final: 0.9162 (t) REVERT: B 289 THR cc_start: 0.8951 (p) cc_final: 0.8647 (t) REVERT: B 293 GLU cc_start: 0.9543 (mp0) cc_final: 0.9266 (pm20) REVERT: B 367 LYS cc_start: 0.8577 (tptt) cc_final: 0.8334 (tptt) REVERT: B 421 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8624 (t80) REVERT: B 438 PHE cc_start: 0.8602 (m-10) cc_final: 0.8385 (m-10) REVERT: C 103 MET cc_start: 0.8913 (mmm) cc_final: 0.8663 (mmm) REVERT: C 132 MET cc_start: 0.8968 (tpt) cc_final: 0.8098 (tpp) REVERT: C 242 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8492 (tm-30) REVERT: C 299 ASP cc_start: 0.9274 (m-30) cc_final: 0.8869 (m-30) REVERT: C 301 GLU cc_start: 0.8971 (tp30) cc_final: 0.8575 (tp30) REVERT: C 385 LYS cc_start: 0.3973 (OUTLIER) cc_final: 0.1575 (mtmm) REVERT: C 386 ASP cc_start: 0.9076 (m-30) cc_final: 0.8811 (m-30) REVERT: C 410 TRP cc_start: 0.9025 (m-90) cc_final: 0.8285 (m-90) REVERT: C 423 VAL cc_start: 0.9419 (p) cc_final: 0.9101 (p) REVERT: C 427 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9182 (mp) REVERT: C 439 HIS cc_start: 0.6973 (OUTLIER) cc_final: 0.5955 (t-170) REVERT: D 197 LYS cc_start: 0.9190 (tppp) cc_final: 0.8870 (tppt) REVERT: D 213 ASP cc_start: 0.9000 (t0) cc_final: 0.8549 (t0) REVERT: D 290 ARG cc_start: 0.8904 (tpp80) cc_final: 0.8588 (tpp80) REVERT: D 306 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8039 (tm-30) REVERT: D 367 LYS cc_start: 0.9223 (ttpt) cc_final: 0.9000 (ttpp) REVERT: D 421 PHE cc_start: 0.9064 (t80) cc_final: 0.8743 (t80) REVERT: P 132 ARG cc_start: 0.8756 (tpp80) cc_final: 0.8139 (tpp80) REVERT: P 135 LYS cc_start: 0.8778 (tttm) cc_final: 0.8483 (tmtt) REVERT: P 181 LYS cc_start: 0.9069 (tmmt) cc_final: 0.8850 (tmmt) REVERT: P 187 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.7983 (p0) REVERT: P 199 ARG cc_start: 0.8811 (tpp-160) cc_final: 0.8549 (tpp-160) REVERT: P 212 SER cc_start: 0.9604 (p) cc_final: 0.9153 (m) REVERT: P 222 ARG cc_start: 0.9516 (ptp90) cc_final: 0.8885 (ptp90) REVERT: P 246 GLN cc_start: 0.9550 (tp40) cc_final: 0.9216 (tm-30) REVERT: P 247 LYS cc_start: 0.9477 (tppt) cc_final: 0.8974 (mmmm) REVERT: Q 117 MET cc_start: 0.9225 (mmm) cc_final: 0.8809 (mmm) REVERT: Q 135 LYS cc_start: 0.7916 (ttpp) cc_final: 0.7022 (ttpp) REVERT: Q 137 LEU cc_start: 0.9431 (mm) cc_final: 0.8787 (mm) REVERT: Q 144 ASP cc_start: 0.7780 (m-30) cc_final: 0.6763 (m-30) REVERT: Q 153 LEU cc_start: 0.9416 (mm) cc_final: 0.9023 (mm) REVERT: Q 154 LYS cc_start: 0.9396 (ptpp) cc_final: 0.8769 (ptpp) REVERT: Q 159 TYR cc_start: 0.9207 (m-80) cc_final: 0.8703 (m-80) REVERT: Q 161 LEU cc_start: 0.9062 (mt) cc_final: 0.8657 (tt) REVERT: Q 162 GLU cc_start: 0.8848 (pt0) cc_final: 0.8437 (pm20) REVERT: Q 166 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8391 (p) REVERT: Q 170 MET cc_start: 0.9180 (pmm) cc_final: 0.8533 (pmm) REVERT: Q 176 GLN cc_start: 0.9144 (pp30) cc_final: 0.8688 (pp30) REVERT: Q 188 TRP cc_start: 0.8258 (t60) cc_final: 0.7772 (t60) REVERT: Q 189 HIS cc_start: 0.9576 (t-170) cc_final: 0.9245 (t-170) REVERT: Q 194 GLN cc_start: 0.8178 (mp10) cc_final: 0.7824 (pm20) REVERT: Q 211 ASP cc_start: 0.8983 (m-30) cc_final: 0.8610 (m-30) REVERT: R 104 MET cc_start: 0.4739 (mmp) cc_final: 0.4192 (mmt) REVERT: R 106 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7384 (mmt) REVERT: R 127 CYS cc_start: 0.8763 (t) cc_final: 0.8554 (m) REVERT: R 170 MET cc_start: 0.9603 (mtm) cc_final: 0.9246 (mtm) REVERT: R 176 GLN cc_start: 0.8872 (pm20) cc_final: 0.8506 (pm20) REVERT: R 199 ARG cc_start: 0.9030 (tpp-160) cc_final: 0.8804 (tpt170) REVERT: R 204 ARG cc_start: 0.9208 (ptm-80) cc_final: 0.8952 (ptm-80) REVERT: R 251 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8390 (m) REVERT: S 104 MET cc_start: 0.4403 (OUTLIER) cc_final: 0.4027 (mpp) REVERT: S 132 ARG cc_start: 0.8992 (ttm110) cc_final: 0.8699 (tpp80) REVERT: S 135 LYS cc_start: 0.8784 (tttm) cc_final: 0.8442 (ptmm) REVERT: S 159 TYR cc_start: 0.8030 (m-80) cc_final: 0.7828 (m-80) REVERT: S 162 GLU cc_start: 0.8943 (tt0) cc_final: 0.8085 (tt0) REVERT: S 214 ARG cc_start: 0.8877 (tpp-160) cc_final: 0.8376 (tpp80) REVERT: S 222 ARG cc_start: 0.8943 (mtm-85) cc_final: 0.8309 (mtm-85) REVERT: S 244 TRP cc_start: 0.9161 (m-90) cc_final: 0.8932 (m-90) REVERT: S 252 LYS cc_start: 0.9168 (ttmt) cc_final: 0.8968 (ttmm) REVERT: a 35 GLU cc_start: 0.7981 (tp30) cc_final: 0.7776 (tp30) REVERT: a 48 GLN cc_start: 0.8762 (mt0) cc_final: 0.8380 (tt0) REVERT: a 52 MET cc_start: 0.8729 (mmm) cc_final: 0.8445 (mmm) REVERT: a 65 MET cc_start: 0.9028 (tpp) cc_final: 0.8618 (tpp) REVERT: a 139 ARG cc_start: 0.9136 (mmt90) cc_final: 0.7485 (mtm110) REVERT: a 165 GLU cc_start: 0.8606 (pp20) cc_final: 0.8097 (pp20) REVERT: a 166 MET cc_start: 0.8077 (mpp) cc_final: 0.7863 (mpp) REVERT: a 172 VAL cc_start: 0.9496 (t) cc_final: 0.9222 (p) REVERT: a 227 LEU cc_start: 0.9136 (mt) cc_final: 0.8916 (mp) REVERT: a 270 GLU cc_start: 0.9291 (tp30) cc_final: 0.8916 (pm20) REVERT: a 310 ARG cc_start: 0.9307 (mtm110) cc_final: 0.9029 (mmt180) REVERT: b 6 PHE cc_start: 0.8194 (t80) cc_final: 0.7750 (t80) REVERT: b 52 MET cc_start: 0.8577 (mmt) cc_final: 0.8201 (mmm) REVERT: b 152 ARG cc_start: 0.8908 (mtp85) cc_final: 0.8536 (mtm-85) REVERT: b 165 GLU cc_start: 0.8486 (pm20) cc_final: 0.8217 (pm20) REVERT: b 246 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.6556 (t0) REVERT: b 371 CYS cc_start: 0.9231 (t) cc_final: 0.9012 (m) REVERT: b 376 MET cc_start: 0.9052 (tmm) cc_final: 0.8795 (tmm) REVERT: c 35 GLU cc_start: 0.8305 (tp30) cc_final: 0.7739 (tp30) REVERT: c 68 MET cc_start: 0.8058 (mmm) cc_final: 0.7035 (mmm) REVERT: c 160 GLN cc_start: 0.8981 (tp40) cc_final: 0.8636 (tp40) REVERT: c 165 GLU cc_start: 0.8549 (pm20) cc_final: 0.8345 (pm20) REVERT: d 3 ASP cc_start: 0.9358 (p0) cc_final: 0.9062 (p0) REVERT: d 6 PHE cc_start: 0.9491 (m-10) cc_final: 0.8962 (m-10) REVERT: d 65 MET cc_start: 0.8603 (ttp) cc_final: 0.8389 (ttp) REVERT: d 166 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6344 (pmm) REVERT: d 272 LEU cc_start: 0.9253 (tp) cc_final: 0.8767 (mm) REVERT: d 342 GLU cc_start: 0.9104 (tp30) cc_final: 0.8655 (tp30) REVERT: d 394 ILE cc_start: 0.8244 (tp) cc_final: 0.8002 (tp) REVERT: d 398 LYS cc_start: 0.9355 (mtpt) cc_final: 0.8926 (ttpt) outliers start: 183 outliers final: 152 residues processed: 817 average time/residue: 0.2122 time to fit residues: 277.8951 Evaluate side-chains 839 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 675 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 408 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 439 HIS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain P residue 128 VAL Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 187 ASN Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 209 LYS Chi-restraints excluded: chain Q residue 113 THR Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain Q residue 193 VAL Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 259 GLU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 239 LEU Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 122 CYS Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 317 THR Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 324 GLU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 369 CYS Chi-restraints excluded: chain a residue 399 LEU Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 124 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 151 ASN Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 246 ASP Chi-restraints excluded: chain b residue 254 VAL Chi-restraints excluded: chain b residue 318 VAL Chi-restraints excluded: chain b residue 379 CYS Chi-restraints excluded: chain b residue 386 LEU Chi-restraints excluded: chain b residue 398 LYS Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 99 ILE Chi-restraints excluded: chain c residue 133 VAL Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 203 ASP Chi-restraints excluded: chain c residue 205 ARG Chi-restraints excluded: chain c residue 215 THR Chi-restraints excluded: chain c residue 234 VAL Chi-restraints excluded: chain c residue 253 HIS Chi-restraints excluded: chain c residue 318 VAL Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 368 LEU Chi-restraints excluded: chain c residue 385 LEU Chi-restraints excluded: chain c residue 398 LYS Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 166 MET Chi-restraints excluded: chain d residue 270 GLU Chi-restraints excluded: chain d residue 326 THR Chi-restraints excluded: chain d residue 335 VAL Chi-restraints excluded: chain d residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 383 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 330 optimal weight: 7.9990 chunk 372 optimal weight: 9.9990 chunk 242 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 155 HIS ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 ASN c 24 HIS c 69 ASN ** c 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.093790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.067278 restraints weight = 81126.504| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.73 r_work: 0.2821 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 1.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 32752 Z= 0.275 Angle : 0.841 11.963 44700 Z= 0.423 Chirality : 0.051 0.345 5000 Planarity : 0.006 0.084 5720 Dihedral : 7.055 61.450 4772 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.34 % Allowed : 28.58 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.11 (0.13), residues: 4054 helix: 0.67 (0.24), residues: 474 sheet: -0.42 (0.16), residues: 1086 loop : -1.18 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG P 204 TYR 0.025 0.002 TYR A 107 PHE 0.036 0.002 PHE C 399 TRP 0.034 0.002 TRP P 188 HIS 0.010 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.27 (32680) covalent geometry : angle 0.83207 / 0.42 (44542) SS BOND : bond 0.00490 / 0.33 ( 58) SS BOND : angle 1.70148 / 1.20 ( 116) hydrogen bonds : bond 0.03733 / 2.46 ( 1064) hydrogen bonds : angle 5.78199 / 3.93 ( 2625) link_BETA1-4 : bond 0.00776 / 0.38 ( 8) link_BETA1-4 : angle 2.65582 / 1.50 ( 24) link_NAG-ASN : bond 0.00746 / 0.49 ( 6) link_NAG-ASN : angle 3.94286 / 2.58 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10435.25 seconds wall clock time: 179 minutes 8.08 seconds (10748.08 seconds total)