Starting phenix.real_space_refine on Tue Aug 26 23:48:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h5s_0142/08_2025/6h5s_0142.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h5s_0142/08_2025/6h5s_0142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6h5s_0142/08_2025/6h5s_0142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h5s_0142/08_2025/6h5s_0142.map" model { file = "/net/cci-nas-00/data/ceres_data/6h5s_0142/08_2025/6h5s_0142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h5s_0142/08_2025/6h5s_0142.cif" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 180 5.16 5 C 28185 2.51 5 N 7740 2.21 5 O 8520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44700 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Restraints were copied for chains: A, D, G, I, K, M, O, Q, S, U, W, Y, 0, 2, B, F, H, J, L, N, P, R, T, V, X, Z, 1, 3 Time building chain proxies: 3.24, per 1000 atoms: 0.07 Number of scatterers: 44700 At special positions: 0 Unit cell: (204, 204.816, 129.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 75 15.00 O 8520 8.00 N 7740 7.00 C 28185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10020 Finding SS restraints... Secondary structure from input PDB file: 330 helices and 15 sheets defined 61.7% alpha, 4.4% beta 0 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG C 6 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 159 through 172 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS C 180 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 181 " --> pdb=" O LEU C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 185 through 187 No H-bonds generated for 'chain 'C' and resid 185 through 187' Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 195 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE C 237 " --> pdb=" O MET C 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY C 291 " --> pdb=" O HIS C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU C 299 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 304 " --> pdb=" O MET C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR C 309 " --> pdb=" O MET C 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 310 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Proline residue: C 311 - end of helix No H-bonds generated for 'chain 'C' and resid 306 through 313' Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN C 321 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN C 322 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER C 328 " --> pdb=" O SER C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 369 " --> pdb=" O GLY C 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 159 through 172 Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR A 309 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 310 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Proline residue: A 311 - end of helix No H-bonds generated for 'chain 'A' and resid 306 through 313' Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN A 321 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 322 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER A 334 " --> pdb=" O PRO A 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 159 through 172 Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS D 180 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 181 " --> pdb=" O LEU D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 181' Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'D' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 226 Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY D 291 " --> pdb=" O HIS D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 304 " --> pdb=" O MET D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR D 309 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 310 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Proline residue: D 311 - end of helix No H-bonds generated for 'chain 'D' and resid 306 through 313' Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN D 321 " --> pdb=" O ASN D 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN D 322 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER D 328 " --> pdb=" O SER D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER D 334 " --> pdb=" O PRO D 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG G 6 " --> pdb=" O ALA G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN G 89 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG G 90 " --> pdb=" O GLN G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 159 through 172 Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS G 180 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA G 181 " --> pdb=" O LEU G 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 177 through 181' Processing helix chain 'G' and resid 185 through 187 No H-bonds generated for 'chain 'G' and resid 185 through 187' Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG G 194 " --> pdb=" O ASP G 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG G 195 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 226 Processing helix chain 'G' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG G 242 " --> pdb=" O LEU G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 258 Processing helix chain 'G' and resid 259 through 261 No H-bonds generated for 'chain 'G' and resid 259 through 261' Processing helix chain 'G' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY G 291 " --> pdb=" O HIS G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU G 299 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN G 304 " --> pdb=" O MET G 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 313 removed outlier: 4.167A pdb=" N THR G 309 " --> pdb=" O MET G 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 310 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Proline residue: G 311 - end of helix No H-bonds generated for 'chain 'G' and resid 306 through 313' Processing helix chain 'G' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN G 321 " --> pdb=" O ASN G 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN G 322 " --> pdb=" O SER G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER G 328 " --> pdb=" O SER G 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 325 through 328' Processing helix chain 'G' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER G 334 " --> pdb=" O PRO G 330 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU G 342 " --> pdb=" O GLY G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 Processing helix chain 'G' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE G 362 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL G 369 " --> pdb=" O GLY G 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG I 48 " --> pdb=" O SER I 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG I 57 " --> pdb=" O ASP I 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 84 through 92 removed outlier: 3.681A pdb=" N GLN I 89 " --> pdb=" O GLY I 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG I 90 " --> pdb=" O GLN I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 159 through 172 Processing helix chain 'I' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS I 180 " --> pdb=" O LEU I 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA I 181 " --> pdb=" O LEU I 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 177 through 181' Processing helix chain 'I' and resid 185 through 187 No H-bonds generated for 'chain 'I' and resid 185 through 187' Processing helix chain 'I' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU I 193 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG I 194 " --> pdb=" O ASP I 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG I 195 " --> pdb=" O SER I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 226 Processing helix chain 'I' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG I 242 " --> pdb=" O LEU I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 258 Processing helix chain 'I' and resid 259 through 261 No H-bonds generated for 'chain 'I' and resid 259 through 261' Processing helix chain 'I' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU I 271 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR I 272 " --> pdb=" O SER I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY I 291 " --> pdb=" O HIS I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU I 299 " --> pdb=" O THR I 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN I 304 " --> pdb=" O MET I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR I 309 " --> pdb=" O MET I 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 310 " --> pdb=" O GLY I 307 " (cutoff:3.500A) Proline residue: I 311 - end of helix No H-bonds generated for 'chain 'I' and resid 306 through 313' Processing helix chain 'I' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN I 321 " --> pdb=" O ASN I 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN I 322 " --> pdb=" O SER I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER I 328 " --> pdb=" O SER I 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 325 through 328' Processing helix chain 'I' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER I 334 " --> pdb=" O PRO I 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU I 342 " --> pdb=" O GLY I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 350 Processing helix chain 'I' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE I 362 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL I 369 " --> pdb=" O GLY I 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG K 6 " --> pdb=" O ALA K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN K 89 " --> pdb=" O GLY K 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG K 90 " --> pdb=" O GLN K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 132 Processing helix chain 'K' and resid 159 through 172 Processing helix chain 'K' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS K 180 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA K 181 " --> pdb=" O LEU K 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 177 through 181' Processing helix chain 'K' and resid 185 through 187 No H-bonds generated for 'chain 'K' and resid 185 through 187' Processing helix chain 'K' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU K 193 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 194 " --> pdb=" O ASP K 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 226 Processing helix chain 'K' and resid 227 through 242 removed outlier: 3.512A pdb=" N ILE K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG K 242 " --> pdb=" O LEU K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 258 Processing helix chain 'K' and resid 259 through 261 No H-bonds generated for 'chain 'K' and resid 259 through 261' Processing helix chain 'K' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU K 271 " --> pdb=" O ALA K 267 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY K 291 " --> pdb=" O HIS K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU K 299 " --> pdb=" O THR K 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN K 304 " --> pdb=" O MET K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR K 309 " --> pdb=" O MET K 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA K 310 " --> pdb=" O GLY K 307 " (cutoff:3.500A) Proline residue: K 311 - end of helix No H-bonds generated for 'chain 'K' and resid 306 through 313' Processing helix chain 'K' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN K 321 " --> pdb=" O ASN K 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN K 322 " --> pdb=" O SER K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER K 328 " --> pdb=" O SER K 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 325 through 328' Processing helix chain 'K' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER K 334 " --> pdb=" O PRO K 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU K 342 " --> pdb=" O GLY K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 350 Processing helix chain 'K' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE K 362 " --> pdb=" O ASP K 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL K 369 " --> pdb=" O GLY K 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG M 6 " --> pdb=" O ALA M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG M 48 " --> pdb=" O SER M 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU M 58 " --> pdb=" O ARG M 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 77 Processing helix chain 'M' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN M 89 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG M 90 " --> pdb=" O GLN M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 159 through 172 Processing helix chain 'M' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS M 180 " --> pdb=" O LEU M 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA M 181 " --> pdb=" O LEU M 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 177 through 181' Processing helix chain 'M' and resid 185 through 187 No H-bonds generated for 'chain 'M' and resid 185 through 187' Processing helix chain 'M' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU M 193 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG M 194 " --> pdb=" O ASP M 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG M 195 " --> pdb=" O SER M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 226 Processing helix chain 'M' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE M 237 " --> pdb=" O MET M 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG M 242 " --> pdb=" O LEU M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 258 Processing helix chain 'M' and resid 259 through 261 No H-bonds generated for 'chain 'M' and resid 259 through 261' Processing helix chain 'M' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU M 271 " --> pdb=" O ALA M 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR M 272 " --> pdb=" O SER M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY M 291 " --> pdb=" O HIS M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU M 299 " --> pdb=" O THR M 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN M 304 " --> pdb=" O MET M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR M 309 " --> pdb=" O MET M 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA M 310 " --> pdb=" O GLY M 307 " (cutoff:3.500A) Proline residue: M 311 - end of helix No H-bonds generated for 'chain 'M' and resid 306 through 313' Processing helix chain 'M' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN M 321 " --> pdb=" O ASN M 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN M 322 " --> pdb=" O SER M 319 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER M 328 " --> pdb=" O SER M 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 325 through 328' Processing helix chain 'M' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER M 334 " --> pdb=" O PRO M 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU M 342 " --> pdb=" O GLY M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 350 Processing helix chain 'M' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE M 362 " --> pdb=" O ASP M 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL M 369 " --> pdb=" O GLY M 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG O 6 " --> pdb=" O ALA O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG O 48 " --> pdb=" O SER O 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG O 57 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU O 58 " --> pdb=" O ARG O 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE O 59 " --> pdb=" O LEU O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 77 Processing helix chain 'O' and resid 84 through 92 removed outlier: 3.681A pdb=" N GLN O 89 " --> pdb=" O GLY O 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG O 90 " --> pdb=" O GLN O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 Processing helix chain 'O' and resid 159 through 172 Processing helix chain 'O' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS O 180 " --> pdb=" O LEU O 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA O 181 " --> pdb=" O LEU O 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 177 through 181' Processing helix chain 'O' and resid 185 through 187 No H-bonds generated for 'chain 'O' and resid 185 through 187' Processing helix chain 'O' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU O 193 " --> pdb=" O ALA O 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG O 194 " --> pdb=" O ASP O 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG O 195 " --> pdb=" O SER O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 226 Processing helix chain 'O' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE O 237 " --> pdb=" O MET O 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG O 242 " --> pdb=" O LEU O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 258 Processing helix chain 'O' and resid 259 through 261 No H-bonds generated for 'chain 'O' and resid 259 through 261' Processing helix chain 'O' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU O 271 " --> pdb=" O ALA O 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR O 272 " --> pdb=" O SER O 268 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU O 299 " --> pdb=" O THR O 295 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN O 304 " --> pdb=" O MET O 300 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR O 309 " --> pdb=" O MET O 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA O 310 " --> pdb=" O GLY O 307 " (cutoff:3.500A) Proline residue: O 311 - end of helix No H-bonds generated for 'chain 'O' and resid 306 through 313' Processing helix chain 'O' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN O 321 " --> pdb=" O ASN O 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN O 322 " --> pdb=" O SER O 319 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER O 328 " --> pdb=" O SER O 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 325 through 328' Processing helix chain 'O' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER O 334 " --> pdb=" O PRO O 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU O 342 " --> pdb=" O GLY O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 345 through 350 Processing helix chain 'O' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE O 362 " --> pdb=" O ASP O 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL O 369 " --> pdb=" O GLY O 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG Q 6 " --> pdb=" O ALA Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG Q 48 " --> pdb=" O SER Q 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG Q 57 " --> pdb=" O ASP Q 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU Q 58 " --> pdb=" O ARG Q 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE Q 59 " --> pdb=" O LEU Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 77 Processing helix chain 'Q' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN Q 89 " --> pdb=" O GLY Q 85 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG Q 90 " --> pdb=" O GLN Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 132 Processing helix chain 'Q' and resid 159 through 172 Processing helix chain 'Q' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS Q 180 " --> pdb=" O LEU Q 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA Q 181 " --> pdb=" O LEU Q 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 177 through 181' Processing helix chain 'Q' and resid 185 through 187 No H-bonds generated for 'chain 'Q' and resid 185 through 187' Processing helix chain 'Q' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU Q 193 " --> pdb=" O ALA Q 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Q 194 " --> pdb=" O ASP Q 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Q 195 " --> pdb=" O SER Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 226 Processing helix chain 'Q' and resid 227 through 242 removed outlier: 3.510A pdb=" N ILE Q 237 " --> pdb=" O MET Q 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG Q 242 " --> pdb=" O LEU Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 258 Processing helix chain 'Q' and resid 259 through 261 No H-bonds generated for 'chain 'Q' and resid 259 through 261' Processing helix chain 'Q' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU Q 271 " --> pdb=" O ALA Q 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR Q 272 " --> pdb=" O SER Q 268 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY Q 291 " --> pdb=" O HIS Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU Q 299 " --> pdb=" O THR Q 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN Q 304 " --> pdb=" O MET Q 300 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR Q 309 " --> pdb=" O MET Q 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA Q 310 " --> pdb=" O GLY Q 307 " (cutoff:3.500A) Proline residue: Q 311 - end of helix No H-bonds generated for 'chain 'Q' and resid 306 through 313' Processing helix chain 'Q' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN Q 321 " --> pdb=" O ASN Q 318 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN Q 322 " --> pdb=" O SER Q 319 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER Q 328 " --> pdb=" O SER Q 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 325 through 328' Processing helix chain 'Q' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER Q 334 " --> pdb=" O PRO Q 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU Q 342 " --> pdb=" O GLY Q 338 " (cutoff:3.500A) Processing helix chain 'Q' and resid 345 through 350 Processing helix chain 'Q' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE Q 362 " --> pdb=" O ASP Q 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL Q 369 " --> pdb=" O GLY Q 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG S 6 " --> pdb=" O ALA S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG S 48 " --> pdb=" O SER S 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG S 57 " --> pdb=" O ASP S 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU S 58 " --> pdb=" O ARG S 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE S 59 " --> pdb=" O LEU S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 77 Processing helix chain 'S' and resid 84 through 92 removed outlier: 3.681A pdb=" N GLN S 89 " --> pdb=" O GLY S 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG S 90 " --> pdb=" O GLN S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 132 Processing helix chain 'S' and resid 159 through 172 Processing helix chain 'S' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS S 180 " --> pdb=" O LEU S 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA S 181 " --> pdb=" O LEU S 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 177 through 181' Processing helix chain 'S' and resid 185 through 187 No H-bonds generated for 'chain 'S' and resid 185 through 187' Processing helix chain 'S' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU S 193 " --> pdb=" O ALA S 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG S 194 " --> pdb=" O ASP S 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG S 195 " --> pdb=" O SER S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 226 Processing helix chain 'S' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE S 237 " --> pdb=" O MET S 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG S 242 " --> pdb=" O LEU S 238 " (cutoff:3.500A) Processing helix chain 'S' and resid 248 through 258 Processing helix chain 'S' and resid 259 through 261 No H-bonds generated for 'chain 'S' and resid 259 through 261' Processing helix chain 'S' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU S 271 " --> pdb=" O ALA S 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR S 272 " --> pdb=" O SER S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY S 291 " --> pdb=" O HIS S 287 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU S 299 " --> pdb=" O THR S 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN S 304 " --> pdb=" O MET S 300 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR S 309 " --> pdb=" O MET S 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA S 310 " --> pdb=" O GLY S 307 " (cutoff:3.500A) Proline residue: S 311 - end of helix No H-bonds generated for 'chain 'S' and resid 306 through 313' Processing helix chain 'S' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN S 321 " --> pdb=" O ASN S 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN S 322 " --> pdb=" O SER S 319 " (cutoff:3.500A) Processing helix chain 'S' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER S 328 " --> pdb=" O SER S 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 325 through 328' Processing helix chain 'S' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER S 334 " --> pdb=" O PRO S 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU S 342 " --> pdb=" O GLY S 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 345 through 350 Processing helix chain 'S' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE S 362 " --> pdb=" O ASP S 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL S 369 " --> pdb=" O GLY S 365 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG U 6 " --> pdb=" O ALA U 2 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG U 48 " --> pdb=" O SER U 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE U 59 " --> pdb=" O LEU U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 77 Processing helix chain 'U' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN U 89 " --> pdb=" O GLY U 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG U 90 " --> pdb=" O GLN U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 132 Processing helix chain 'U' and resid 159 through 172 Processing helix chain 'U' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS U 180 " --> pdb=" O LEU U 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA U 181 " --> pdb=" O LEU U 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 177 through 181' Processing helix chain 'U' and resid 185 through 187 No H-bonds generated for 'chain 'U' and resid 185 through 187' Processing helix chain 'U' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU U 193 " --> pdb=" O ALA U 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG U 194 " --> pdb=" O ASP U 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG U 195 " --> pdb=" O SER U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 226 Processing helix chain 'U' and resid 227 through 242 removed outlier: 3.512A pdb=" N ILE U 237 " --> pdb=" O MET U 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG U 242 " --> pdb=" O LEU U 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 248 through 258 Processing helix chain 'U' and resid 259 through 261 No H-bonds generated for 'chain 'U' and resid 259 through 261' Processing helix chain 'U' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU U 271 " --> pdb=" O ALA U 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR U 272 " --> pdb=" O SER U 268 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY U 291 " --> pdb=" O HIS U 287 " (cutoff:3.500A) Processing helix chain 'U' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU U 299 " --> pdb=" O THR U 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN U 304 " --> pdb=" O MET U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR U 309 " --> pdb=" O MET U 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA U 310 " --> pdb=" O GLY U 307 " (cutoff:3.500A) Proline residue: U 311 - end of helix No H-bonds generated for 'chain 'U' and resid 306 through 313' Processing helix chain 'U' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN U 321 " --> pdb=" O ASN U 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN U 322 " --> pdb=" O SER U 319 " (cutoff:3.500A) Processing helix chain 'U' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER U 328 " --> pdb=" O SER U 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 325 through 328' Processing helix chain 'U' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER U 334 " --> pdb=" O PRO U 330 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU U 342 " --> pdb=" O GLY U 338 " (cutoff:3.500A) Processing helix chain 'U' and resid 345 through 350 Processing helix chain 'U' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE U 362 " --> pdb=" O ASP U 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL U 369 " --> pdb=" O GLY U 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG W 6 " --> pdb=" O ALA W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG W 48 " --> pdb=" O SER W 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG W 57 " --> pdb=" O ASP W 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU W 58 " --> pdb=" O ARG W 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE W 59 " --> pdb=" O LEU W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'W' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN W 89 " --> pdb=" O GLY W 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG W 90 " --> pdb=" O GLN W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 132 Processing helix chain 'W' and resid 159 through 172 Processing helix chain 'W' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS W 180 " --> pdb=" O LEU W 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA W 181 " --> pdb=" O LEU W 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 177 through 181' Processing helix chain 'W' and resid 185 through 187 No H-bonds generated for 'chain 'W' and resid 185 through 187' Processing helix chain 'W' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU W 193 " --> pdb=" O ALA W 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG W 194 " --> pdb=" O ASP W 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG W 195 " --> pdb=" O SER W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 226 Processing helix chain 'W' and resid 227 through 242 removed outlier: 3.512A pdb=" N ILE W 237 " --> pdb=" O MET W 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG W 242 " --> pdb=" O LEU W 238 " (cutoff:3.500A) Processing helix chain 'W' and resid 248 through 258 Processing helix chain 'W' and resid 259 through 261 No H-bonds generated for 'chain 'W' and resid 259 through 261' Processing helix chain 'W' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU W 271 " --> pdb=" O ALA W 267 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR W 272 " --> pdb=" O SER W 268 " (cutoff:3.500A) Processing helix chain 'W' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY W 291 " --> pdb=" O HIS W 287 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU W 299 " --> pdb=" O THR W 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN W 304 " --> pdb=" O MET W 300 " (cutoff:3.500A) Processing helix chain 'W' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR W 309 " --> pdb=" O MET W 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA W 310 " --> pdb=" O GLY W 307 " (cutoff:3.500A) Proline residue: W 311 - end of helix No H-bonds generated for 'chain 'W' and resid 306 through 313' Processing helix chain 'W' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN W 321 " --> pdb=" O ASN W 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN W 322 " --> pdb=" O SER W 319 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER W 328 " --> pdb=" O SER W 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 325 through 328' Processing helix chain 'W' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER W 334 " --> pdb=" O PRO W 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU W 342 " --> pdb=" O GLY W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 345 through 350 Processing helix chain 'W' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE W 362 " --> pdb=" O ASP W 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL W 369 " --> pdb=" O GLY W 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG Y 6 " --> pdb=" O ALA Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG Y 48 " --> pdb=" O SER Y 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG Y 57 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU Y 58 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE Y 59 " --> pdb=" O LEU Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 77 Processing helix chain 'Y' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN Y 89 " --> pdb=" O GLY Y 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG Y 90 " --> pdb=" O GLN Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 127 through 132 Processing helix chain 'Y' and resid 159 through 172 Processing helix chain 'Y' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS Y 180 " --> pdb=" O LEU Y 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA Y 181 " --> pdb=" O LEU Y 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 177 through 181' Processing helix chain 'Y' and resid 185 through 187 No H-bonds generated for 'chain 'Y' and resid 185 through 187' Processing helix chain 'Y' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU Y 193 " --> pdb=" O ALA Y 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Y 194 " --> pdb=" O ASP Y 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Y 195 " --> pdb=" O SER Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 226 Processing helix chain 'Y' and resid 227 through 242 removed outlier: 3.512A pdb=" N ILE Y 237 " --> pdb=" O MET Y 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG Y 242 " --> pdb=" O LEU Y 238 " (cutoff:3.500A) Processing helix chain 'Y' and resid 248 through 258 Processing helix chain 'Y' and resid 259 through 261 No H-bonds generated for 'chain 'Y' and resid 259 through 261' Processing helix chain 'Y' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU Y 271 " --> pdb=" O ALA Y 267 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR Y 272 " --> pdb=" O SER Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY Y 291 " --> pdb=" O HIS Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU Y 299 " --> pdb=" O THR Y 295 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN Y 304 " --> pdb=" O MET Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR Y 309 " --> pdb=" O MET Y 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA Y 310 " --> pdb=" O GLY Y 307 " (cutoff:3.500A) Proline residue: Y 311 - end of helix No H-bonds generated for 'chain 'Y' and resid 306 through 313' Processing helix chain 'Y' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN Y 321 " --> pdb=" O ASN Y 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN Y 322 " --> pdb=" O SER Y 319 " (cutoff:3.500A) Processing helix chain 'Y' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER Y 328 " --> pdb=" O SER Y 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 325 through 328' Processing helix chain 'Y' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER Y 334 " --> pdb=" O PRO Y 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU Y 342 " --> pdb=" O GLY Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 345 through 350 Processing helix chain 'Y' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE Y 362 " --> pdb=" O ASP Y 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL Y 369 " --> pdb=" O GLY Y 365 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG 0 6 " --> pdb=" O ALA 0 2 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG 0 48 " --> pdb=" O SER 0 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG 0 57 " --> pdb=" O ASP 0 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 0 58 " --> pdb=" O ARG 0 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE 0 59 " --> pdb=" O LEU 0 55 " (cutoff:3.500A) Processing helix chain '0' and resid 65 through 77 Processing helix chain '0' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN 0 89 " --> pdb=" O GLY 0 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG 0 90 " --> pdb=" O GLN 0 86 " (cutoff:3.500A) Processing helix chain '0' and resid 127 through 132 Processing helix chain '0' and resid 159 through 172 Processing helix chain '0' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS 0 180 " --> pdb=" O LEU 0 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA 0 181 " --> pdb=" O LEU 0 178 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 177 through 181' Processing helix chain '0' and resid 185 through 187 No H-bonds generated for 'chain '0' and resid 185 through 187' Processing helix chain '0' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU 0 193 " --> pdb=" O ALA 0 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG 0 194 " --> pdb=" O ASP 0 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG 0 195 " --> pdb=" O SER 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 212 through 226 Processing helix chain '0' and resid 227 through 242 removed outlier: 3.510A pdb=" N ILE 0 237 " --> pdb=" O MET 0 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG 0 242 " --> pdb=" O LEU 0 238 " (cutoff:3.500A) Processing helix chain '0' and resid 248 through 258 Processing helix chain '0' and resid 259 through 261 No H-bonds generated for 'chain '0' and resid 259 through 261' Processing helix chain '0' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU 0 271 " --> pdb=" O ALA 0 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR 0 272 " --> pdb=" O SER 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY 0 291 " --> pdb=" O HIS 0 287 " (cutoff:3.500A) Processing helix chain '0' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU 0 299 " --> pdb=" O THR 0 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN 0 304 " --> pdb=" O MET 0 300 " (cutoff:3.500A) Processing helix chain '0' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR 0 309 " --> pdb=" O MET 0 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA 0 310 " --> pdb=" O GLY 0 307 " (cutoff:3.500A) Proline residue: 0 311 - end of helix No H-bonds generated for 'chain '0' and resid 306 through 313' Processing helix chain '0' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN 0 321 " --> pdb=" O ASN 0 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN 0 322 " --> pdb=" O SER 0 319 " (cutoff:3.500A) Processing helix chain '0' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER 0 328 " --> pdb=" O SER 0 325 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 325 through 328' Processing helix chain '0' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER 0 334 " --> pdb=" O PRO 0 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU 0 342 " --> pdb=" O GLY 0 338 " (cutoff:3.500A) Processing helix chain '0' and resid 345 through 350 Processing helix chain '0' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE 0 362 " --> pdb=" O ASP 0 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL 0 369 " --> pdb=" O GLY 0 365 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG 2 6 " --> pdb=" O ALA 2 2 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG 2 48 " --> pdb=" O SER 2 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG 2 57 " --> pdb=" O ASP 2 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU 2 58 " --> pdb=" O ARG 2 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE 2 59 " --> pdb=" O LEU 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 77 Processing helix chain '2' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN 2 89 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG 2 90 " --> pdb=" O GLN 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 127 through 132 Processing helix chain '2' and resid 159 through 172 Processing helix chain '2' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS 2 180 " --> pdb=" O LEU 2 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA 2 181 " --> pdb=" O LEU 2 178 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 177 through 181' Processing helix chain '2' and resid 185 through 187 No H-bonds generated for 'chain '2' and resid 185 through 187' Processing helix chain '2' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU 2 193 " --> pdb=" O ALA 2 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG 2 194 " --> pdb=" O ASP 2 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG 2 195 " --> pdb=" O SER 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 226 Processing helix chain '2' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE 2 237 " --> pdb=" O MET 2 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG 2 242 " --> pdb=" O LEU 2 238 " (cutoff:3.500A) Processing helix chain '2' and resid 248 through 258 Processing helix chain '2' and resid 259 through 261 No H-bonds generated for 'chain '2' and resid 259 through 261' Processing helix chain '2' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU 2 271 " --> pdb=" O ALA 2 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR 2 272 " --> pdb=" O SER 2 268 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY 2 291 " --> pdb=" O HIS 2 287 " (cutoff:3.500A) Processing helix chain '2' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU 2 299 " --> pdb=" O THR 2 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN 2 304 " --> pdb=" O MET 2 300 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 313 removed outlier: 4.165A pdb=" N THR 2 309 " --> pdb=" O MET 2 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA 2 310 " --> pdb=" O GLY 2 307 " (cutoff:3.500A) Proline residue: 2 311 - end of helix No H-bonds generated for 'chain '2' and resid 306 through 313' Processing helix chain '2' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN 2 321 " --> pdb=" O ASN 2 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN 2 322 " --> pdb=" O SER 2 319 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER 2 328 " --> pdb=" O SER 2 325 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 325 through 328' Processing helix chain '2' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER 2 334 " --> pdb=" O PRO 2 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU 2 342 " --> pdb=" O GLY 2 338 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 350 Processing helix chain '2' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE 2 362 " --> pdb=" O ASP 2 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL 2 369 " --> pdb=" O GLY 2 365 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'C' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE C 35 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 102 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 37 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 104 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 39 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN C 106 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE A 35 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 102 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 37 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 39 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN A 106 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'D' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE D 35 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU D 102 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL D 37 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL D 104 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE D 39 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN D 106 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'G' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE G 35 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU G 102 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL G 37 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL G 104 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE G 39 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN G 106 " --> pdb=" O ILE G 39 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'I' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE I 35 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU I 102 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL I 37 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL I 104 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE I 39 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN I 106 " --> pdb=" O ILE I 39 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'K' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE K 35 " --> pdb=" O ARG K 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU K 102 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL K 37 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL K 104 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE K 39 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN K 106 " --> pdb=" O ILE K 39 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'M' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE M 35 " --> pdb=" O ARG M 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU M 102 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL M 37 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL M 104 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE M 39 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N GLN M 106 " --> pdb=" O ILE M 39 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'O' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE O 35 " --> pdb=" O ARG O 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU O 102 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL O 37 " --> pdb=" O LEU O 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL O 104 " --> pdb=" O VAL O 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE O 39 " --> pdb=" O VAL O 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN O 106 " --> pdb=" O ILE O 39 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'Q' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE Q 35 " --> pdb=" O ARG Q 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU Q 102 " --> pdb=" O ILE Q 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL Q 37 " --> pdb=" O LEU Q 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL Q 104 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE Q 39 " --> pdb=" O VAL Q 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN Q 106 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'S' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE S 35 " --> pdb=" O ARG S 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU S 102 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL S 37 " --> pdb=" O LEU S 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL S 104 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE S 39 " --> pdb=" O VAL S 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN S 106 " --> pdb=" O ILE S 39 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'U' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE U 35 " --> pdb=" O ARG U 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU U 102 " --> pdb=" O ILE U 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL U 37 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL U 104 " --> pdb=" O VAL U 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE U 39 " --> pdb=" O VAL U 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN U 106 " --> pdb=" O ILE U 39 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'W' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE W 35 " --> pdb=" O ARG W 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU W 102 " --> pdb=" O ILE W 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL W 37 " --> pdb=" O LEU W 102 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL W 104 " --> pdb=" O VAL W 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE W 39 " --> pdb=" O VAL W 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN W 106 " --> pdb=" O ILE W 39 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'Y' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE Y 35 " --> pdb=" O ARG Y 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU Y 102 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL Y 37 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL Y 104 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE Y 39 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN Y 106 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain '0' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE 0 35 " --> pdb=" O ARG 0 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU 0 102 " --> pdb=" O ILE 0 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL 0 37 " --> pdb=" O LEU 0 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL 0 104 " --> pdb=" O VAL 0 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN 0 106 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain '2' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE 2 35 " --> pdb=" O ARG 2 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU 2 102 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL 2 37 " --> pdb=" O LEU 2 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL 2 104 " --> pdb=" O VAL 2 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE 2 39 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN 2 106 " --> pdb=" O ILE 2 39 " (cutoff:3.500A) 1710 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 8.03 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 13815 1.33 - 1.45: 6865 1.45 - 1.57: 24515 1.57 - 1.69: 150 1.69 - 1.80: 345 Bond restraints: 45690 Sorted by residual: bond pdb=" CB VAL Q 314 " pdb=" CG1 VAL Q 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB VAL 2 314 " pdb=" CG1 VAL 2 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB VAL G 314 " pdb=" CG1 VAL G 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CB VAL A 314 " pdb=" CG1 VAL A 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CB VAL K 314 " pdb=" CG1 VAL K 314 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.13e+00 ... (remaining 45685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 60016 2.63 - 5.25: 1878 5.25 - 7.88: 161 7.88 - 10.50: 75 10.50 - 13.13: 15 Bond angle restraints: 62145 Sorted by residual: angle pdb=" N ILE M 28 " pdb=" CA ILE M 28 " pdb=" C ILE M 28 " ideal model delta sigma weight residual 113.71 106.84 6.87 9.50e-01 1.11e+00 5.22e+01 angle pdb=" N ILE 0 28 " pdb=" CA ILE 0 28 " pdb=" C ILE 0 28 " ideal model delta sigma weight residual 113.71 106.86 6.85 9.50e-01 1.11e+00 5.21e+01 angle pdb=" N ILE U 28 " pdb=" CA ILE U 28 " pdb=" C ILE U 28 " ideal model delta sigma weight residual 113.71 106.86 6.85 9.50e-01 1.11e+00 5.20e+01 angle pdb=" N ILE Y 28 " pdb=" CA ILE Y 28 " pdb=" C ILE Y 28 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.19e+01 angle pdb=" N ILE I 28 " pdb=" CA ILE I 28 " pdb=" C ILE I 28 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.19e+01 ... (remaining 62140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 25486 15.16 - 30.32: 1664 30.32 - 45.47: 330 45.47 - 60.63: 90 60.63 - 75.79: 75 Dihedral angle restraints: 27645 sinusoidal: 12075 harmonic: 15570 Sorted by residual: dihedral pdb=" CA LYS Q 150 " pdb=" C LYS Q 150 " pdb=" N GLU Q 151 " pdb=" CA GLU Q 151 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS K 150 " pdb=" C LYS K 150 " pdb=" N GLU K 151 " pdb=" CA GLU K 151 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS 2 150 " pdb=" C LYS 2 150 " pdb=" N GLU 2 151 " pdb=" CA GLU 2 151 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 27642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5739 0.075 - 0.151: 1221 0.151 - 0.226: 120 0.226 - 0.302: 15 0.302 - 0.377: 15 Chirality restraints: 7110 Sorted by residual: chirality pdb=" CA ASP O 42 " pdb=" N ASP O 42 " pdb=" C ASP O 42 " pdb=" CB ASP O 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ASP I 42 " pdb=" N ASP I 42 " pdb=" C ASP I 42 " pdb=" CB ASP I 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ASP Y 42 " pdb=" N ASP Y 42 " pdb=" C ASP Y 42 " pdb=" CB ASP Y 42 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 7107 not shown) Planarity restraints: 7650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 281 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO S 282 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO S 282 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 282 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 0 281 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO 0 282 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO 0 282 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 0 282 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 281 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO A 282 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " -0.031 5.00e-02 4.00e+02 ... (remaining 7647 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 155 2.43 - 3.05: 26374 3.05 - 3.67: 70678 3.67 - 4.28: 108487 4.28 - 4.90: 175372 Nonbonded interactions: 381066 Sorted by model distance: nonbonded pdb=" O GLY A 23 " pdb=" OE2 GLU 0 342 " model vdw 1.817 3.040 nonbonded pdb=" O GLY D 23 " pdb=" OE2 GLU 2 342 " model vdw 1.817 3.040 nonbonded pdb=" OG SER Y 334 " pdb=" O PHE Y 357 " model vdw 2.272 3.040 nonbonded pdb=" OG SER S 334 " pdb=" O PHE S 357 " model vdw 2.272 3.040 nonbonded pdb=" OG SER W 334 " pdb=" O PHE W 357 " model vdw 2.272 3.040 ... (remaining 381061 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: 0.16 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain '0' selection = chain '2' } ncs_group { reference = chain 'E' selection = chain 'B' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain '1' selection = chain '3' } 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 32.420 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.010 0.060 45690 Z= 0.405 Angle : 1.118 13.127 62145 Z= 0.607 Chirality : 0.063 0.377 7110 Planarity : 0.007 0.056 7650 Dihedral : 11.844 75.788 17625 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.65 % Allowed : 4.19 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -5.39 (0.08), residues: 5355 helix: -4.22 (0.04), residues: 3030 sheet: -1.96 (0.26), residues: 390 loop : -2.39 (0.12), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 370 TYR 0.029 0.005 TYR O 281 PHE 0.020 0.004 PHE G 324 TRP 0.022 0.003 TRP Y 215 HIS 0.004 0.001 HIS O 287 Details of bonding type rmsd covalent geometry : bond 0.00964 (45690) covalent geometry : angle 1.11843 (62145) hydrogen bonds : bond 0.28744 ( 1710) hydrogen bonds : angle 10.61113 ( 4950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 1244 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8344 (ptp-110) cc_final: 0.8029 (ptp-110) REVERT: C 143 ARG cc_start: 0.7223 (pmt170) cc_final: 0.6689 (ptm-80) REVERT: C 166 ILE cc_start: 0.9019 (mm) cc_final: 0.8814 (mt) REVERT: C 256 ASP cc_start: 0.8847 (t70) cc_final: 0.8252 (t0) REVERT: C 306 MET cc_start: 0.8949 (mtp) cc_final: 0.8705 (mtp) REVERT: A 143 ARG cc_start: 0.7317 (pmt170) cc_final: 0.6829 (ttp-110) REVERT: A 156 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6601 (tm-30) REVERT: A 320 ILE cc_start: 0.9108 (tt) cc_final: 0.8776 (tt) REVERT: A 367 GLU cc_start: 0.7353 (tt0) cc_final: 0.7031 (tt0) REVERT: D 29 ARG cc_start: 0.8407 (ptp-110) cc_final: 0.8067 (ptp-110) REVERT: D 53 ASP cc_start: 0.8341 (t0) cc_final: 0.7861 (t0) REVERT: D 76 ILE cc_start: 0.8588 (pt) cc_final: 0.8245 (pt) REVERT: D 143 ARG cc_start: 0.7375 (pmt170) cc_final: 0.6961 (ptt-90) REVERT: D 297 GLU cc_start: 0.7808 (tt0) cc_final: 0.7576 (tt0) REVERT: D 320 ILE cc_start: 0.9164 (tt) cc_final: 0.8869 (tt) REVERT: G 13 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7156 (mtm110) REVERT: G 156 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6656 (tm-30) REVERT: G 297 GLU cc_start: 0.7905 (tt0) cc_final: 0.7629 (tt0) REVERT: G 306 MET cc_start: 0.8946 (mtp) cc_final: 0.8675 (mtp) REVERT: I 53 ASP cc_start: 0.8188 (t0) cc_final: 0.7979 (t0) REVERT: I 57 ARG cc_start: 0.8188 (ptp-110) cc_final: 0.7927 (ttp-170) REVERT: I 123 MET cc_start: 0.6115 (mtm) cc_final: 0.5910 (ptt) REVERT: I 143 ARG cc_start: 0.7443 (pmt170) cc_final: 0.7143 (ptt-90) REVERT: I 159 ASP cc_start: 0.8641 (p0) cc_final: 0.8378 (p0) REVERT: I 297 GLU cc_start: 0.7796 (tt0) cc_final: 0.7552 (tt0) REVERT: I 320 ILE cc_start: 0.9104 (tt) cc_final: 0.8855 (tt) REVERT: K 156 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6555 (tm-30) REVERT: K 158 GLN cc_start: 0.7966 (mp10) cc_final: 0.7602 (mm-40) REVERT: K 252 GLU cc_start: 0.8119 (tp30) cc_final: 0.7818 (tp30) REVERT: K 297 GLU cc_start: 0.7735 (tt0) cc_final: 0.7442 (tt0) REVERT: K 320 ILE cc_start: 0.9068 (tt) cc_final: 0.8827 (tt) REVERT: M 3 THR cc_start: 0.8878 (t) cc_final: 0.8632 (m) REVERT: M 29 ARG cc_start: 0.8372 (ptp-110) cc_final: 0.8148 (ptp-110) REVERT: M 53 ASP cc_start: 0.8202 (t0) cc_final: 0.7989 (t0) REVERT: M 143 ARG cc_start: 0.7485 (pmt170) cc_final: 0.7110 (ptt-90) REVERT: M 156 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6144 (tm-30) REVERT: M 158 GLN cc_start: 0.8036 (mp10) cc_final: 0.7767 (mm-40) REVERT: M 166 ILE cc_start: 0.8987 (mm) cc_final: 0.8775 (mt) REVERT: M 263 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7850 (mt-10) REVERT: M 320 ILE cc_start: 0.9049 (tt) cc_final: 0.8748 (tt) REVERT: M 371 ARG cc_start: 0.7307 (mtp180) cc_final: 0.7087 (mtp180) REVERT: O 29 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.7938 (ptp-110) REVERT: O 53 ASP cc_start: 0.8342 (t0) cc_final: 0.8057 (t0) REVERT: O 143 ARG cc_start: 0.7331 (pmt170) cc_final: 0.6889 (ptm-80) REVERT: O 217 ASP cc_start: 0.7574 (m-30) cc_final: 0.7208 (m-30) REVERT: O 320 ILE cc_start: 0.9103 (tt) cc_final: 0.8842 (tt) REVERT: O 371 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6871 (mtp180) REVERT: Q 10 LEU cc_start: 0.9043 (mt) cc_final: 0.8803 (mp) REVERT: Q 29 ARG cc_start: 0.8393 (ptp-110) cc_final: 0.8060 (ptp-110) REVERT: Q 53 ASP cc_start: 0.8358 (t0) cc_final: 0.7935 (t0) REVERT: Q 109 GLN cc_start: 0.7236 (tm-30) cc_final: 0.7035 (tm-30) REVERT: Q 143 ARG cc_start: 0.7297 (pmt170) cc_final: 0.7038 (ptm-80) REVERT: Q 217 ASP cc_start: 0.7541 (m-30) cc_final: 0.7083 (m-30) REVERT: Q 253 MET cc_start: 0.8187 (ttm) cc_final: 0.7968 (ttp) REVERT: Q 371 ARG cc_start: 0.7311 (mtp180) cc_final: 0.7043 (mtp180) REVERT: S 13 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.7053 (mtm110) REVERT: S 166 ILE cc_start: 0.9061 (mm) cc_final: 0.8836 (mt) REVERT: S 256 ASP cc_start: 0.8764 (t70) cc_final: 0.8106 (t0) REVERT: S 304 GLN cc_start: 0.7935 (pt0) cc_final: 0.7710 (pt0) REVERT: U 29 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.8148 (ptp-110) REVERT: U 143 ARG cc_start: 0.7374 (pmt170) cc_final: 0.6980 (mtp-110) REVERT: U 159 ASP cc_start: 0.8672 (p0) cc_final: 0.8409 (p0) REVERT: U 166 ILE cc_start: 0.9116 (mm) cc_final: 0.8890 (mt) REVERT: U 256 ASP cc_start: 0.8707 (t70) cc_final: 0.7959 (t0) REVERT: U 306 MET cc_start: 0.8921 (mtp) cc_final: 0.8670 (mtm) REVERT: U 371 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6899 (mtp180) REVERT: W 5 LEU cc_start: 0.8707 (mm) cc_final: 0.8507 (mm) REVERT: W 10 LEU cc_start: 0.8950 (mt) cc_final: 0.8666 (mt) REVERT: W 111 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7538 (tp40) REVERT: W 143 ARG cc_start: 0.7218 (pmt170) cc_final: 0.6645 (ptm-80) REVERT: W 367 GLU cc_start: 0.7472 (tt0) cc_final: 0.7271 (tt0) REVERT: W 371 ARG cc_start: 0.7317 (mtp180) cc_final: 0.7066 (mtp180) REVERT: Y 31 ILE cc_start: 0.8835 (tp) cc_final: 0.8571 (tp) REVERT: Y 53 ASP cc_start: 0.8570 (t0) cc_final: 0.8333 (t0) REVERT: Y 123 MET cc_start: 0.5922 (mtm) cc_final: 0.5454 (mtp) REVERT: Y 166 ILE cc_start: 0.9054 (mm) cc_final: 0.8814 (mt) REVERT: Y 209 PHE cc_start: 0.8582 (m-10) cc_final: 0.8320 (m-80) REVERT: Y 337 MET cc_start: 0.8494 (mmp) cc_final: 0.8275 (mmp) REVERT: Y 367 GLU cc_start: 0.7488 (tt0) cc_final: 0.7262 (tt0) REVERT: Y 371 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6934 (mtp180) REVERT: 0 53 ASP cc_start: 0.8687 (t0) cc_final: 0.8300 (t0) REVERT: 0 337 MET cc_start: 0.8589 (mmp) cc_final: 0.8310 (mmp) REVERT: 0 371 ARG cc_start: 0.7213 (mtp180) cc_final: 0.6742 (mtp180) REVERT: 2 3 THR cc_start: 0.8554 (t) cc_final: 0.8256 (m) REVERT: 2 10 LEU cc_start: 0.9044 (mt) cc_final: 0.8808 (mt) REVERT: 2 29 ARG cc_start: 0.8365 (ptp-110) cc_final: 0.7918 (ptp90) REVERT: 2 256 ASP cc_start: 0.8711 (t70) cc_final: 0.8005 (t0) REVERT: 2 274 LYS cc_start: 0.8670 (tttp) cc_final: 0.8439 (ttmt) REVERT: 2 320 ILE cc_start: 0.9108 (tt) cc_final: 0.8887 (tt) REVERT: 2 371 ARG cc_start: 0.7273 (mtp180) cc_final: 0.6887 (mtp180) outliers start: 30 outliers final: 7 residues processed: 1267 average time/residue: 0.2640 time to fit residues: 528.5992 Evaluate side-chains 844 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 837 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain S residue 236 LEU Chi-restraints excluded: chain 0 residue 236 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 0.8980 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 33 HIS C 61 ASN C 164 ASN C 351 ASN A 33 HIS A 61 ASN A 304 GLN A 351 ASN D 61 ASN D 246 ASN D 322 ASN D 351 ASN G 33 HIS G 61 ASN G 246 ASN G 351 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN I 351 ASN K 33 HIS K 61 ASN K 149 ASN K 164 ASN K 246 ASN K 322 ASN K 351 ASN M 33 HIS M 61 ASN M 149 ASN M 202 GLN M 246 ASN M 351 ASN O 33 HIS O 61 ASN O 164 ASN O 246 ASN O 304 GLN O 351 ASN ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS Q 61 ASN Q 246 ASN Q 351 ASN S 33 HIS S 61 ASN S 351 ASN U 33 HIS U 61 ASN U 164 ASN U 351 ASN W 14 ASN W 33 HIS W 61 ASN ** W 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 351 ASN Y 14 ASN Y 33 HIS Y 61 ASN ** Y 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 351 ASN 0 14 ASN 0 33 HIS 0 61 ASN 0 164 ASN 2 14 ASN 2 33 HIS 2 61 ASN 2 164 ASN 2 351 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.093617 restraints weight = 68141.877| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.98 r_work: 0.2916 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 45690 Z= 0.127 Angle : 0.635 9.420 62145 Z= 0.331 Chirality : 0.044 0.266 7110 Planarity : 0.005 0.047 7650 Dihedral : 10.977 73.576 7184 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.24 % Allowed : 9.01 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.37 (0.10), residues: 5355 helix: -2.01 (0.08), residues: 3120 sheet: -2.10 (0.26), residues: 375 loop : -2.36 (0.12), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 231 TYR 0.012 0.001 TYR 0 361 PHE 0.016 0.002 PHE A 163 TRP 0.009 0.001 TRP M 333 HIS 0.005 0.001 HIS S 33 Details of bonding type rmsd covalent geometry : bond 0.00277 (45690) covalent geometry : angle 0.63465 (62145) hydrogen bonds : bond 0.04621 ( 1710) hydrogen bonds : angle 4.87086 ( 4950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 940 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8743 (ptp-110) cc_final: 0.8474 (ptp-110) REVERT: C 53 ASP cc_start: 0.8758 (t0) cc_final: 0.8416 (t0) REVERT: C 143 ARG cc_start: 0.7708 (pmt170) cc_final: 0.6732 (ptm-80) REVERT: C 209 PHE cc_start: 0.8915 (m-10) cc_final: 0.8683 (m-10) REVERT: C 371 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7484 (mtp180) REVERT: A 143 ARG cc_start: 0.7661 (pmt170) cc_final: 0.7453 (ptt-90) REVERT: A 367 GLU cc_start: 0.8253 (tt0) cc_final: 0.7987 (tt0) REVERT: D 143 ARG cc_start: 0.7762 (pmt170) cc_final: 0.7383 (ptt-90) REVERT: D 320 ILE cc_start: 0.9282 (tt) cc_final: 0.9082 (tt) REVERT: D 344 GLU cc_start: 0.8240 (mp0) cc_final: 0.7992 (mp0) REVERT: G 53 ASP cc_start: 0.8843 (t0) cc_final: 0.8600 (t0) REVERT: G 55 LEU cc_start: 0.8572 (tp) cc_final: 0.8335 (tp) REVERT: G 306 MET cc_start: 0.8908 (mtp) cc_final: 0.8668 (mtp) REVERT: I 53 ASP cc_start: 0.8627 (t0) cc_final: 0.8400 (t0) REVERT: I 57 ARG cc_start: 0.8308 (ptp-110) cc_final: 0.8033 (ttp-170) REVERT: I 123 MET cc_start: 0.6421 (mtm) cc_final: 0.6110 (ptt) REVERT: I 129 GLN cc_start: 0.8511 (mp10) cc_final: 0.8279 (mp10) REVERT: I 143 ARG cc_start: 0.7950 (pmt170) cc_final: 0.7465 (ptt-90) REVERT: K 13 ARG cc_start: 0.7910 (mtp180) cc_final: 0.7560 (mtm110) REVERT: K 29 ARG cc_start: 0.8693 (ptp-110) cc_final: 0.8422 (ptp90) REVERT: K 156 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7154 (tm-30) REVERT: K 158 GLN cc_start: 0.8276 (mp10) cc_final: 0.8065 (mm-40) REVERT: K 159 ASP cc_start: 0.8399 (p0) cc_final: 0.8013 (p0) REVERT: K 256 ASP cc_start: 0.8674 (t70) cc_final: 0.8289 (t0) REVERT: K 320 ILE cc_start: 0.9185 (tt) cc_final: 0.8921 (tt) REVERT: K 344 GLU cc_start: 0.8159 (mp0) cc_final: 0.7892 (mp0) REVERT: K 371 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7635 (mtp180) REVERT: M 143 ARG cc_start: 0.7814 (pmt170) cc_final: 0.7163 (ptt-90) REVERT: M 156 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6534 (tm-30) REVERT: M 158 GLN cc_start: 0.8302 (mp10) cc_final: 0.8007 (mm-40) REVERT: M 217 ASP cc_start: 0.7803 (m-30) cc_final: 0.7302 (m-30) REVERT: M 227 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8678 (tp) REVERT: M 371 ARG cc_start: 0.7873 (mtp180) cc_final: 0.7338 (mtp180) REVERT: O 82 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: O 100 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8377 (tmm160) REVERT: O 143 ARG cc_start: 0.7754 (pmt170) cc_final: 0.6921 (ptm-80) REVERT: O 212 GLU cc_start: 0.8644 (pt0) cc_final: 0.8420 (pt0) REVERT: O 217 ASP cc_start: 0.7913 (m-30) cc_final: 0.7483 (m-30) REVERT: O 367 GLU cc_start: 0.8486 (tt0) cc_final: 0.8053 (tt0) REVERT: O 371 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7389 (mtp180) REVERT: Q 53 ASP cc_start: 0.8765 (t0) cc_final: 0.8455 (t0) REVERT: Q 57 ARG cc_start: 0.8472 (ptp-110) cc_final: 0.8199 (ptm160) REVERT: Q 109 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6913 (tm-30) REVERT: Q 143 ARG cc_start: 0.7713 (pmt170) cc_final: 0.6988 (ptm-80) REVERT: Q 213 ARG cc_start: 0.8269 (mtp-110) cc_final: 0.7876 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7908 (m-30) cc_final: 0.7554 (m-30) REVERT: Q 371 ARG cc_start: 0.7772 (mtp180) cc_final: 0.7412 (mtp180) REVERT: S 143 ARG cc_start: 0.7407 (ptt-90) cc_final: 0.6449 (ttp-110) REVERT: S 280 MET cc_start: 0.9004 (mmm) cc_final: 0.8598 (mmt) REVERT: S 371 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7462 (mtp180) REVERT: U 143 ARG cc_start: 0.7797 (pmt170) cc_final: 0.6990 (mtp-110) REVERT: U 371 ARG cc_start: 0.7818 (mtp180) cc_final: 0.7425 (mtp180) REVERT: W 111 GLN cc_start: 0.8292 (tp-100) cc_final: 0.7760 (tp40) REVERT: W 143 ARG cc_start: 0.7535 (pmt170) cc_final: 0.6663 (ptm-80) REVERT: W 332 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9208 (tp) REVERT: W 371 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7516 (mtp180) REVERT: Y 6 ARG cc_start: 0.8505 (ptp90) cc_final: 0.8112 (mtm110) REVERT: Y 100 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7802 (tmm160) REVERT: Y 123 MET cc_start: 0.6088 (mtm) cc_final: 0.5604 (mtp) REVERT: Y 258 ASP cc_start: 0.8902 (t70) cc_final: 0.8623 (t0) REVERT: Y 367 GLU cc_start: 0.8378 (tt0) cc_final: 0.8078 (tt0) REVERT: Y 371 ARG cc_start: 0.7782 (mtp180) cc_final: 0.7480 (mtp180) REVERT: 0 53 ASP cc_start: 0.8969 (t0) cc_final: 0.8710 (t0) REVERT: 0 123 MET cc_start: 0.7283 (mtp) cc_final: 0.6791 (mtp) REVERT: 0 225 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: 0 371 ARG cc_start: 0.7794 (mtp180) cc_final: 0.7237 (mtp180) REVERT: 2 10 LEU cc_start: 0.9131 (mt) cc_final: 0.8863 (mm) REVERT: 2 53 ASP cc_start: 0.8990 (t0) cc_final: 0.8636 (t0) REVERT: 2 258 ASP cc_start: 0.8941 (t70) cc_final: 0.8713 (t0) REVERT: 2 274 LYS cc_start: 0.8956 (tttp) cc_final: 0.8709 (ttmt) REVERT: 2 317 GLU cc_start: 0.6230 (tm-30) cc_final: 0.5513 (tm-30) REVERT: 2 371 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7265 (mtp180) outliers start: 104 outliers final: 57 residues processed: 1019 average time/residue: 0.3077 time to fit residues: 489.8920 Evaluate side-chains 883 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 822 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 150 LYS Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 150 LYS Chi-restraints excluded: chain K residue 225 GLU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 150 LYS Chi-restraints excluded: chain Q residue 225 GLU Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain S residue 186 ASP Chi-restraints excluded: chain S residue 355 SER Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 150 LYS Chi-restraints excluded: chain W residue 227 LEU Chi-restraints excluded: chain W residue 332 LEU Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 225 GLU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 236 LEU Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 249 optimal weight: 0.4980 chunk 142 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 442 optimal weight: 8.9990 chunk 488 optimal weight: 10.0000 chunk 339 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 417 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 137 optimal weight: 0.1980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN A 33 HIS A 304 GLN D 33 HIS D 246 ASN ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 33 HIS G 246 ASN I 14 ASN I 33 HIS ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS K 246 ASN K 304 GLN K 322 ASN M 33 HIS M 246 ASN O 33 HIS O 246 ASN Q 14 ASN Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN S 33 HIS U 33 HIS U 164 ASN U 304 GLN W 33 HIS W 304 GLN Y 33 HIS Y 164 ASN 0 33 HIS 2 33 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.093350 restraints weight = 67873.155| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.94 r_work: 0.2820 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 45690 Z= 0.187 Angle : 0.604 8.097 62145 Z= 0.310 Chirality : 0.046 0.213 7110 Planarity : 0.004 0.038 7650 Dihedral : 10.624 73.596 7170 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.62 % Allowed : 9.87 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.79 (0.11), residues: 5355 helix: -0.69 (0.09), residues: 3090 sheet: -1.69 (0.27), residues: 390 loop : -1.71 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 100 TYR 0.015 0.002 TYR G 303 PHE 0.011 0.002 PHE U 163 TRP 0.008 0.001 TRP U 333 HIS 0.006 0.001 HIS I 33 Details of bonding type rmsd covalent geometry : bond 0.00445 (45690) covalent geometry : angle 0.60350 (62145) hydrogen bonds : bond 0.03865 ( 1710) hydrogen bonds : angle 4.29541 ( 4950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 886 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8819 (ptp-110) cc_final: 0.8504 (ptp-110) REVERT: C 53 ASP cc_start: 0.8831 (t0) cc_final: 0.8462 (t0) REVERT: C 143 ARG cc_start: 0.7707 (pmt170) cc_final: 0.7163 (ptt-90) REVERT: C 201 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: C 217 ASP cc_start: 0.7879 (m-30) cc_final: 0.7429 (m-30) REVERT: C 271 LEU cc_start: 0.8899 (mt) cc_final: 0.8693 (mt) REVERT: C 371 ARG cc_start: 0.7707 (mtp180) cc_final: 0.7362 (mtp180) REVERT: A 143 ARG cc_start: 0.7675 (pmt170) cc_final: 0.7396 (ptt-90) REVERT: A 280 MET cc_start: 0.9063 (mmt) cc_final: 0.8735 (mmt) REVERT: A 297 GLU cc_start: 0.7561 (tt0) cc_final: 0.7327 (tt0) REVERT: A 304 GLN cc_start: 0.8076 (mt0) cc_final: 0.7702 (mm110) REVERT: A 367 GLU cc_start: 0.8327 (tt0) cc_final: 0.8096 (tt0) REVERT: D 143 ARG cc_start: 0.7713 (pmt170) cc_final: 0.7219 (ptt-90) REVERT: D 201 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.7740 (mp10) REVERT: D 249 ARG cc_start: 0.8770 (ttt-90) cc_final: 0.8534 (ttt-90) REVERT: D 320 ILE cc_start: 0.9368 (tt) cc_final: 0.9123 (tt) REVERT: G 53 ASP cc_start: 0.8963 (t0) cc_final: 0.8723 (t0) REVERT: G 201 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: G 227 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8579 (tp) REVERT: I 53 ASP cc_start: 0.8688 (t0) cc_final: 0.8459 (t0) REVERT: I 57 ARG cc_start: 0.8340 (ptp-110) cc_final: 0.7958 (ttp-170) REVERT: I 123 MET cc_start: 0.6520 (mtm) cc_final: 0.6243 (ptt) REVERT: I 143 ARG cc_start: 0.7966 (pmt170) cc_final: 0.7616 (ptt-90) REVERT: I 201 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: I 227 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8679 (tp) REVERT: I 271 LEU cc_start: 0.8854 (mt) cc_final: 0.8574 (mt) REVERT: I 344 GLU cc_start: 0.8339 (mp0) cc_final: 0.8120 (mt-10) REVERT: K 5 LEU cc_start: 0.8857 (mm) cc_final: 0.8613 (mm) REVERT: K 29 ARG cc_start: 0.8742 (ptp-110) cc_final: 0.8409 (ptp90) REVERT: K 102 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8573 (pp) REVERT: K 158 GLN cc_start: 0.8369 (mp10) cc_final: 0.8164 (mm-40) REVERT: K 201 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: K 227 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8629 (tp) REVERT: K 320 ILE cc_start: 0.9228 (tt) cc_final: 0.8886 (tt) REVERT: K 371 ARG cc_start: 0.7895 (mtp180) cc_final: 0.7652 (mtp180) REVERT: M 143 ARG cc_start: 0.7827 (pmt170) cc_final: 0.7373 (ptt-90) REVERT: M 156 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6613 (tm-30) REVERT: M 158 GLN cc_start: 0.8369 (mp10) cc_final: 0.8049 (mm-40) REVERT: M 201 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: M 217 ASP cc_start: 0.7846 (m-30) cc_final: 0.7339 (m-30) REVERT: M 263 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8457 (mt-10) REVERT: M 371 ARG cc_start: 0.7763 (mtp180) cc_final: 0.7289 (mtp180) REVERT: O 6 ARG cc_start: 0.8548 (ptp90) cc_final: 0.8228 (ttp-110) REVERT: O 100 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8429 (tmm160) REVERT: O 143 ARG cc_start: 0.7721 (pmt170) cc_final: 0.7292 (ptt-90) REVERT: O 212 GLU cc_start: 0.8749 (pt0) cc_final: 0.8382 (pt0) REVERT: O 217 ASP cc_start: 0.7961 (m-30) cc_final: 0.7587 (m-30) REVERT: O 367 GLU cc_start: 0.8505 (tt0) cc_final: 0.8108 (tt0) REVERT: O 371 ARG cc_start: 0.7713 (mtp180) cc_final: 0.7425 (mtp180) REVERT: Q 53 ASP cc_start: 0.8779 (t0) cc_final: 0.8499 (t0) REVERT: Q 57 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.8158 (ptm160) REVERT: Q 143 ARG cc_start: 0.7654 (pmt170) cc_final: 0.6864 (ptm-80) REVERT: Q 213 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7886 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7949 (m-30) cc_final: 0.7604 (m-30) REVERT: Q 371 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7518 (mtp180) REVERT: S 143 ARG cc_start: 0.7441 (ptt-90) cc_final: 0.6645 (ptm-80) REVERT: S 201 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: S 280 MET cc_start: 0.8976 (mmm) cc_final: 0.8572 (mmt) REVERT: S 371 ARG cc_start: 0.7708 (mtp180) cc_final: 0.7288 (mtp180) REVERT: U 143 ARG cc_start: 0.7844 (pmt170) cc_final: 0.6977 (ttp-110) REVERT: U 201 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: U 209 PHE cc_start: 0.8390 (m-10) cc_final: 0.8044 (m-10) REVERT: U 227 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8638 (tp) REVERT: U 258 ASP cc_start: 0.8944 (t70) cc_final: 0.8712 (t0) REVERT: W 54 ARG cc_start: 0.8268 (mmp80) cc_final: 0.8003 (mmt-90) REVERT: W 111 GLN cc_start: 0.8310 (tp-100) cc_final: 0.7755 (tp40) REVERT: W 143 ARG cc_start: 0.7691 (pmt170) cc_final: 0.6698 (ptm-80) REVERT: W 371 ARG cc_start: 0.7837 (mtp180) cc_final: 0.7548 (mtp180) REVERT: Y 6 ARG cc_start: 0.8531 (ptp90) cc_final: 0.8055 (mtm110) REVERT: Y 10 LEU cc_start: 0.8966 (mt) cc_final: 0.8748 (mt) REVERT: Y 123 MET cc_start: 0.6112 (mtm) cc_final: 0.5554 (mtp) REVERT: Y 225 GLU cc_start: 0.8694 (tt0) cc_final: 0.8268 (tt0) REVERT: Y 258 ASP cc_start: 0.8989 (t70) cc_final: 0.8777 (t0) REVERT: Y 301 ASN cc_start: 0.8401 (m110) cc_final: 0.8184 (m-40) REVERT: Y 371 ARG cc_start: 0.7844 (mtp180) cc_final: 0.7315 (mtp180) REVERT: 0 53 ASP cc_start: 0.9020 (t0) cc_final: 0.8712 (t0) REVERT: 0 201 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: 0 371 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7138 (mtp180) REVERT: 2 10 LEU cc_start: 0.9139 (mt) cc_final: 0.8894 (mm) REVERT: 2 123 MET cc_start: 0.3667 (mtm) cc_final: 0.3454 (ttm) REVERT: 2 201 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: 2 274 LYS cc_start: 0.8947 (tttp) cc_final: 0.8694 (ttmt) REVERT: 2 317 GLU cc_start: 0.6142 (tm-30) cc_final: 0.5147 (tm-30) REVERT: 2 371 ARG cc_start: 0.7772 (mtp180) cc_final: 0.7301 (mtp180) outliers start: 122 outliers final: 61 residues processed: 978 average time/residue: 0.3032 time to fit residues: 466.2330 Evaluate side-chains 865 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 789 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 213 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 201 GLN Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 109 GLN Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 150 LYS Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 57 ARG Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 201 GLN Chi-restraints excluded: chain S residue 355 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 150 LYS Chi-restraints excluded: chain W residue 259 THR Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 225 GLU Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 236 LEU Chi-restraints excluded: chain 2 residue 259 THR Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 264 optimal weight: 5.9990 chunk 405 optimal weight: 4.9990 chunk 495 optimal weight: 0.0870 chunk 435 optimal weight: 9.9990 chunk 505 optimal weight: 5.9990 chunk 492 optimal weight: 4.9990 chunk 395 optimal weight: 0.9990 chunk 272 optimal weight: 0.9980 chunk 385 optimal weight: 0.8980 chunk 313 optimal weight: 0.6980 chunk 267 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN D 33 HIS D 164 ASN G 33 HIS G 164 ASN G 246 ASN G 301 ASN G 304 GLN I 33 HIS K 14 ASN K 164 ASN K 246 ASN M 33 HIS M 246 ASN O 33 HIS O 164 ASN O 246 ASN Q 14 ASN Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 33 HIS U 33 HIS U 322 ASN W 33 HIS W 304 GLN W 322 ASN Y 33 HIS 0 33 HIS 2 33 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.095905 restraints weight = 68054.719| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.07 r_work: 0.2942 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 45690 Z= 0.100 Angle : 0.529 6.908 62145 Z= 0.273 Chirality : 0.042 0.149 7110 Planarity : 0.003 0.034 7650 Dihedral : 10.500 73.520 7170 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.92 % Rotamer: Outliers : 2.28 % Allowed : 10.39 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.10 (0.12), residues: 5355 helix: -0.08 (0.10), residues: 3105 sheet: -1.68 (0.26), residues: 390 loop : -1.44 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 213 TYR 0.017 0.001 TYR D 303 PHE 0.012 0.001 PHE U 163 TRP 0.008 0.001 TRP U 333 HIS 0.005 0.001 HIS S 33 Details of bonding type rmsd covalent geometry : bond 0.00225 (45690) covalent geometry : angle 0.52905 (62145) hydrogen bonds : bond 0.03362 ( 1710) hydrogen bonds : angle 3.92596 ( 4950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 905 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8827 (ptp-110) cc_final: 0.8545 (ptp-110) REVERT: C 53 ASP cc_start: 0.8818 (t0) cc_final: 0.8462 (t0) REVERT: C 143 ARG cc_start: 0.7706 (pmt170) cc_final: 0.7175 (ptt-90) REVERT: C 213 ARG cc_start: 0.8022 (mtp-110) cc_final: 0.7786 (ttm-80) REVERT: C 371 ARG cc_start: 0.7810 (mtp180) cc_final: 0.7523 (mtp180) REVERT: A 123 MET cc_start: 0.6791 (mtm) cc_final: 0.6444 (ptp) REVERT: A 143 ARG cc_start: 0.7712 (pmt170) cc_final: 0.7441 (ptt-90) REVERT: A 212 GLU cc_start: 0.8805 (pt0) cc_final: 0.8590 (pt0) REVERT: A 256 ASP cc_start: 0.8447 (t70) cc_final: 0.8117 (t70) REVERT: A 280 MET cc_start: 0.9095 (mmt) cc_final: 0.8779 (mmm) REVERT: A 297 GLU cc_start: 0.7657 (tt0) cc_final: 0.7444 (tt0) REVERT: A 304 GLN cc_start: 0.8028 (mt0) cc_final: 0.7706 (mm110) REVERT: A 367 GLU cc_start: 0.8266 (tt0) cc_final: 0.8007 (tt0) REVERT: A 371 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7563 (mtp180) REVERT: D 143 ARG cc_start: 0.7725 (pmt170) cc_final: 0.7225 (ptt-90) REVERT: D 150 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8218 (mttt) REVERT: D 320 ILE cc_start: 0.9281 (tt) cc_final: 0.9030 (tt) REVERT: G 53 ASP cc_start: 0.8916 (t0) cc_final: 0.8653 (t0) REVERT: G 201 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: I 57 ARG cc_start: 0.8300 (ptp-110) cc_final: 0.8026 (ttp-170) REVERT: I 123 MET cc_start: 0.6504 (mtm) cc_final: 0.6267 (ptt) REVERT: I 143 ARG cc_start: 0.7895 (pmt170) cc_final: 0.7571 (ptt-90) REVERT: I 156 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7240 (tm-30) REVERT: I 159 ASP cc_start: 0.8177 (p0) cc_final: 0.7864 (p0) REVERT: I 192 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7880 (mt-10) REVERT: I 201 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: I 271 LEU cc_start: 0.8822 (mt) cc_final: 0.8587 (mt) REVERT: K 5 LEU cc_start: 0.8846 (mm) cc_final: 0.8627 (mm) REVERT: K 29 ARG cc_start: 0.8743 (ptp-110) cc_final: 0.8284 (ptp90) REVERT: K 53 ASP cc_start: 0.8779 (t0) cc_final: 0.8548 (t0) REVERT: K 57 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7934 (ttp-170) REVERT: K 102 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8365 (pp) REVERT: K 150 LYS cc_start: 0.8881 (mtmm) cc_final: 0.8274 (mtpt) REVERT: K 159 ASP cc_start: 0.8347 (p0) cc_final: 0.7991 (p0) REVERT: K 201 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: K 320 ILE cc_start: 0.9137 (tt) cc_final: 0.8849 (tt) REVERT: M 102 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8429 (pp) REVERT: M 143 ARG cc_start: 0.7891 (pmt170) cc_final: 0.7441 (ptt-90) REVERT: M 156 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7171 (tm-30) REVERT: M 371 ARG cc_start: 0.7850 (mtp180) cc_final: 0.7373 (mtp180) REVERT: O 6 ARG cc_start: 0.8559 (ptp90) cc_final: 0.8195 (ttp-110) REVERT: O 82 GLU cc_start: 0.8407 (tt0) cc_final: 0.8184 (mt-10) REVERT: O 93 ASP cc_start: 0.7694 (p0) cc_final: 0.7406 (t70) REVERT: O 100 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8382 (tmm160) REVERT: O 143 ARG cc_start: 0.7689 (pmt170) cc_final: 0.7259 (ptt-90) REVERT: O 209 PHE cc_start: 0.8511 (m-10) cc_final: 0.8300 (m-10) REVERT: O 212 GLU cc_start: 0.8721 (pt0) cc_final: 0.8386 (pt0) REVERT: O 280 MET cc_start: 0.8985 (mmm) cc_final: 0.8745 (mmt) REVERT: Q 53 ASP cc_start: 0.8751 (t0) cc_final: 0.8477 (t0) REVERT: Q 57 ARG cc_start: 0.8432 (ptp-110) cc_final: 0.8151 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7647 (pmt170) cc_final: 0.6868 (ptm-80) REVERT: Q 158 GLN cc_start: 0.8425 (mp10) cc_final: 0.8146 (mp10) REVERT: Q 213 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7846 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7933 (m-30) cc_final: 0.7559 (m-30) REVERT: Q 303 TYR cc_start: 0.9478 (t80) cc_final: 0.9250 (t80) REVERT: Q 371 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7654 (mtp180) REVERT: S 143 ARG cc_start: 0.7369 (ptt-90) cc_final: 0.6332 (ttp-110) REVERT: S 371 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7390 (mtp180) REVERT: U 143 ARG cc_start: 0.7768 (pmt170) cc_final: 0.6945 (ttp-110) REVERT: U 201 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.7563 (mt0) REVERT: U 227 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8630 (tp) REVERT: U 258 ASP cc_start: 0.8941 (t70) cc_final: 0.8713 (t0) REVERT: W 31 ILE cc_start: 0.9042 (tp) cc_final: 0.8822 (tp) REVERT: W 111 GLN cc_start: 0.8327 (tp-100) cc_final: 0.7781 (tp40) REVERT: W 143 ARG cc_start: 0.7680 (pmt170) cc_final: 0.6703 (ptm-80) REVERT: W 225 GLU cc_start: 0.8654 (tt0) cc_final: 0.8417 (tt0) REVERT: W 371 ARG cc_start: 0.7882 (mtp180) cc_final: 0.7480 (mtp180) REVERT: Y 6 ARG cc_start: 0.8534 (ptp90) cc_final: 0.8021 (mtm110) REVERT: Y 10 LEU cc_start: 0.9070 (mt) cc_final: 0.8723 (mt) REVERT: Y 123 MET cc_start: 0.6033 (mtm) cc_final: 0.5648 (mtp) REVERT: Y 126 GLU cc_start: 0.7782 (tm-30) cc_final: 0.6928 (tt0) REVERT: Y 225 GLU cc_start: 0.8687 (tt0) cc_final: 0.8339 (tt0) REVERT: Y 301 ASN cc_start: 0.8321 (m110) cc_final: 0.8026 (m-40) REVERT: Y 371 ARG cc_start: 0.7908 (mtp180) cc_final: 0.7380 (mtp180) REVERT: 0 53 ASP cc_start: 0.9034 (t0) cc_final: 0.8814 (t0) REVERT: 0 123 MET cc_start: 0.7183 (mtp) cc_final: 0.6919 (mtp) REVERT: 0 201 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: 0 209 PHE cc_start: 0.8286 (m-10) cc_final: 0.8060 (m-80) REVERT: 0 225 GLU cc_start: 0.8401 (pt0) cc_final: 0.8182 (tt0) REVERT: 0 371 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7233 (mtp180) REVERT: 2 10 LEU cc_start: 0.9099 (mt) cc_final: 0.8886 (mm) REVERT: 2 53 ASP cc_start: 0.9098 (t0) cc_final: 0.8828 (t0) REVERT: 2 102 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8339 (pp) REVERT: 2 123 MET cc_start: 0.3783 (mtm) cc_final: 0.3516 (ttm) REVERT: 2 256 ASP cc_start: 0.8978 (t70) cc_final: 0.8470 (t0) REVERT: 2 274 LYS cc_start: 0.8953 (tttp) cc_final: 0.8722 (ttmt) REVERT: 2 317 GLU cc_start: 0.6020 (tm-30) cc_final: 0.4949 (tm-30) REVERT: 2 371 ARG cc_start: 0.7721 (mtp180) cc_final: 0.7319 (mtp180) outliers start: 106 outliers final: 53 residues processed: 980 average time/residue: 0.3219 time to fit residues: 493.6079 Evaluate side-chains 843 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 780 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 57 ARG Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 129 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 187 THR Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 534 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 487 optimal weight: 2.9990 chunk 474 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 387 optimal weight: 7.9990 chunk 373 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN D 33 HIS D 304 GLN G 33 HIS G 246 ASN I 33 HIS K 33 HIS K 164 ASN K 246 ASN K 304 GLN M 33 HIS M 246 ASN O 33 HIS O 304 GLN Q 33 HIS Q 246 ASN S 33 HIS S 304 GLN U 14 ASN U 33 HIS U 304 GLN U 322 ASN W 33 HIS W 322 ASN Y 33 HIS ** Y 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.109490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.092018 restraints weight = 68506.826| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.10 r_work: 0.2775 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45690 Z= 0.144 Angle : 0.550 9.500 62145 Z= 0.281 Chirality : 0.043 0.163 7110 Planarity : 0.004 0.034 7650 Dihedral : 10.474 73.535 7170 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.73 % Favored : 96.15 % Rotamer: Outliers : 2.62 % Allowed : 11.66 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.80 (0.12), residues: 5355 helix: 0.17 (0.10), residues: 3120 sheet: -1.78 (0.25), residues: 390 loop : -1.31 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 0 213 TYR 0.019 0.001 TYR D 303 PHE 0.011 0.001 PHE G 324 TRP 0.005 0.001 TRP W 333 HIS 0.005 0.001 HIS S 33 Details of bonding type rmsd covalent geometry : bond 0.00344 (45690) covalent geometry : angle 0.54997 (62145) hydrogen bonds : bond 0.03293 ( 1710) hydrogen bonds : angle 3.87474 ( 4950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 843 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8812 (ptp-110) cc_final: 0.8534 (ptp-110) REVERT: C 53 ASP cc_start: 0.8887 (t0) cc_final: 0.8516 (t0) REVERT: C 55 LEU cc_start: 0.8985 (tp) cc_final: 0.8575 (mt) REVERT: C 93 ASP cc_start: 0.8011 (p0) cc_final: 0.7798 (p0) REVERT: C 143 ARG cc_start: 0.7621 (pmt170) cc_final: 0.7090 (ptt-90) REVERT: C 256 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8297 (t0) REVERT: C 371 ARG cc_start: 0.7871 (mtp180) cc_final: 0.7519 (mtp180) REVERT: A 143 ARG cc_start: 0.7706 (pmt170) cc_final: 0.7382 (ptt-90) REVERT: A 212 GLU cc_start: 0.8823 (pt0) cc_final: 0.8507 (pt0) REVERT: A 256 ASP cc_start: 0.8495 (t70) cc_final: 0.8109 (t70) REVERT: A 280 MET cc_start: 0.9088 (mmt) cc_final: 0.8758 (mmm) REVERT: A 304 GLN cc_start: 0.8111 (mt0) cc_final: 0.7630 (mm110) REVERT: A 323 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8840 (ttmm) REVERT: A 367 GLU cc_start: 0.8237 (tt0) cc_final: 0.7925 (tt0) REVERT: A 371 ARG cc_start: 0.7828 (mtp180) cc_final: 0.7438 (mtp180) REVERT: D 143 ARG cc_start: 0.7705 (pmt170) cc_final: 0.7163 (ptt-90) REVERT: D 150 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8230 (mttt) REVERT: D 320 ILE cc_start: 0.9329 (tt) cc_final: 0.9085 (tt) REVERT: G 201 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: G 371 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7632 (mtp180) REVERT: I 53 ASP cc_start: 0.8676 (t0) cc_final: 0.8437 (t0) REVERT: I 57 ARG cc_start: 0.8344 (ptp-110) cc_final: 0.8026 (ttp-170) REVERT: I 123 MET cc_start: 0.6462 (mtm) cc_final: 0.6064 (ptt) REVERT: I 143 ARG cc_start: 0.7877 (pmt170) cc_final: 0.7535 (ptt-90) REVERT: I 159 ASP cc_start: 0.8159 (p0) cc_final: 0.7844 (p0) REVERT: I 201 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.7796 (mt0) REVERT: I 228 SER cc_start: 0.9104 (p) cc_final: 0.8891 (m) REVERT: I 256 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8460 (t70) REVERT: I 271 LEU cc_start: 0.8749 (mt) cc_final: 0.8458 (mt) REVERT: K 5 LEU cc_start: 0.8880 (mm) cc_final: 0.8608 (mm) REVERT: K 53 ASP cc_start: 0.8873 (t0) cc_final: 0.8580 (t0) REVERT: K 57 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7962 (ttp-170) REVERT: K 102 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8309 (pp) REVERT: K 159 ASP cc_start: 0.8286 (p0) cc_final: 0.7961 (p0) REVERT: K 201 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: M 102 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8361 (pp) REVERT: M 103 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8243 (mt-10) REVERT: M 143 ARG cc_start: 0.7836 (pmt170) cc_final: 0.7369 (ptt-90) REVERT: M 156 GLU cc_start: 0.7757 (tm-30) cc_final: 0.6732 (tm-30) REVERT: M 371 ARG cc_start: 0.7748 (mtp180) cc_final: 0.7258 (mtp180) REVERT: O 6 ARG cc_start: 0.8505 (ptp90) cc_final: 0.8267 (ttp-110) REVERT: O 53 ASP cc_start: 0.8900 (t0) cc_final: 0.8625 (t0) REVERT: O 54 ARG cc_start: 0.8353 (mmp80) cc_final: 0.8026 (mmp80) REVERT: O 82 GLU cc_start: 0.8499 (tt0) cc_final: 0.8244 (mt-10) REVERT: O 93 ASP cc_start: 0.7801 (p0) cc_final: 0.7402 (t70) REVERT: O 100 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8346 (tmm160) REVERT: O 143 ARG cc_start: 0.7651 (pmt170) cc_final: 0.7206 (ptt-90) REVERT: O 212 GLU cc_start: 0.8691 (pt0) cc_final: 0.8432 (pt0) REVERT: O 371 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7430 (mtp180) REVERT: Q 53 ASP cc_start: 0.8829 (t0) cc_final: 0.8539 (t0) REVERT: Q 57 ARG cc_start: 0.8443 (ptp-110) cc_final: 0.8165 (ttp-170) REVERT: Q 93 ASP cc_start: 0.7918 (p0) cc_final: 0.7709 (p0) REVERT: Q 143 ARG cc_start: 0.7570 (pmt170) cc_final: 0.6670 (ptm-80) REVERT: Q 158 GLN cc_start: 0.8464 (mp10) cc_final: 0.8240 (mp10) REVERT: Q 213 ARG cc_start: 0.8182 (mtp-110) cc_final: 0.7887 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7952 (m-30) cc_final: 0.7622 (m-30) REVERT: Q 351 ASN cc_start: 0.8829 (t0) cc_final: 0.8597 (t0) REVERT: S 29 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8417 (ptp-110) REVERT: S 55 LEU cc_start: 0.8866 (tp) cc_final: 0.8662 (mt) REVERT: S 143 ARG cc_start: 0.7376 (ptt-90) cc_final: 0.6240 (ttp-110) REVERT: S 149 ASN cc_start: 0.8892 (t0) cc_final: 0.8667 (t0) REVERT: S 150 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8029 (mttm) REVERT: S 228 SER cc_start: 0.8957 (p) cc_final: 0.8703 (m) REVERT: S 371 ARG cc_start: 0.7749 (mtp180) cc_final: 0.7383 (mtp180) REVERT: U 143 ARG cc_start: 0.7739 (pmt170) cc_final: 0.6794 (ttp-110) REVERT: U 201 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: U 227 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8685 (tp) REVERT: U 258 ASP cc_start: 0.9051 (t70) cc_final: 0.8819 (t0) REVERT: W 31 ILE cc_start: 0.8967 (tp) cc_final: 0.8727 (tp) REVERT: W 111 GLN cc_start: 0.8440 (tp-100) cc_final: 0.7868 (tp40) REVERT: W 143 ARG cc_start: 0.7707 (pmt170) cc_final: 0.6610 (ptm-80) REVERT: W 225 GLU cc_start: 0.8671 (tt0) cc_final: 0.8448 (tt0) REVERT: W 371 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7442 (mtp180) REVERT: Y 6 ARG cc_start: 0.8553 (ptp90) cc_final: 0.8144 (mtm110) REVERT: Y 123 MET cc_start: 0.5987 (mtm) cc_final: 0.5508 (mtp) REVERT: Y 126 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7598 (tt0) REVERT: Y 225 GLU cc_start: 0.8700 (tt0) cc_final: 0.8377 (tt0) REVERT: Y 301 ASN cc_start: 0.8229 (m110) cc_final: 0.7922 (m-40) REVERT: Y 371 ARG cc_start: 0.7850 (mtp180) cc_final: 0.7321 (mtp180) REVERT: 0 53 ASP cc_start: 0.9107 (t0) cc_final: 0.8855 (t0) REVERT: 0 201 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: 0 292 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: 0 371 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7294 (mtp180) REVERT: 2 10 LEU cc_start: 0.9014 (mt) cc_final: 0.8810 (mm) REVERT: 2 102 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8289 (pp) REVERT: 2 123 MET cc_start: 0.4086 (mtm) cc_final: 0.3798 (ttm) REVERT: 2 201 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: 2 208 GLU cc_start: 0.7904 (mp0) cc_final: 0.7614 (mm-30) REVERT: 2 209 PHE cc_start: 0.8059 (m-10) cc_final: 0.7684 (m-10) REVERT: 2 274 LYS cc_start: 0.8903 (tttp) cc_final: 0.8626 (ttmt) REVERT: 2 317 GLU cc_start: 0.6013 (tm-30) cc_final: 0.4223 (tm-30) REVERT: 2 371 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7334 (mtp180) outliers start: 122 outliers final: 76 residues processed: 937 average time/residue: 0.3077 time to fit residues: 454.6368 Evaluate side-chains 895 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 803 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 256 ASP Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 259 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 164 ASN Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 225 GLU Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 57 ARG Chi-restraints excluded: chain S residue 91 ILE Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 123 MET Chi-restraints excluded: chain W residue 186 ASP Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 187 THR Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 0 residue 292 GLU Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 259 THR Chi-restraints excluded: chain 2 residue 304 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 65 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 538 optimal weight: 0.9980 chunk 410 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 263 optimal weight: 20.0000 chunk 520 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 246 ASN C 304 GLN A 164 ASN D 33 HIS G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 164 ASN K 246 ASN ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS Q 33 HIS Q 164 ASN S 33 HIS U 33 HIS U 304 GLN U 322 ASN W 33 HIS W 322 ASN Y 33 HIS 0 33 HIS 0 322 ASN 2 89 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.100771 restraints weight = 66936.901| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.02 r_work: 0.2880 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 45690 Z= 0.106 Angle : 0.520 8.482 62145 Z= 0.266 Chirality : 0.042 0.237 7110 Planarity : 0.003 0.037 7650 Dihedral : 10.415 73.442 7170 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.01 % Favored : 96.86 % Rotamer: Outliers : 2.41 % Allowed : 12.47 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.61 (0.12), residues: 5355 helix: 0.31 (0.10), residues: 3150 sheet: -1.86 (0.25), residues: 390 loop : -1.18 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 213 TYR 0.019 0.001 TYR D 303 PHE 0.018 0.001 PHE 0 209 TRP 0.007 0.001 TRP U 333 HIS 0.005 0.001 HIS S 33 Details of bonding type rmsd covalent geometry : bond 0.00247 (45690) covalent geometry : angle 0.52042 (62145) hydrogen bonds : bond 0.03123 ( 1710) hydrogen bonds : angle 3.71458 ( 4950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 855 time to evaluate : 1.855 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: C 53 ASP cc_start: 0.8856 (t0) cc_final: 0.8520 (t0) REVERT: C 93 ASP cc_start: 0.8014 (p0) cc_final: 0.7801 (p0) REVERT: C 143 ARG cc_start: 0.7601 (pmt170) cc_final: 0.7097 (ptt-90) REVERT: C 150 LYS cc_start: 0.8579 (mtmm) cc_final: 0.7867 (mttp) REVERT: C 213 ARG cc_start: 0.7984 (mtp-110) cc_final: 0.7764 (ttm-80) REVERT: C 371 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7624 (mtp180) REVERT: A 82 GLU cc_start: 0.4192 (mp0) cc_final: 0.3982 (mp0) REVERT: A 143 ARG cc_start: 0.7675 (pmt170) cc_final: 0.7366 (ptt-90) REVERT: A 212 GLU cc_start: 0.8822 (pt0) cc_final: 0.8416 (pt0) REVERT: A 280 MET cc_start: 0.9099 (mmt) cc_final: 0.8826 (mmm) REVERT: A 304 GLN cc_start: 0.8050 (mt0) cc_final: 0.7667 (mm-40) REVERT: A 367 GLU cc_start: 0.8234 (tt0) cc_final: 0.7934 (tt0) REVERT: A 371 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7519 (mtp180) REVERT: D 143 ARG cc_start: 0.7688 (pmt170) cc_final: 0.7180 (ptt-90) REVERT: D 150 LYS cc_start: 0.8894 (mtmm) cc_final: 0.8336 (mttt) REVERT: D 212 GLU cc_start: 0.8721 (pt0) cc_final: 0.8375 (pt0) REVERT: D 256 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8342 (t0) REVERT: G 201 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: G 256 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8339 (t70) REVERT: G 371 ARG cc_start: 0.8044 (mtp180) cc_final: 0.7714 (mtp180) REVERT: I 53 ASP cc_start: 0.8705 (t0) cc_final: 0.8453 (t0) REVERT: I 57 ARG cc_start: 0.8299 (ptp-110) cc_final: 0.8047 (ttp-170) REVERT: I 123 MET cc_start: 0.6454 (mtm) cc_final: 0.6192 (ptt) REVERT: I 143 ARG cc_start: 0.7868 (pmt170) cc_final: 0.7540 (ptt-90) REVERT: I 159 ASP cc_start: 0.8154 (p0) cc_final: 0.7826 (p0) REVERT: I 201 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: I 271 LEU cc_start: 0.8766 (mt) cc_final: 0.8516 (mt) REVERT: I 371 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7694 (mtp180) REVERT: K 5 LEU cc_start: 0.8927 (mm) cc_final: 0.8689 (mm) REVERT: K 53 ASP cc_start: 0.8868 (t0) cc_final: 0.8583 (t0) REVERT: K 57 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8021 (ttp-170) REVERT: K 102 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8266 (pp) REVERT: K 150 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8356 (mtpt) REVERT: K 201 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: M 102 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8362 (pp) REVERT: M 103 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8226 (mt-10) REVERT: M 143 ARG cc_start: 0.7826 (pmt170) cc_final: 0.7361 (ptt-90) REVERT: M 371 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7350 (mtp180) REVERT: O 6 ARG cc_start: 0.8510 (ptp90) cc_final: 0.8297 (ttp-110) REVERT: O 53 ASP cc_start: 0.8798 (t0) cc_final: 0.8455 (t0) REVERT: O 54 ARG cc_start: 0.8155 (mmp80) cc_final: 0.7735 (mmp80) REVERT: O 82 GLU cc_start: 0.8437 (tt0) cc_final: 0.8218 (mt-10) REVERT: O 93 ASP cc_start: 0.7732 (p0) cc_final: 0.7430 (t70) REVERT: O 100 ARG cc_start: 0.8651 (ttp80) cc_final: 0.8360 (tmm160) REVERT: O 143 ARG cc_start: 0.7654 (pmt170) cc_final: 0.7224 (ptt-90) REVERT: O 212 GLU cc_start: 0.8675 (pt0) cc_final: 0.8408 (pt0) REVERT: O 371 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7486 (mtp180) REVERT: Q 53 ASP cc_start: 0.8805 (t0) cc_final: 0.8524 (t0) REVERT: Q 57 ARG cc_start: 0.8483 (ptp-110) cc_final: 0.8234 (ttp-170) REVERT: Q 93 ASP cc_start: 0.7822 (p0) cc_final: 0.7617 (p0) REVERT: Q 143 ARG cc_start: 0.7593 (pmt170) cc_final: 0.6743 (ptm-80) REVERT: Q 212 GLU cc_start: 0.8789 (pt0) cc_final: 0.8498 (pt0) REVERT: Q 213 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7860 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7893 (m-30) cc_final: 0.7534 (m-30) REVERT: Q 301 ASN cc_start: 0.8201 (m-40) cc_final: 0.7902 (m-40) REVERT: S 111 GLN cc_start: 0.8442 (tp40) cc_final: 0.7869 (tp40) REVERT: S 143 ARG cc_start: 0.7336 (ptt-90) cc_final: 0.6274 (ttp-110) REVERT: S 149 ASN cc_start: 0.8863 (t0) cc_final: 0.8653 (t0) REVERT: S 150 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8064 (mttt) REVERT: S 161 GLU cc_start: 0.7891 (pt0) cc_final: 0.7628 (pt0) REVERT: S 228 SER cc_start: 0.8937 (p) cc_final: 0.8693 (m) REVERT: S 371 ARG cc_start: 0.7751 (mtp180) cc_final: 0.7413 (mtp180) REVERT: U 31 ILE cc_start: 0.8942 (tp) cc_final: 0.8705 (tp) REVERT: U 143 ARG cc_start: 0.7642 (pmt170) cc_final: 0.6807 (ttp-110) REVERT: U 201 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: U 227 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8630 (tp) REVERT: U 258 ASP cc_start: 0.9042 (t70) cc_final: 0.8833 (t0) REVERT: U 371 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7469 (mtp180) REVERT: W 31 ILE cc_start: 0.9008 (tp) cc_final: 0.8791 (tp) REVERT: W 111 GLN cc_start: 0.8419 (tp-100) cc_final: 0.7866 (tp40) REVERT: W 143 ARG cc_start: 0.7686 (pmt170) cc_final: 0.6666 (ptm-80) REVERT: W 371 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7392 (mtp180) REVERT: Y 6 ARG cc_start: 0.8541 (ptp90) cc_final: 0.8085 (mtm110) REVERT: Y 123 MET cc_start: 0.5982 (mtm) cc_final: 0.5536 (mtp) REVERT: Y 126 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7591 (tt0) REVERT: Y 150 LYS cc_start: 0.8532 (ptpp) cc_final: 0.7951 (mttt) REVERT: Y 225 GLU cc_start: 0.8629 (tt0) cc_final: 0.8400 (tt0) REVERT: Y 301 ASN cc_start: 0.8272 (m110) cc_final: 0.8018 (m-40) REVERT: Y 371 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7436 (mtp180) REVERT: 0 53 ASP cc_start: 0.9074 (t0) cc_final: 0.8853 (t0) REVERT: 0 123 MET cc_start: 0.7152 (mtp) cc_final: 0.6720 (mtp) REVERT: 0 201 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: 0 351 ASN cc_start: 0.8785 (t0) cc_final: 0.8567 (t0) REVERT: 0 371 ARG cc_start: 0.7818 (mtp180) cc_final: 0.7366 (mtp180) REVERT: 2 53 ASP cc_start: 0.9147 (t0) cc_final: 0.8890 (t0) REVERT: 2 102 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8297 (pp) REVERT: 2 123 MET cc_start: 0.4155 (mtm) cc_final: 0.3954 (ttm) REVERT: 2 201 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: 2 208 GLU cc_start: 0.7731 (mp0) cc_final: 0.7465 (mm-30) REVERT: 2 209 PHE cc_start: 0.7858 (m-10) cc_final: 0.7508 (m-10) REVERT: 2 274 LYS cc_start: 0.8929 (tttp) cc_final: 0.8680 (ttmt) REVERT: 2 317 GLU cc_start: 0.6060 (tm-30) cc_final: 0.4281 (tm-30) REVERT: 2 371 ARG cc_start: 0.7719 (mtp180) cc_final: 0.6877 (mtp180) outliers start: 112 outliers final: 70 residues processed: 937 average time/residue: 0.3118 time to fit residues: 457.8963 Evaluate side-chains 882 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 798 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 256 ASP Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 164 ASN Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 57 ARG Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 237 ILE Chi-restraints excluded: chain S residue 256 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 228 SER Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 304 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 76 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 423 optimal weight: 7.9990 chunk 224 optimal weight: 0.0980 chunk 82 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 451 optimal weight: 0.4980 chunk 250 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 528 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 246 ASN C 304 GLN D 33 HIS G 14 ASN G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS O 304 GLN Q 33 HIS ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 HIS U 304 GLN U 322 ASN W 33 HIS Y 33 HIS Y 246 ASN Y 304 GLN 0 33 HIS 2 89 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.094500 restraints weight = 67721.259| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.08 r_work: 0.2945 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 45690 Z= 0.106 Angle : 0.517 8.120 62145 Z= 0.264 Chirality : 0.042 0.121 7110 Planarity : 0.003 0.037 7650 Dihedral : 10.371 73.424 7170 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.94 % Rotamer: Outliers : 2.47 % Allowed : 12.95 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.43 (0.12), residues: 5355 helix: 0.43 (0.10), residues: 3135 sheet: -1.80 (0.25), residues: 390 loop : -1.03 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 249 TYR 0.021 0.001 TYR Q 303 PHE 0.018 0.001 PHE 0 209 TRP 0.006 0.001 TRP S 333 HIS 0.005 0.001 HIS S 33 Details of bonding type rmsd covalent geometry : bond 0.00249 (45690) covalent geometry : angle 0.51700 (62145) hydrogen bonds : bond 0.03036 ( 1710) hydrogen bonds : angle 3.65031 ( 4950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 844 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.8864 (t0) cc_final: 0.8530 (t0) REVERT: C 143 ARG cc_start: 0.7618 (pmt170) cc_final: 0.7129 (ptt-90) REVERT: C 150 LYS cc_start: 0.8576 (mtmm) cc_final: 0.7944 (mttp) REVERT: C 371 ARG cc_start: 0.8011 (mtp180) cc_final: 0.7760 (mtp180) REVERT: A 143 ARG cc_start: 0.7682 (pmt170) cc_final: 0.7257 (ptt-90) REVERT: A 150 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8243 (mttt) REVERT: A 212 GLU cc_start: 0.8835 (pt0) cc_final: 0.8292 (pt0) REVERT: A 256 ASP cc_start: 0.8429 (t70) cc_final: 0.8077 (t70) REVERT: A 280 MET cc_start: 0.9125 (mmt) cc_final: 0.8866 (mmm) REVERT: A 304 GLN cc_start: 0.8028 (mt0) cc_final: 0.7677 (mm-40) REVERT: A 367 GLU cc_start: 0.8260 (tt0) cc_final: 0.7987 (tt0) REVERT: A 371 ARG cc_start: 0.7891 (mtp180) cc_final: 0.7530 (mtp180) REVERT: D 143 ARG cc_start: 0.7708 (pmt170) cc_final: 0.7206 (ptt-90) REVERT: D 150 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8382 (mttt) REVERT: D 212 GLU cc_start: 0.8746 (pt0) cc_final: 0.8410 (pt0) REVERT: D 256 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8295 (t0) REVERT: D 304 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8312 (mm-40) REVERT: G 150 LYS cc_start: 0.8662 (ptpp) cc_final: 0.7974 (mttp) REVERT: G 201 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: G 256 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8378 (t70) REVERT: G 371 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7802 (mtp180) REVERT: I 53 ASP cc_start: 0.8700 (t0) cc_final: 0.8452 (t0) REVERT: I 57 ARG cc_start: 0.8258 (ptp-110) cc_final: 0.8057 (ttp-170) REVERT: I 123 MET cc_start: 0.6582 (mtm) cc_final: 0.6363 (ptt) REVERT: I 143 ARG cc_start: 0.7929 (pmt170) cc_final: 0.7616 (ptt-90) REVERT: I 150 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8330 (mttt) REVERT: I 156 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7648 (tm-30) REVERT: I 159 ASP cc_start: 0.8150 (p0) cc_final: 0.7753 (p0) REVERT: I 227 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8593 (tp) REVERT: I 256 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8418 (t70) REVERT: I 271 LEU cc_start: 0.8788 (mt) cc_final: 0.8558 (mt) REVERT: I 371 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7671 (mtp180) REVERT: K 5 LEU cc_start: 0.8971 (mm) cc_final: 0.8741 (mm) REVERT: K 53 ASP cc_start: 0.8895 (t0) cc_final: 0.8613 (t0) REVERT: K 57 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8063 (ttp-170) REVERT: K 102 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8238 (pp) REVERT: K 150 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8299 (mttt) REVERT: K 159 ASP cc_start: 0.8295 (p0) cc_final: 0.7982 (p0) REVERT: K 201 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.7669 (mt0) REVERT: M 102 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8372 (pp) REVERT: M 143 ARG cc_start: 0.7849 (pmt170) cc_final: 0.7394 (ptt-90) REVERT: M 156 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7459 (tm-30) REVERT: M 371 ARG cc_start: 0.7849 (mtp180) cc_final: 0.7412 (mtp180) REVERT: O 6 ARG cc_start: 0.8532 (ptp90) cc_final: 0.8311 (ttp-110) REVERT: O 53 ASP cc_start: 0.8736 (t0) cc_final: 0.8397 (t0) REVERT: O 54 ARG cc_start: 0.8007 (mmp80) cc_final: 0.7581 (mmp80) REVERT: O 82 GLU cc_start: 0.8444 (tt0) cc_final: 0.8219 (mt-10) REVERT: O 93 ASP cc_start: 0.7738 (p0) cc_final: 0.7467 (t70) REVERT: O 100 ARG cc_start: 0.8636 (ttp80) cc_final: 0.8359 (tmm160) REVERT: O 143 ARG cc_start: 0.7680 (pmt170) cc_final: 0.7250 (ptt-90) REVERT: O 212 GLU cc_start: 0.8676 (pt0) cc_final: 0.8364 (pt0) REVERT: O 371 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7550 (mtp180) REVERT: Q 53 ASP cc_start: 0.8821 (t0) cc_final: 0.8542 (t0) REVERT: Q 57 ARG cc_start: 0.8464 (ptp-110) cc_final: 0.8168 (ttp-170) REVERT: Q 93 ASP cc_start: 0.7911 (p0) cc_final: 0.7700 (p0) REVERT: Q 143 ARG cc_start: 0.7587 (pmt170) cc_final: 0.6775 (ptm-80) REVERT: Q 212 GLU cc_start: 0.8807 (pt0) cc_final: 0.8506 (pt0) REVERT: Q 213 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.7884 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7893 (m-30) cc_final: 0.7535 (m-30) REVERT: S 143 ARG cc_start: 0.7346 (ptt-90) cc_final: 0.6310 (ttp-110) REVERT: S 150 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8298 (mtpt) REVERT: S 161 GLU cc_start: 0.7937 (pt0) cc_final: 0.7692 (pt0) REVERT: S 228 SER cc_start: 0.8910 (p) cc_final: 0.8684 (m) REVERT: S 256 ASP cc_start: 0.8750 (t70) cc_final: 0.8169 (t0) REVERT: S 371 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7528 (mtp180) REVERT: U 31 ILE cc_start: 0.8943 (tp) cc_final: 0.8716 (tp) REVERT: U 143 ARG cc_start: 0.7632 (pmt170) cc_final: 0.6859 (ttp-110) REVERT: U 201 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: U 209 PHE cc_start: 0.8073 (m-10) cc_final: 0.7722 (m-10) REVERT: U 256 ASP cc_start: 0.8714 (t70) cc_final: 0.8073 (t0) REVERT: U 332 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9250 (tm) REVERT: U 371 ARG cc_start: 0.7818 (mtp180) cc_final: 0.7526 (mtp180) REVERT: W 111 GLN cc_start: 0.8383 (tp-100) cc_final: 0.7838 (tp40) REVERT: W 143 ARG cc_start: 0.7666 (pmt170) cc_final: 0.6649 (ptm-80) REVERT: W 258 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8792 (t0) REVERT: W 371 ARG cc_start: 0.7893 (mtp180) cc_final: 0.7496 (mtp180) REVERT: Y 6 ARG cc_start: 0.8507 (ptp90) cc_final: 0.8116 (mtm110) REVERT: Y 14 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.8002 (m-40) REVERT: Y 123 MET cc_start: 0.6044 (mtm) cc_final: 0.5612 (mtp) REVERT: Y 126 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7605 (tt0) REVERT: Y 150 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8030 (mtpt) REVERT: Y 201 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8673 (mp10) REVERT: Y 209 PHE cc_start: 0.8367 (m-10) cc_final: 0.8154 (m-10) REVERT: Y 371 ARG cc_start: 0.7941 (mtp180) cc_final: 0.7481 (mtp180) REVERT: 0 53 ASP cc_start: 0.9071 (t0) cc_final: 0.8871 (t0) REVERT: 0 123 MET cc_start: 0.7183 (mtp) cc_final: 0.6781 (mtp) REVERT: 0 201 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: 0 225 GLU cc_start: 0.8713 (tt0) cc_final: 0.8382 (tt0) REVERT: 0 325 SER cc_start: 0.9305 (t) cc_final: 0.9025 (p) REVERT: 0 371 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7428 (mtp180) REVERT: 2 102 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8351 (pp) REVERT: 2 123 MET cc_start: 0.4317 (mtm) cc_final: 0.4111 (ttm) REVERT: 2 201 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: 2 209 PHE cc_start: 0.7752 (m-10) cc_final: 0.7500 (m-10) REVERT: 2 256 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8340 (t0) REVERT: 2 274 LYS cc_start: 0.8983 (tttp) cc_final: 0.8748 (ttmt) REVERT: 2 317 GLU cc_start: 0.6143 (tm-30) cc_final: 0.4249 (tm-30) REVERT: 2 371 ARG cc_start: 0.7738 (mtp180) cc_final: 0.7133 (mtp180) outliers start: 115 outliers final: 78 residues processed: 929 average time/residue: 0.2979 time to fit residues: 435.6085 Evaluate side-chains 894 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 795 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 304 GLN Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 256 ASP Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 164 ASN Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 91 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 186 ASP Chi-restraints excluded: chain W residue 258 ASP Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Y residue 201 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 228 SER Chi-restraints excluded: chain 0 residue 256 ASP Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 256 ASP Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 262 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 510 optimal weight: 0.7980 chunk 477 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 486 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN D 33 HIS G 14 ASN G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS I 246 ASN ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS Q 33 HIS S 33 HIS S 246 ASN U 33 HIS U 304 GLN U 322 ASN W 33 HIS Y 33 HIS Y 246 ASN 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.094584 restraints weight = 67833.731| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.05 r_work: 0.2983 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 45690 Z= 0.113 Angle : 0.522 8.754 62145 Z= 0.267 Chirality : 0.042 0.150 7110 Planarity : 0.003 0.037 7650 Dihedral : 10.344 73.429 7170 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 2.45 % Allowed : 13.66 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.34 (0.12), residues: 5355 helix: 0.48 (0.10), residues: 3135 sheet: -1.75 (0.25), residues: 390 loop : -0.93 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 249 TYR 0.020 0.001 TYR Q 303 PHE 0.019 0.001 PHE 0 209 TRP 0.007 0.001 TRP W 333 HIS 0.008 0.001 HIS U 33 Details of bonding type rmsd covalent geometry : bond 0.00267 (45690) covalent geometry : angle 0.52182 (62145) hydrogen bonds : bond 0.03000 ( 1710) hydrogen bonds : angle 3.60338 ( 4950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 845 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.8900 (t0) cc_final: 0.8629 (t0) REVERT: C 143 ARG cc_start: 0.7624 (pmt170) cc_final: 0.7120 (ptt-90) REVERT: C 150 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8137 (mmmt) REVERT: C 225 GLU cc_start: 0.8377 (pt0) cc_final: 0.8163 (tt0) REVERT: C 371 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7706 (mtp180) REVERT: A 143 ARG cc_start: 0.7651 (pmt170) cc_final: 0.7245 (ptt-90) REVERT: A 150 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8057 (mptt) REVERT: A 212 GLU cc_start: 0.8839 (pt0) cc_final: 0.8622 (pt0) REVERT: A 256 ASP cc_start: 0.8491 (t70) cc_final: 0.8117 (t70) REVERT: A 280 MET cc_start: 0.9108 (mmt) cc_final: 0.8866 (mmm) REVERT: A 304 GLN cc_start: 0.7988 (mt0) cc_final: 0.7648 (mm-40) REVERT: A 367 GLU cc_start: 0.8379 (tt0) cc_final: 0.8091 (tt0) REVERT: A 371 ARG cc_start: 0.7882 (mtp180) cc_final: 0.7519 (mtp180) REVERT: D 143 ARG cc_start: 0.7705 (pmt170) cc_final: 0.7218 (ptt-90) REVERT: D 150 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8426 (mttt) REVERT: D 212 GLU cc_start: 0.8807 (pt0) cc_final: 0.8474 (pt0) REVERT: D 256 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.7999 (t0) REVERT: D 304 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8261 (mm-40) REVERT: G 150 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8005 (mttp) REVERT: G 201 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: G 371 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7798 (mtp180) REVERT: I 53 ASP cc_start: 0.8694 (t0) cc_final: 0.8441 (t0) REVERT: I 143 ARG cc_start: 0.7915 (pmt170) cc_final: 0.7600 (ptt-90) REVERT: I 156 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7743 (tm-30) REVERT: I 159 ASP cc_start: 0.8202 (p0) cc_final: 0.7792 (p0) REVERT: I 227 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8599 (tp) REVERT: I 271 LEU cc_start: 0.8769 (mt) cc_final: 0.8530 (mt) REVERT: I 371 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7755 (mtp180) REVERT: K 53 ASP cc_start: 0.8963 (t0) cc_final: 0.8695 (t0) REVERT: K 57 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8076 (ttp-170) REVERT: K 102 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8264 (pp) REVERT: K 150 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8350 (mttt) REVERT: K 159 ASP cc_start: 0.8292 (p0) cc_final: 0.8053 (p0) REVERT: K 201 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: K 256 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8206 (t0) REVERT: M 102 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8408 (pp) REVERT: M 143 ARG cc_start: 0.7804 (pmt170) cc_final: 0.7370 (ptt-90) REVERT: M 156 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7501 (tm-30) REVERT: M 371 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7455 (mtp180) REVERT: O 6 ARG cc_start: 0.8561 (ptp90) cc_final: 0.8358 (ttp-110) REVERT: O 53 ASP cc_start: 0.8803 (t0) cc_final: 0.8491 (t0) REVERT: O 54 ARG cc_start: 0.8091 (mmp80) cc_final: 0.7753 (mmp80) REVERT: O 82 GLU cc_start: 0.8423 (tt0) cc_final: 0.8222 (mt-10) REVERT: O 93 ASP cc_start: 0.7755 (p0) cc_final: 0.7472 (t70) REVERT: O 100 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8306 (tmm160) REVERT: O 143 ARG cc_start: 0.7631 (pmt170) cc_final: 0.7223 (ptt-90) REVERT: O 212 GLU cc_start: 0.8672 (pt0) cc_final: 0.8347 (pt0) REVERT: O 297 GLU cc_start: 0.8468 (tt0) cc_final: 0.8249 (tt0) REVERT: O 371 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7711 (mtp180) REVERT: Q 53 ASP cc_start: 0.8824 (t0) cc_final: 0.8531 (t0) REVERT: Q 57 ARG cc_start: 0.8469 (ptp-110) cc_final: 0.8182 (ttp-170) REVERT: Q 93 ASP cc_start: 0.7820 (p0) cc_final: 0.7604 (p0) REVERT: Q 143 ARG cc_start: 0.7534 (pmt170) cc_final: 0.6680 (ttp-110) REVERT: Q 212 GLU cc_start: 0.8779 (pt0) cc_final: 0.8500 (pt0) REVERT: Q 213 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7898 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7808 (m-30) cc_final: 0.7453 (m-30) REVERT: S 143 ARG cc_start: 0.7350 (ptt-90) cc_final: 0.6319 (ttp-110) REVERT: S 150 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8334 (mtpt) REVERT: S 161 GLU cc_start: 0.7940 (pt0) cc_final: 0.7686 (pt0) REVERT: S 213 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7720 (ttt180) REVERT: S 228 SER cc_start: 0.8912 (p) cc_final: 0.8699 (m) REVERT: S 371 ARG cc_start: 0.7910 (mtp180) cc_final: 0.7620 (mtp180) REVERT: U 31 ILE cc_start: 0.8970 (tp) cc_final: 0.8761 (tp) REVERT: U 143 ARG cc_start: 0.7683 (pmt170) cc_final: 0.6837 (ttp-110) REVERT: U 201 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: U 209 PHE cc_start: 0.8019 (m-10) cc_final: 0.7678 (m-10) REVERT: U 332 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9218 (tm) REVERT: U 371 ARG cc_start: 0.7792 (mtp180) cc_final: 0.7536 (mtp180) REVERT: W 111 GLN cc_start: 0.8262 (tp-100) cc_final: 0.7741 (tp40) REVERT: W 143 ARG cc_start: 0.7714 (pmt170) cc_final: 0.6693 (ptm-80) REVERT: W 371 ARG cc_start: 0.7786 (mtp180) cc_final: 0.7358 (mtp180) REVERT: Y 6 ARG cc_start: 0.8440 (ptp90) cc_final: 0.8075 (mtm110) REVERT: Y 123 MET cc_start: 0.6132 (mtm) cc_final: 0.5662 (mtp) REVERT: Y 126 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7629 (tt0) REVERT: Y 150 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8040 (mttt) REVERT: Y 201 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8655 (mp10) REVERT: Y 209 PHE cc_start: 0.8271 (m-10) cc_final: 0.8066 (m-10) REVERT: Y 304 GLN cc_start: 0.8624 (tt0) cc_final: 0.8389 (mt0) REVERT: Y 371 ARG cc_start: 0.7844 (mtp180) cc_final: 0.7428 (mtp180) REVERT: 0 53 ASP cc_start: 0.9103 (t0) cc_final: 0.8858 (t0) REVERT: 0 123 MET cc_start: 0.7163 (mtp) cc_final: 0.6845 (mtp) REVERT: 0 201 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: 0 225 GLU cc_start: 0.8658 (tt0) cc_final: 0.8382 (tt0) REVERT: 0 313 MET cc_start: 0.8726 (ptp) cc_final: 0.8456 (ptm) REVERT: 0 325 SER cc_start: 0.9294 (t) cc_final: 0.9034 (p) REVERT: 0 371 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7460 (mtp180) REVERT: 2 102 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8345 (pp) REVERT: 2 123 MET cc_start: 0.4467 (mtm) cc_final: 0.4184 (ttm) REVERT: 2 126 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7830 (tm-30) REVERT: 2 201 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8364 (mt0) REVERT: 2 209 PHE cc_start: 0.7639 (m-10) cc_final: 0.7378 (m-10) REVERT: 2 256 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8343 (t0) REVERT: 2 274 LYS cc_start: 0.8991 (tttp) cc_final: 0.8756 (ttmt) REVERT: 2 317 GLU cc_start: 0.6168 (tm-30) cc_final: 0.4180 (tm-30) REVERT: 2 371 ARG cc_start: 0.7900 (mtp180) cc_final: 0.7350 (mtp180) outliers start: 114 outliers final: 83 residues processed: 926 average time/residue: 0.2749 time to fit residues: 402.2285 Evaluate side-chains 911 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 810 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 304 GLN Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 164 ASN Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 57 ARG Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 237 ILE Chi-restraints excluded: chain S residue 256 ASP Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 186 ASP Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Y residue 201 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 57 ARG Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 228 SER Chi-restraints excluded: chain 0 residue 256 ASP Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 256 ASP Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 355 SER Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 145 optimal weight: 0.4980 chunk 126 optimal weight: 8.9990 chunk 508 optimal weight: 0.0870 chunk 313 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 457 optimal weight: 0.9980 chunk 277 optimal weight: 0.2980 chunk 183 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 437 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN D 164 ASN G 14 ASN G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 304 GLN M 33 HIS M 246 ASN O 33 HIS Q 33 HIS ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 ASN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 304 GLN U 322 ASN W 33 HIS W 304 GLN Y 164 ASN Y 246 ASN 0 33 HIS 2 86 GLN 2 246 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.101384 restraints weight = 66332.815| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.01 r_work: 0.2956 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 45690 Z= 0.095 Angle : 0.511 8.037 62145 Z= 0.261 Chirality : 0.041 0.152 7110 Planarity : 0.003 0.042 7650 Dihedral : 10.280 73.346 7170 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.11 % Allowed : 14.32 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.22 (0.12), residues: 5355 helix: 0.57 (0.10), residues: 3150 sheet: -1.68 (0.25), residues: 390 loop : -0.90 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 249 TYR 0.020 0.001 TYR Q 303 PHE 0.022 0.001 PHE 0 209 TRP 0.009 0.001 TRP 2 175 HIS 0.007 0.001 HIS U 33 Details of bonding type rmsd covalent geometry : bond 0.00212 (45690) covalent geometry : angle 0.51060 (62145) hydrogen bonds : bond 0.02850 ( 1710) hydrogen bonds : angle 3.48225 ( 4950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 909 time to evaluate : 1.301 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: C 53 ASP cc_start: 0.8895 (t0) cc_final: 0.8689 (t0) REVERT: C 143 ARG cc_start: 0.7527 (pmt170) cc_final: 0.7026 (ptt-90) REVERT: C 150 LYS cc_start: 0.8671 (mtmm) cc_final: 0.8201 (mmmt) REVERT: C 201 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: A 143 ARG cc_start: 0.7602 (pmt170) cc_final: 0.7203 (ptt-90) REVERT: A 150 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8130 (mptt) REVERT: A 201 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: A 212 GLU cc_start: 0.8773 (pt0) cc_final: 0.8562 (pt0) REVERT: A 280 MET cc_start: 0.9104 (mmt) cc_final: 0.8901 (mmt) REVERT: A 304 GLN cc_start: 0.8003 (mt0) cc_final: 0.7623 (mm-40) REVERT: A 367 GLU cc_start: 0.8349 (tt0) cc_final: 0.8065 (tt0) REVERT: A 371 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7530 (mtp180) REVERT: D 21 THR cc_start: 0.7601 (p) cc_final: 0.7296 (p) REVERT: D 57 ARG cc_start: 0.8333 (ptp-110) cc_final: 0.8046 (ttp-170) REVERT: D 123 MET cc_start: 0.6112 (ptt) cc_final: 0.5810 (ptp) REVERT: D 143 ARG cc_start: 0.7712 (pmt170) cc_final: 0.7224 (ptt-90) REVERT: D 150 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8466 (mmtt) REVERT: D 212 GLU cc_start: 0.8730 (pt0) cc_final: 0.8428 (pt0) REVERT: D 256 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.7978 (t0) REVERT: G 5 LEU cc_start: 0.8862 (mm) cc_final: 0.8597 (mm) REVERT: G 103 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8163 (mt-10) REVERT: G 150 LYS cc_start: 0.8594 (ptpp) cc_final: 0.8059 (mttp) REVERT: G 201 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: G 371 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7787 (mtp180) REVERT: I 53 ASP cc_start: 0.8649 (t0) cc_final: 0.8412 (t0) REVERT: I 103 GLU cc_start: 0.8200 (mp0) cc_final: 0.7985 (mp0) REVERT: I 143 ARG cc_start: 0.7839 (pmt170) cc_final: 0.7543 (ptt-90) REVERT: I 150 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8388 (mmtt) REVERT: I 156 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7804 (tm-30) REVERT: I 159 ASP cc_start: 0.8138 (p0) cc_final: 0.7698 (p0) REVERT: I 227 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8572 (tp) REVERT: I 256 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8252 (t70) REVERT: I 371 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7803 (mtp180) REVERT: K 53 ASP cc_start: 0.8972 (t0) cc_final: 0.8691 (t0) REVERT: K 57 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8097 (ttp-170) REVERT: K 102 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8115 (pp) REVERT: K 150 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8387 (mmmt) REVERT: K 159 ASP cc_start: 0.8235 (p0) cc_final: 0.8009 (p0) REVERT: K 201 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: M 102 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8250 (pp) REVERT: M 143 ARG cc_start: 0.7780 (pmt170) cc_final: 0.7350 (ptt-90) REVERT: M 150 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8195 (mmtm) REVERT: M 371 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7451 (mtp180) REVERT: O 53 ASP cc_start: 0.8745 (t0) cc_final: 0.8447 (t0) REVERT: O 54 ARG cc_start: 0.8097 (mmp80) cc_final: 0.7767 (mmp80) REVERT: O 93 ASP cc_start: 0.7736 (p0) cc_final: 0.7478 (t70) REVERT: O 100 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8217 (tmm160) REVERT: O 143 ARG cc_start: 0.7517 (pmt170) cc_final: 0.7110 (ptt-90) REVERT: O 150 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8035 (mmtm) REVERT: O 201 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: O 212 GLU cc_start: 0.8649 (pt0) cc_final: 0.8377 (pt0) REVERT: Q 5 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7774 (mm) REVERT: Q 53 ASP cc_start: 0.8814 (t0) cc_final: 0.8534 (t0) REVERT: Q 57 ARG cc_start: 0.8437 (ptp-110) cc_final: 0.8223 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7551 (pmt170) cc_final: 0.6721 (ttp-110) REVERT: Q 212 GLU cc_start: 0.8732 (pt0) cc_final: 0.8491 (pt0) REVERT: Q 213 ARG cc_start: 0.8214 (mtp-110) cc_final: 0.7888 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7793 (m-30) cc_final: 0.7464 (m-30) REVERT: Q 256 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8202 (t0) REVERT: S 143 ARG cc_start: 0.7319 (ptt-90) cc_final: 0.6276 (ttp-110) REVERT: S 150 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8238 (mttt) REVERT: S 161 GLU cc_start: 0.7937 (pt0) cc_final: 0.7685 (pt0) REVERT: S 213 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7700 (ttt180) REVERT: S 228 SER cc_start: 0.8928 (p) cc_final: 0.8723 (m) REVERT: S 371 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7638 (mtp180) REVERT: U 143 ARG cc_start: 0.7613 (pmt170) cc_final: 0.6810 (ttp-110) REVERT: U 201 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: U 209 PHE cc_start: 0.7909 (m-10) cc_final: 0.7589 (m-10) REVERT: U 332 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9196 (tm) REVERT: W 54 ARG cc_start: 0.8272 (mmt-90) cc_final: 0.7795 (mmt-90) REVERT: W 111 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7710 (tp40) REVERT: W 143 ARG cc_start: 0.7639 (pmt170) cc_final: 0.6667 (ptm-80) REVERT: W 325 SER cc_start: 0.9314 (t) cc_final: 0.9069 (p) REVERT: W 371 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7415 (mtp180) REVERT: Y 6 ARG cc_start: 0.8435 (ptp90) cc_final: 0.8084 (mtm110) REVERT: Y 123 MET cc_start: 0.6096 (mtm) cc_final: 0.5638 (mtp) REVERT: Y 126 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7672 (tt0) REVERT: Y 201 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8674 (mp10) REVERT: Y 209 PHE cc_start: 0.8214 (m-10) cc_final: 0.7997 (m-10) REVERT: Y 304 GLN cc_start: 0.8595 (tt0) cc_final: 0.8346 (mt0) REVERT: Y 371 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7404 (mtp180) REVERT: 0 53 ASP cc_start: 0.9114 (t0) cc_final: 0.8856 (t0) REVERT: 0 123 MET cc_start: 0.7109 (mtp) cc_final: 0.6802 (mtp) REVERT: 0 201 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: 0 213 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7702 (mtt-85) REVERT: 0 225 GLU cc_start: 0.8630 (tt0) cc_final: 0.8279 (tt0) REVERT: 0 313 MET cc_start: 0.8604 (ptp) cc_final: 0.8339 (ptm) REVERT: 0 325 SER cc_start: 0.9270 (t) cc_final: 0.9042 (p) REVERT: 0 371 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7467 (mtp180) REVERT: 2 53 ASP cc_start: 0.9098 (t0) cc_final: 0.8843 (t0) REVERT: 2 54 ARG cc_start: 0.8176 (mmp80) cc_final: 0.7788 (mmt-90) REVERT: 2 102 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8247 (pp) REVERT: 2 123 MET cc_start: 0.4449 (mtm) cc_final: 0.4200 (ttm) REVERT: 2 126 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7855 (tm-30) REVERT: 2 150 LYS cc_start: 0.8419 (ptpp) cc_final: 0.7743 (mttm) REVERT: 2 161 GLU cc_start: 0.8265 (pt0) cc_final: 0.7972 (pt0) REVERT: 2 201 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: 2 209 PHE cc_start: 0.7438 (m-10) cc_final: 0.7234 (m-10) REVERT: 2 212 GLU cc_start: 0.8401 (pt0) cc_final: 0.7903 (pt0) REVERT: 2 256 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8329 (t0) REVERT: 2 274 LYS cc_start: 0.8964 (tttp) cc_final: 0.8731 (ttmt) REVERT: 2 317 GLU cc_start: 0.6167 (tm-30) cc_final: 0.4240 (tm-30) REVERT: 2 371 ARG cc_start: 0.7881 (mtp180) cc_final: 0.7335 (mtp180) outliers start: 98 outliers final: 63 residues processed: 979 average time/residue: 0.2631 time to fit residues: 407.0560 Evaluate side-chains 927 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 843 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 228 SER Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 201 GLN Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 256 ASP Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 237 ILE Chi-restraints excluded: chain S residue 256 ASP Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 129 GLN Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 237 ILE Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 228 SER Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 201 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 256 ASP Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 256 ASP Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 355 SER Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 471 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 512 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 52 optimal weight: 0.0010 chunk 422 optimal weight: 0.0040 chunk 368 optimal weight: 3.9990 chunk 454 optimal weight: 2.9990 chunk 474 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS I 33 HIS K 322 ASN M 33 HIS M 246 ASN O 33 HIS Q 33 HIS Q 164 ASN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 ASN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN U 322 ASN W 33 HIS W 322 ASN Y 33 HIS Y 164 ASN Y 246 ASN 0 33 HIS 2 33 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.093867 restraints weight = 67964.408| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.95 r_work: 0.2906 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 45690 Z= 0.118 Angle : 0.527 8.040 62145 Z= 0.269 Chirality : 0.042 0.134 7110 Planarity : 0.004 0.038 7650 Dihedral : 10.294 73.413 7170 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 2.11 % Allowed : 14.97 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.17 (0.12), residues: 5355 helix: 0.67 (0.10), residues: 3090 sheet: -1.65 (0.25), residues: 390 loop : -0.95 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 249 TYR 0.021 0.001 TYR Q 303 PHE 0.021 0.001 PHE 0 209 TRP 0.006 0.001 TRP U 175 HIS 0.007 0.002 HIS U 33 Details of bonding type rmsd covalent geometry : bond 0.00281 (45690) covalent geometry : angle 0.52705 (62145) hydrogen bonds : bond 0.02891 ( 1710) hydrogen bonds : angle 3.50930 ( 4950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 850 time to evaluate : 1.446 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: C 29 ARG cc_start: 0.8827 (ptp-110) cc_final: 0.8626 (ptp-110) REVERT: C 143 ARG cc_start: 0.7558 (pmt170) cc_final: 0.7037 (ptt-90) REVERT: C 150 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8200 (mmmt) REVERT: C 201 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: C 368 MET cc_start: 0.7998 (ttm) cc_final: 0.7792 (mtp) REVERT: A 143 ARG cc_start: 0.7627 (pmt170) cc_final: 0.7204 (ptt-90) REVERT: A 150 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8115 (mptt) REVERT: A 201 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7663 (mp10) REVERT: A 212 GLU cc_start: 0.8797 (pt0) cc_final: 0.8573 (pt0) REVERT: A 280 MET cc_start: 0.9115 (mmt) cc_final: 0.8868 (mmm) REVERT: A 304 GLN cc_start: 0.8008 (mt0) cc_final: 0.7569 (mm-40) REVERT: A 367 GLU cc_start: 0.8340 (tt0) cc_final: 0.8015 (tt0) REVERT: A 371 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7465 (mtp180) REVERT: D 21 THR cc_start: 0.7546 (p) cc_final: 0.7254 (p) REVERT: D 57 ARG cc_start: 0.8360 (ptp-110) cc_final: 0.8056 (ttp-170) REVERT: D 123 MET cc_start: 0.6134 (ptt) cc_final: 0.5893 (ptp) REVERT: D 143 ARG cc_start: 0.7696 (pmt170) cc_final: 0.7180 (ptt-90) REVERT: D 150 LYS cc_start: 0.8828 (mtmm) cc_final: 0.8451 (mmtt) REVERT: D 212 GLU cc_start: 0.8721 (pt0) cc_final: 0.8325 (pt0) REVERT: D 256 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8001 (t0) REVERT: G 5 LEU cc_start: 0.8910 (mm) cc_final: 0.8607 (mm) REVERT: G 103 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8136 (mt-10) REVERT: G 123 MET cc_start: 0.5974 (ptt) cc_final: 0.5527 (ptp) REVERT: G 150 LYS cc_start: 0.8582 (ptpp) cc_final: 0.8061 (mttp) REVERT: G 201 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: G 371 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7761 (mtp180) REVERT: I 53 ASP cc_start: 0.8706 (t0) cc_final: 0.8462 (t0) REVERT: I 103 GLU cc_start: 0.8223 (mp0) cc_final: 0.8018 (mp0) REVERT: I 143 ARG cc_start: 0.7897 (pmt170) cc_final: 0.7573 (ptt-90) REVERT: I 150 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8336 (mmtt) REVERT: I 156 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7806 (tm-30) REVERT: I 159 ASP cc_start: 0.8121 (p0) cc_final: 0.7665 (p0) REVERT: I 256 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8299 (t70) REVERT: I 271 LEU cc_start: 0.8601 (mt) cc_final: 0.8358 (mt) REVERT: I 371 ARG cc_start: 0.7980 (mtp180) cc_final: 0.7702 (mtp180) REVERT: K 53 ASP cc_start: 0.8969 (t0) cc_final: 0.8673 (t0) REVERT: K 57 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8129 (ttp-170) REVERT: K 102 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8177 (pp) REVERT: K 150 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8391 (mmmt) REVERT: K 159 ASP cc_start: 0.8154 (p0) cc_final: 0.7902 (p0) REVERT: K 201 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.7514 (mt0) REVERT: M 102 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8297 (pp) REVERT: M 143 ARG cc_start: 0.7747 (pmt170) cc_final: 0.7287 (ptt-90) REVERT: M 371 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7370 (mtp180) REVERT: O 53 ASP cc_start: 0.8776 (t0) cc_final: 0.8437 (t0) REVERT: O 54 ARG cc_start: 0.8159 (mmp80) cc_final: 0.7787 (mmp80) REVERT: O 93 ASP cc_start: 0.7751 (p0) cc_final: 0.7449 (t70) REVERT: O 100 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8208 (tmm160) REVERT: O 143 ARG cc_start: 0.7474 (pmt170) cc_final: 0.6602 (ttp-110) REVERT: O 150 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8268 (mmmt) REVERT: O 201 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: O 212 GLU cc_start: 0.8625 (pt0) cc_final: 0.8237 (pt0) REVERT: O 371 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7637 (mtp180) REVERT: Q 53 ASP cc_start: 0.8835 (t0) cc_final: 0.8542 (t0) REVERT: Q 57 ARG cc_start: 0.8449 (ptp-110) cc_final: 0.8207 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7548 (pmt170) cc_final: 0.6671 (ttp-110) REVERT: Q 212 GLU cc_start: 0.8780 (pt0) cc_final: 0.8318 (pt0) REVERT: Q 213 ARG cc_start: 0.8251 (mtp-110) cc_final: 0.7892 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7833 (m-30) cc_final: 0.7498 (m-30) REVERT: Q 256 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8241 (t0) REVERT: S 143 ARG cc_start: 0.7324 (ptt-90) cc_final: 0.6227 (ttp-110) REVERT: S 150 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8285 (mttt) REVERT: S 161 GLU cc_start: 0.7872 (pt0) cc_final: 0.7614 (pt0) REVERT: S 213 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7730 (ttt180) REVERT: S 228 SER cc_start: 0.8940 (p) cc_final: 0.8718 (m) REVERT: U 10 LEU cc_start: 0.8941 (mp) cc_final: 0.8693 (mm) REVERT: U 143 ARG cc_start: 0.7639 (pmt170) cc_final: 0.6747 (ttp-110) REVERT: U 201 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: U 209 PHE cc_start: 0.7954 (m-10) cc_final: 0.7618 (m-10) REVERT: U 332 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9198 (tm) REVERT: W 54 ARG cc_start: 0.8271 (mmt-90) cc_final: 0.7790 (mmt-90) REVERT: W 111 GLN cc_start: 0.8325 (tp-100) cc_final: 0.7774 (tp40) REVERT: W 143 ARG cc_start: 0.7611 (pmt170) cc_final: 0.6631 (ptm-80) REVERT: W 325 SER cc_start: 0.9294 (t) cc_final: 0.9036 (p) REVERT: W 371 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7421 (mtp180) REVERT: Y 6 ARG cc_start: 0.8439 (ptp90) cc_final: 0.8104 (mtm110) REVERT: Y 15 LYS cc_start: 0.8842 (ptmm) cc_final: 0.8563 (ptmm) REVERT: Y 201 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8653 (mp10) REVERT: Y 209 PHE cc_start: 0.8215 (m-10) cc_final: 0.7979 (m-10) REVERT: Y 304 GLN cc_start: 0.8665 (tt0) cc_final: 0.8401 (mt0) REVERT: Y 371 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7337 (mtp180) REVERT: 0 53 ASP cc_start: 0.9114 (t0) cc_final: 0.8868 (t0) REVERT: 0 123 MET cc_start: 0.7257 (mtp) cc_final: 0.6895 (mtp) REVERT: 0 201 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: 0 213 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7662 (mtt-85) REVERT: 0 225 GLU cc_start: 0.8670 (tt0) cc_final: 0.8313 (tt0) REVERT: 0 313 MET cc_start: 0.8684 (ptp) cc_final: 0.8468 (ptm) REVERT: 0 325 SER cc_start: 0.9257 (t) cc_final: 0.9046 (p) REVERT: 0 371 ARG cc_start: 0.7805 (mtp180) cc_final: 0.7430 (mtp180) REVERT: 2 53 ASP cc_start: 0.9125 (t0) cc_final: 0.8781 (t0) REVERT: 2 54 ARG cc_start: 0.8171 (mmp80) cc_final: 0.7968 (mmt-90) REVERT: 2 98 SER cc_start: 0.9018 (t) cc_final: 0.8726 (p) REVERT: 2 102 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8230 (pp) REVERT: 2 123 MET cc_start: 0.4428 (mtm) cc_final: 0.4191 (ttm) REVERT: 2 126 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7826 (tm-30) REVERT: 2 150 LYS cc_start: 0.8468 (ptpp) cc_final: 0.7793 (mttm) REVERT: 2 161 GLU cc_start: 0.8269 (pt0) cc_final: 0.7958 (pt0) REVERT: 2 201 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: 2 209 PHE cc_start: 0.7612 (m-10) cc_final: 0.7393 (m-10) REVERT: 2 256 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8310 (t0) REVERT: 2 274 LYS cc_start: 0.8964 (tttp) cc_final: 0.8717 (ttmt) REVERT: 2 317 GLU cc_start: 0.6110 (tm-30) cc_final: 0.4456 (tm-30) REVERT: 2 371 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7314 (mtp180) outliers start: 98 outliers final: 67 residues processed: 920 average time/residue: 0.2654 time to fit residues: 388.1013 Evaluate side-chains 908 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 822 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 228 SER Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 201 GLN Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 256 ASP Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 57 ARG Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 237 ILE Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 228 SER Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 201 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 368 MET Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 227 LEU Chi-restraints excluded: chain 0 residue 256 ASP Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 256 ASP Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 355 SER Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 480 optimal weight: 0.8980 chunk 182 optimal weight: 0.2980 chunk 491 optimal weight: 1.9990 chunk 211 optimal weight: 0.0670 chunk 474 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 502 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 398 optimal weight: 5.9990 chunk 470 optimal weight: 6.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 33 HIS D 164 ASN G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 33 HIS K 322 ASN M 33 HIS M 246 ASN O 33 HIS ** O 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 ASN S 322 ASN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 164 ASN U 322 ASN W 33 HIS W 322 ASN Y 33 HIS Y 164 ASN 0 33 HIS 2 33 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.103591 restraints weight = 66104.489| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.99 r_work: 0.2908 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 45690 Z= 0.096 Angle : 0.515 7.845 62145 Z= 0.264 Chirality : 0.041 0.130 7110 Planarity : 0.004 0.059 7650 Dihedral : 10.259 73.368 7170 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 1.94 % Allowed : 15.31 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.09 (0.12), residues: 5355 helix: 0.73 (0.10), residues: 3090 sheet: -1.59 (0.25), residues: 390 loop : -0.91 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 249 TYR 0.022 0.001 TYR Q 303 PHE 0.021 0.001 PHE 0 209 TRP 0.008 0.001 TRP W 333 HIS 0.008 0.002 HIS M 33 Details of bonding type rmsd covalent geometry : bond 0.00220 (45690) covalent geometry : angle 0.51539 (62145) hydrogen bonds : bond 0.02815 ( 1710) hydrogen bonds : angle 3.44407 ( 4950) =============================================================================== Job complete usr+sys time: 13108.06 seconds wall clock time: 224 minutes 42.59 seconds (13482.59 seconds total)