Starting phenix.real_space_refine on Tue Sep 15 18:52:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6h5s_0142/09_2026/6h5s_0142.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h5s_0142/09_2026/6h5s_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_0142/09_2026/6h5s_0142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h5s_0142/09_2026/6h5s_0142.map" model { file = "/net/cci-nas-00/data/ceres_data/6h5s_0142/09_2026/6h5s_0142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h5s_0142/09_2026/6h5s_0142.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6h5s_0142/09_2026/6h5s_0142.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6h5s_0142/09_2026/6h5s_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): 0.07s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 6.59, per 1000 atoms: 0.15 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: 4.36 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 5.35 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: 9.51 Time building geometry restraints manager: 5.64 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: 59866 2.63 - 5.25: 2028 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: 25276 15.16 - 30.32: 1664 30.32 - 45.47: 360 45.47 - 60.63: 105 60.63 - 75.79: 30 Dihedral angle restraints: 27435 sinusoidal: 11865 harmonic: 15570 Sorted by residual: dihedral pdb=" C4' C Z 2 " pdb=" C3' C Z 2 " pdb=" C2' C Z 2 " pdb=" C1' C Z 2 " ideal model delta sinusoidal sigma weight residual 36.34 -34.44 70.79 1 3.10e+00 1.04e-01 6.70e+02 dihedral pdb=" C4' C X 2 " pdb=" C3' C X 2 " pdb=" C2' C X 2 " pdb=" C1' C X 2 " ideal model delta sinusoidal sigma weight residual 36.34 -34.44 70.78 1 3.10e+00 1.04e-01 6.70e+02 dihedral pdb=" C4' C L 2 " pdb=" C3' C L 2 " pdb=" C2' C L 2 " pdb=" C1' C L 2 " ideal model delta sinusoidal sigma weight residual 36.34 -34.43 70.78 1 3.10e+00 1.04e-01 6.70e+02 ... (remaining 27432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5651 0.075 - 0.151: 1219 0.151 - 0.226: 164 0.226 - 0.302: 61 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: 0.18 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.960 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 43.130 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 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= 0.403 Angle : 1.135 13.127 62145 Z= 0.607 Chirality : 0.069 0.377 7110 Planarity : 0.007 0.056 7650 Dihedral : 11.525 75.788 17415 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 are 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/Z covalent geometry : bond 0.00966 / 0.40 (45690) covalent geometry : angle 1.13526 / 0.61 (62145) hydrogen bonds : bond 0.28744 / 18.93 ( 1710) hydrogen bonds : angle 10.61113 / 7.16 ( 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 : 1.710 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: 0.7318 (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: 0.7226 (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: 0.8945 (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: 0.7161 (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: 0.7373 (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: 0.3050 time to fit residues: 618.5093 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 : 1.754 ------------------------------------------------------------------------------- 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... 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 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 351 ASN Y 14 ASN Y 33 HIS Y 61 ASN 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: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099959 restraints weight = 66780.678| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.95 r_work: 0.2915 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 45690 Z= 0.136 Angle : 0.754 10.069 62145 Z= 0.358 Chirality : 0.059 0.651 7110 Planarity : 0.005 0.046 7650 Dihedral : 8.849 59.312 6974 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.26 % Allowed : 8.84 % Favored : 88.90 % 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 are 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 : -2.35 (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 0.015 0.002 PHE K 324 TRP 0.009 0.001 TRP M 333 HIS 0.005 0.001 HIS S 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (45690) covalent geometry : angle 0.75356 / 0.36 (62145) hydrogen bonds : bond 0.04671 / 3.06 ( 1710) hydrogen bonds : angle 4.87382 / 3.33 ( 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 1039 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 934 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8729 (ptp-110) cc_final: 0.8456 (ptp-110) REVERT: C 53 ASP cc_start: 0.8769 (t0) cc_final: 0.8425 (t0) REVERT: C 143 ARG cc_start: 0.7689 (pmt170) cc_final: 0.6727 (ptm-80) REVERT: C 332 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9194 (tp) REVERT: C 371 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7410 (mtp180) REVERT: A 123 MET cc_start: 0.6811 (mtm) cc_final: 0.6452 (ptp) REVERT: A 143 ARG cc_start: 0.7663 (pmt170) cc_final: 0.7453 (ptt-90) REVERT: A 367 GLU cc_start: 0.8229 (tt0) cc_final: 0.7950 (tt0) REVERT: D 143 ARG cc_start: 0.7739 (pmt170) cc_final: 0.7356 (ptt-90) REVERT: D 320 ILE cc_start: 0.9285 (tt) cc_final: 0.9078 (tt) REVERT: D 344 GLU cc_start: 0.8253 (mp0) cc_final: 0.7980 (mp0) REVERT: G 53 ASP cc_start: 0.8850 (t0) cc_final: 0.8608 (t0) REVERT: G 192 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7856 (mt-10) REVERT: G 306 MET cc_start: 0.8925 (mtp) cc_final: 0.8668 (mtp) REVERT: I 53 ASP cc_start: 0.8633 (t0) cc_final: 0.8390 (t0) REVERT: I 57 ARG cc_start: 0.8310 (ptp-110) cc_final: 0.8032 (ttp-170) REVERT: I 123 MET cc_start: 0.6398 (mtm) cc_final: 0.6080 (ptt) REVERT: I 129 GLN cc_start: 0.8518 (mp10) cc_final: 0.8289 (mp10) REVERT: I 143 ARG cc_start: 0.7911 (pmt170) cc_final: 0.7433 (ptt-90) REVERT: K 13 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7625 (mtm110) REVERT: K 29 ARG cc_start: 0.8694 (ptp-110) cc_final: 0.8424 (ptp90) REVERT: K 156 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7127 (tm-30) REVERT: K 158 GLN cc_start: 0.8274 (mp10) cc_final: 0.8067 (mm-40) REVERT: K 159 ASP cc_start: 0.8401 (p0) cc_final: 0.8015 (p0) REVERT: K 256 ASP cc_start: 0.8688 (t70) cc_final: 0.8254 (t0) REVERT: K 320 ILE cc_start: 0.9191 (tt) cc_final: 0.8916 (tt) REVERT: K 344 GLU cc_start: 0.8157 (mp0) cc_final: 0.7842 (mm-30) REVERT: K 371 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7621 (mtp180) REVERT: M 143 ARG cc_start: 0.7819 (pmt170) cc_final: 0.7164 (ptt-90) REVERT: M 156 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6509 (tm-30) REVERT: M 158 GLN cc_start: 0.8297 (mp10) cc_final: 0.7998 (mm-40) REVERT: M 217 ASP cc_start: 0.7803 (m-30) cc_final: 0.7299 (m-30) REVERT: M 227 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8646 (tp) REVERT: M 371 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7344 (mtp180) REVERT: O 82 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: O 100 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8369 (tmm160) REVERT: O 143 ARG cc_start: 0.7743 (pmt170) cc_final: 0.6914 (ptm-80) REVERT: O 212 GLU cc_start: 0.8631 (pt0) cc_final: 0.8412 (pt0) REVERT: O 217 ASP cc_start: 0.7937 (m-30) cc_final: 0.7531 (m-30) REVERT: O 320 ILE cc_start: 0.9242 (tt) cc_final: 0.9032 (tt) REVERT: O 367 GLU cc_start: 0.8463 (tt0) cc_final: 0.8027 (tt0) REVERT: O 371 ARG cc_start: 0.7720 (mtp180) cc_final: 0.7386 (mtp180) REVERT: Q 53 ASP cc_start: 0.8758 (t0) cc_final: 0.8436 (t0) REVERT: Q 57 ARG cc_start: 0.8478 (ptp-110) cc_final: 0.8208 (ptm160) REVERT: Q 109 GLN cc_start: 0.7121 (tm-30) cc_final: 0.6917 (tm-30) REVERT: Q 143 ARG cc_start: 0.7695 (pmt170) cc_final: 0.6978 (ptm-80) REVERT: Q 213 ARG cc_start: 0.8261 (mtp-110) cc_final: 0.7839 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7881 (m-30) cc_final: 0.7499 (m-30) REVERT: Q 371 ARG cc_start: 0.7753 (mtp180) cc_final: 0.7397 (mtp180) REVERT: S 143 ARG cc_start: 0.7373 (ptt-90) cc_final: 0.6419 (ttp-110) REVERT: S 280 MET cc_start: 0.8981 (mmm) cc_final: 0.8565 (mmt) REVERT: S 371 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7449 (mtp180) REVERT: U 143 ARG cc_start: 0.7801 (pmt170) cc_final: 0.6986 (mtp-110) REVERT: U 371 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7401 (mtp180) REVERT: W 111 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7771 (tp40) REVERT: W 143 ARG cc_start: 0.7544 (pmt170) cc_final: 0.6654 (ptm-80) REVERT: W 332 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9197 (tp) REVERT: W 371 ARG cc_start: 0.7842 (mtp180) cc_final: 0.7498 (mtp180) REVERT: Y 6 ARG cc_start: 0.8509 (ptp90) cc_final: 0.8116 (mtm110) REVERT: Y 100 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7784 (tmm160) REVERT: Y 123 MET cc_start: 0.6103 (mtm) cc_final: 0.5617 (mtp) REVERT: Y 258 ASP cc_start: 0.8917 (t70) cc_final: 0.8645 (t0) REVERT: Y 367 GLU cc_start: 0.8361 (tt0) cc_final: 0.8028 (tt0) REVERT: Y 371 ARG cc_start: 0.7771 (mtp180) cc_final: 0.7074 (mtp180) REVERT: 0 53 ASP cc_start: 0.8974 (t0) cc_final: 0.8716 (t0) REVERT: 0 225 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: 0 371 ARG cc_start: 0.7751 (mtp180) cc_final: 0.7193 (mtp180) REVERT: 2 10 LEU cc_start: 0.9125 (mt) cc_final: 0.8859 (mm) REVERT: 2 53 ASP cc_start: 0.8982 (t0) cc_final: 0.8614 (t0) REVERT: 2 258 ASP cc_start: 0.8938 (t70) cc_final: 0.8716 (t0) REVERT: 2 274 LYS cc_start: 0.8939 (tttp) cc_final: 0.8692 (ttmt) REVERT: 2 317 GLU cc_start: 0.6237 (tm-30) cc_final: 0.5535 (tm-30) REVERT: 2 371 ARG cc_start: 0.7781 (mtp180) cc_final: 0.7262 (mtp180) outliers start: 105 outliers final: 58 residues processed: 1013 average time/residue: 0.3181 time to fit residues: 505.3383 Evaluate side-chains 894 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 831 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 332 LEU Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 186 ASP 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 47 THR 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 355 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 249 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 442 optimal weight: 0.0980 chunk 488 optimal weight: 7.9990 chunk 339 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 417 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 137 optimal weight: 0.3980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 G 14 ASN G 33 HIS G 246 ASN I 14 ASN I 33 HIS K 33 HIS K 246 ASN K 304 GLN K 322 ASN M 33 HIS M 246 ASN O 33 HIS O 246 ASN O 304 GLN 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 ** W 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 33 HIS Y 164 ASN 0 33 HIS 2 33 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.094532 restraints weight = 67725.777| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.93 r_work: 0.2886 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 45690 Z= 0.183 Angle : 0.664 8.150 62145 Z= 0.321 Chirality : 0.050 0.330 7110 Planarity : 0.004 0.041 7650 Dihedral : 8.884 74.811 6960 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.54 % Allowed : 9.76 % Favored : 87.70 % 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 are not related in a simple way. whole: -1.77 (0.11), residues: 5355 helix: -0.67 (0.09), residues: 3090 sheet: -1.70 (0.27), residues: 390 loop : -1.70 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 100 TYR 0.016 0.002 TYR G 303 PHE 0.012 0.002 PHE O 232 TRP 0.008 0.001 TRP U 333 HIS 0.006 0.001 HIS I 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (45690) covalent geometry : angle 0.66404 / 0.32 (62145) hydrogen bonds : bond 0.03826 / 2.48 ( 1710) hydrogen bonds : angle 4.27665 / 2.93 ( 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 1023 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 905 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8816 (ptp-110) cc_final: 0.8503 (ptp-110) REVERT: C 53 ASP cc_start: 0.8817 (t0) cc_final: 0.8456 (t0) REVERT: C 143 ARG cc_start: 0.7688 (pmt170) cc_final: 0.7152 (ptt-90) REVERT: C 201 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: C 209 PHE cc_start: 0.9083 (m-10) cc_final: 0.8880 (m-10) REVERT: C 217 ASP cc_start: 0.7853 (m-30) cc_final: 0.7404 (m-30) REVERT: C 332 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9173 (tp) REVERT: C 371 ARG cc_start: 0.7782 (mtp180) cc_final: 0.7449 (mtp180) REVERT: A 143 ARG cc_start: 0.7690 (pmt170) cc_final: 0.7419 (ptt-90) REVERT: A 280 MET cc_start: 0.9059 (mmt) cc_final: 0.8815 (mmm) REVERT: A 297 GLU cc_start: 0.7592 (tt0) cc_final: 0.7363 (tt0) REVERT: A 304 GLN cc_start: 0.8059 (mt0) cc_final: 0.7689 (mm110) REVERT: A 367 GLU cc_start: 0.8345 (tt0) cc_final: 0.8109 (tt0) REVERT: D 143 ARG cc_start: 0.7719 (pmt170) cc_final: 0.7234 (ptt-90) REVERT: D 201 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: D 249 ARG cc_start: 0.8764 (ttt-90) cc_final: 0.8527 (ttt-90) REVERT: D 320 ILE cc_start: 0.9356 (tt) cc_final: 0.9121 (tt) REVERT: G 13 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7563 (mtm110) REVERT: G 53 ASP cc_start: 0.8955 (t0) cc_final: 0.8723 (t0) REVERT: G 156 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7538 (tm-30) REVERT: G 201 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: G 227 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8567 (tp) REVERT: I 53 ASP cc_start: 0.8691 (t0) cc_final: 0.8470 (t0) REVERT: I 57 ARG cc_start: 0.8330 (ptp-110) cc_final: 0.7978 (ttp-170) REVERT: I 143 ARG cc_start: 0.7921 (pmt170) cc_final: 0.7574 (ptt-90) REVERT: I 159 ASP cc_start: 0.8278 (p0) cc_final: 0.7947 (p0) REVERT: I 201 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: I 227 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8670 (tp) REVERT: I 271 LEU cc_start: 0.8863 (mt) cc_final: 0.8576 (mt) REVERT: I 344 GLU cc_start: 0.8319 (mp0) cc_final: 0.8045 (mt-10) REVERT: K 5 LEU cc_start: 0.8857 (mm) cc_final: 0.8619 (mm) REVERT: K 29 ARG cc_start: 0.8749 (ptp-110) cc_final: 0.8428 (ptp90) REVERT: K 102 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8570 (pp) REVERT: K 156 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7166 (tm-30) REVERT: K 158 GLN cc_start: 0.8359 (mp10) cc_final: 0.8154 (mm-40) REVERT: K 201 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: K 227 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8592 (tp) REVERT: K 320 ILE cc_start: 0.9217 (tt) cc_final: 0.8879 (tt) REVERT: K 371 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7634 (mtp180) REVERT: M 143 ARG cc_start: 0.7837 (pmt170) cc_final: 0.7387 (ptt-90) REVERT: M 156 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6586 (tm-30) REVERT: M 158 GLN cc_start: 0.8354 (mp10) cc_final: 0.8039 (mm-40) REVERT: M 201 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: M 217 ASP cc_start: 0.7799 (m-30) cc_final: 0.7306 (m-30) REVERT: M 371 ARG cc_start: 0.7771 (mtp180) cc_final: 0.7317 (mtp180) REVERT: O 6 ARG cc_start: 0.8559 (ptp90) cc_final: 0.8237 (ttp-110) REVERT: O 100 ARG cc_start: 0.8667 (ttp80) cc_final: 0.8425 (tmm160) REVERT: O 143 ARG cc_start: 0.7698 (pmt170) cc_final: 0.7271 (ptt-90) REVERT: O 212 GLU cc_start: 0.8730 (pt0) cc_final: 0.8384 (pt0) REVERT: O 217 ASP cc_start: 0.7906 (m-30) cc_final: 0.7537 (m-30) REVERT: O 320 ILE cc_start: 0.9250 (tt) cc_final: 0.9019 (tt) REVERT: O 367 GLU cc_start: 0.8516 (tt0) cc_final: 0.8124 (tt0) REVERT: O 371 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7431 (mtp180) REVERT: Q 53 ASP cc_start: 0.8760 (t0) cc_final: 0.8503 (t0) REVERT: Q 143 ARG cc_start: 0.7662 (pmt170) cc_final: 0.6902 (ptm-80) REVERT: Q 213 ARG cc_start: 0.8214 (mtp-110) cc_final: 0.7869 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7932 (m-30) cc_final: 0.7573 (m-30) REVERT: Q 308 GLU cc_start: 0.8706 (pm20) cc_final: 0.8421 (pm20) REVERT: S 143 ARG cc_start: 0.7419 (ptt-90) cc_final: 0.6629 (ptm-80) REVERT: S 201 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: S 280 MET cc_start: 0.8993 (mmm) cc_final: 0.8606 (mmt) REVERT: S 371 ARG cc_start: 0.7705 (mtp180) cc_final: 0.7294 (mtp180) REVERT: U 143 ARG cc_start: 0.7839 (pmt170) cc_final: 0.6983 (ttp-110) REVERT: U 201 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: U 227 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8623 (tp) REVERT: U 258 ASP cc_start: 0.8931 (t70) cc_final: 0.8713 (t0) REVERT: U 371 ARG cc_start: 0.7794 (mtp180) cc_final: 0.7330 (mtp180) REVERT: W 54 ARG cc_start: 0.8270 (mmp80) cc_final: 0.8022 (mmt-90) REVERT: W 93 ASP cc_start: 0.7917 (p0) cc_final: 0.7670 (p0) REVERT: W 111 GLN cc_start: 0.8305 (tp-100) cc_final: 0.7756 (tp40) REVERT: W 143 ARG cc_start: 0.7665 (pmt170) cc_final: 0.6697 (ptm-80) REVERT: W 371 ARG cc_start: 0.7872 (mtp180) cc_final: 0.7578 (mtp180) REVERT: Y 6 ARG cc_start: 0.8491 (ptp90) cc_final: 0.8017 (mtm110) REVERT: Y 10 LEU cc_start: 0.8988 (mt) cc_final: 0.8772 (mt) REVERT: Y 123 MET cc_start: 0.6168 (mtm) cc_final: 0.5618 (mtp) REVERT: Y 225 GLU cc_start: 0.8634 (tt0) cc_final: 0.8209 (tt0) REVERT: Y 301 ASN cc_start: 0.8404 (m110) cc_final: 0.8182 (m-40) REVERT: Y 371 ARG cc_start: 0.7790 (mtp180) cc_final: 0.7268 (mtp180) REVERT: 0 53 ASP cc_start: 0.9015 (t0) cc_final: 0.8776 (t0) REVERT: 0 201 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: 0 371 ARG cc_start: 0.7764 (mtp180) cc_final: 0.7173 (mtp180) REVERT: 2 10 LEU cc_start: 0.9145 (mt) cc_final: 0.8898 (mm) REVERT: 2 123 MET cc_start: 0.3665 (mtm) cc_final: 0.3445 (ttm) REVERT: 2 274 LYS cc_start: 0.8962 (tttp) cc_final: 0.8710 (ttmt) REVERT: 2 317 GLU cc_start: 0.6219 (tm-30) cc_final: 0.5229 (tm-30) REVERT: 2 371 ARG cc_start: 0.7763 (mtp180) cc_final: 0.7290 (mtp180) outliers start: 118 outliers final: 58 residues processed: 995 average time/residue: 0.3127 time to fit residues: 492.7443 Evaluate side-chains 866 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 793 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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 332 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 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 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 186 ASP 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 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 227 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: 7.9990 chunk 405 optimal weight: 5.9990 chunk 495 optimal weight: 0.0270 chunk 435 optimal weight: 4.9990 chunk 505 optimal weight: 7.9990 chunk 492 optimal weight: 5.9990 chunk 395 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 385 optimal weight: 0.9990 chunk 313 optimal weight: 0.6980 chunk 267 optimal weight: 0.9990 overall best weight: 0.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 K 322 ASN M 33 HIS M 246 ASN O 33 HIS O 164 ASN O 246 ASN Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 33 HIS U 33 HIS U 304 GLN U 322 ASN W 33 HIS W 304 GLN W 322 ASN Y 33 HIS 0 33 HIS 0 304 GLN 2 33 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.113139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.095987 restraints weight = 67948.562| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.06 r_work: 0.2931 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 45690 Z= 0.104 Angle : 0.571 7.013 62145 Z= 0.281 Chirality : 0.045 0.231 7110 Planarity : 0.004 0.034 7650 Dihedral : 8.781 86.674 6960 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 2.32 % Allowed : 10.17 % 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 are not related in a simple way. whole: -1.16 (0.12), residues: 5355 helix: -0.18 (0.10), residues: 3165 sheet: -1.68 (0.26), residues: 390 loop : -1.42 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 213 TYR 0.014 0.001 TYR D 303 PHE 0.014 0.001 PHE U 163 TRP 0.008 0.001 TRP S 333 HIS 0.005 0.001 HIS S 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (45690) covalent geometry : angle 0.57066 / 0.28 (62145) hydrogen bonds : bond 0.03362 / 2.18 ( 1710) hydrogen bonds : angle 3.94101 / 2.70 ( 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 995 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 887 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8847 (ptp-110) cc_final: 0.8563 (ptp-110) REVERT: C 53 ASP cc_start: 0.8816 (t0) cc_final: 0.8482 (t0) REVERT: C 143 ARG cc_start: 0.7698 (pmt170) cc_final: 0.7166 (ptt-90) REVERT: C 213 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7769 (ttm-80) REVERT: C 332 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9133 (tp) REVERT: C 371 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7502 (mtp180) REVERT: A 123 MET cc_start: 0.6699 (mtm) cc_final: 0.6399 (ptp) REVERT: A 143 ARG cc_start: 0.7757 (pmt170) cc_final: 0.7477 (ptt-90) REVERT: A 256 ASP cc_start: 0.8418 (t70) cc_final: 0.8081 (t70) REVERT: A 280 MET cc_start: 0.9096 (mmt) cc_final: 0.8775 (mmm) REVERT: A 297 GLU cc_start: 0.7625 (tt0) cc_final: 0.7412 (tt0) REVERT: A 304 GLN cc_start: 0.8025 (mt0) cc_final: 0.7695 (mm110) REVERT: A 367 GLU cc_start: 0.8292 (tt0) cc_final: 0.8026 (tt0) REVERT: A 371 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7560 (mtp180) REVERT: D 143 ARG cc_start: 0.7739 (pmt170) cc_final: 0.7241 (ptt-90) REVERT: D 150 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8207 (mttt) REVERT: D 320 ILE cc_start: 0.9284 (tt) cc_final: 0.9045 (tt) REVERT: G 53 ASP cc_start: 0.8919 (t0) cc_final: 0.8651 (t0) REVERT: G 156 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7518 (tm-30) REVERT: G 201 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: I 53 ASP cc_start: 0.8718 (t0) cc_final: 0.8515 (t0) REVERT: I 57 ARG cc_start: 0.8293 (ptp-110) cc_final: 0.8044 (ttp-170) REVERT: I 143 ARG cc_start: 0.7851 (pmt170) cc_final: 0.7528 (ptt-90) REVERT: I 159 ASP cc_start: 0.8176 (p0) cc_final: 0.7870 (p0) REVERT: I 201 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.7832 (mt0) REVERT: I 271 LEU cc_start: 0.8807 (mt) cc_final: 0.8554 (mt) REVERT: K 5 LEU cc_start: 0.8859 (mm) cc_final: 0.8641 (mm) REVERT: K 29 ARG cc_start: 0.8749 (ptp-110) cc_final: 0.8301 (ptp90) REVERT: K 53 ASP cc_start: 0.8765 (t0) cc_final: 0.8537 (t0) REVERT: K 57 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7928 (ttp-170) REVERT: K 102 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8359 (pp) REVERT: K 156 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7234 (tm-30) REVERT: K 201 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7737 (mt0) REVERT: K 320 ILE cc_start: 0.9124 (tt) cc_final: 0.8824 (tt) REVERT: M 102 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8419 (pp) REVERT: M 143 ARG cc_start: 0.7908 (pmt170) cc_final: 0.7454 (ptt-90) REVERT: M 156 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7134 (tm-30) REVERT: M 371 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7365 (mtp180) REVERT: O 6 ARG cc_start: 0.8579 (ptp90) cc_final: 0.8210 (ttp-110) REVERT: O 53 ASP cc_start: 0.8807 (t0) cc_final: 0.8595 (t0) REVERT: O 54 ARG cc_start: 0.8542 (mmp80) cc_final: 0.8224 (mmp80) REVERT: O 82 GLU cc_start: 0.8429 (tt0) cc_final: 0.8172 (mt-10) REVERT: O 93 ASP cc_start: 0.7663 (p0) cc_final: 0.7387 (t70) REVERT: O 100 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8384 (tmm160) REVERT: O 143 ARG cc_start: 0.7667 (pmt170) cc_final: 0.7241 (ptt-90) REVERT: O 212 GLU cc_start: 0.8721 (pt0) cc_final: 0.8406 (pt0) REVERT: O 280 MET cc_start: 0.9007 (mmm) cc_final: 0.8790 (mmt) REVERT: Q 53 ASP cc_start: 0.8753 (t0) cc_final: 0.8475 (t0) REVERT: Q 143 ARG cc_start: 0.7691 (pmt170) cc_final: 0.6931 (ptm-80) REVERT: Q 158 GLN cc_start: 0.8420 (mp10) cc_final: 0.8134 (mp10) REVERT: Q 213 ARG cc_start: 0.8251 (mtp-110) cc_final: 0.7883 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7950 (m-30) cc_final: 0.7555 (m-30) REVERT: Q 351 ASN cc_start: 0.8815 (t0) cc_final: 0.8577 (t0) REVERT: S 143 ARG cc_start: 0.7339 (ptt-90) cc_final: 0.6324 (ttp-110) REVERT: S 371 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7427 (mtp180) REVERT: U 143 ARG cc_start: 0.7769 (pmt170) cc_final: 0.6974 (ttp-110) REVERT: U 201 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: U 227 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8617 (tp) REVERT: U 258 ASP cc_start: 0.8957 (t70) cc_final: 0.8744 (t0) REVERT: W 31 ILE cc_start: 0.9045 (tp) cc_final: 0.8820 (tp) REVERT: W 93 ASP cc_start: 0.7875 (p0) cc_final: 0.7660 (p0) REVERT: W 111 GLN cc_start: 0.8356 (tp-100) cc_final: 0.7809 (tp40) REVERT: W 143 ARG cc_start: 0.7676 (pmt170) cc_final: 0.6683 (ptm-80) REVERT: W 225 GLU cc_start: 0.8623 (tt0) cc_final: 0.8382 (tt0) REVERT: W 371 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7499 (mtp180) REVERT: Y 6 ARG cc_start: 0.8531 (ptp90) cc_final: 0.8013 (mtm110) REVERT: Y 10 LEU cc_start: 0.9067 (mt) cc_final: 0.8697 (mt) REVERT: Y 55 LEU cc_start: 0.8803 (tp) cc_final: 0.8561 (mt) REVERT: Y 123 MET cc_start: 0.6099 (mtm) cc_final: 0.5717 (mtp) REVERT: Y 126 GLU cc_start: 0.7748 (tm-30) cc_final: 0.6896 (tt0) REVERT: Y 225 GLU cc_start: 0.8642 (tt0) cc_final: 0.8268 (tt0) REVERT: Y 301 ASN cc_start: 0.8313 (m110) cc_final: 0.8007 (m-40) REVERT: Y 371 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7416 (mtp180) REVERT: 0 53 ASP cc_start: 0.9042 (t0) cc_final: 0.8814 (t0) REVERT: 0 165 MET cc_start: 0.8606 (tpp) cc_final: 0.8200 (mmp) REVERT: 0 201 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: 0 209 PHE cc_start: 0.8327 (m-10) cc_final: 0.8058 (m-80) REVERT: 0 225 GLU cc_start: 0.8393 (pt0) cc_final: 0.8180 (tt0) REVERT: 0 371 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7294 (mtp180) REVERT: 2 10 LEU cc_start: 0.9113 (mt) cc_final: 0.8892 (mm) REVERT: 2 53 ASP cc_start: 0.9086 (t0) cc_final: 0.8806 (t0) REVERT: 2 102 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8382 (pp) REVERT: 2 201 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: 2 256 ASP cc_start: 0.9061 (t70) cc_final: 0.8425 (t0) REVERT: 2 274 LYS cc_start: 0.8961 (tttp) cc_final: 0.8731 (ttmt) REVERT: 2 317 GLU cc_start: 0.6038 (tm-30) cc_final: 0.4999 (tm-30) REVERT: 2 371 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7314 (mtp180) outliers start: 108 outliers final: 54 residues processed: 966 average time/residue: 0.3059 time to fit residues: 468.2089 Evaluate side-chains 863 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 797 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain C residue 332 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 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 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 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 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 186 ASP 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 186 ASP 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 86 GLN 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 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 259 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 5 optimal weight: 0.8980 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: 7.9990 chunk 474 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 198 optimal weight: 0.1980 chunk 387 optimal weight: 7.9990 chunk 373 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN A 14 ASN D 33 HIS G 33 HIS G 246 ASN I 33 HIS K 304 GLN M 33 HIS M 246 ASN ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 14 ASN O 33 HIS Q 14 ASN Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 33 HIS S 304 GLN U 33 HIS U 304 GLN U 322 ASN W 33 HIS W 322 ASN Y 33 HIS 0 33 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.096804 restraints weight = 67775.191| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.07 r_work: 0.2987 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 45690 Z= 0.103 Angle : 0.558 9.495 62145 Z= 0.273 Chirality : 0.045 0.213 7110 Planarity : 0.003 0.034 7650 Dihedral : 8.389 76.819 6960 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 2.22 % Allowed : 11.51 % Favored : 86.28 % 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 are not related in a simple way. whole: -0.72 (0.12), residues: 5355 helix: 0.31 (0.10), residues: 3030 sheet: -1.69 (0.26), residues: 390 loop : -1.37 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 0 213 TYR 0.021 0.001 TYR Q 303 PHE 0.011 0.001 PHE U 163 TRP 0.006 0.001 TRP U 333 HIS 0.004 0.001 HIS S 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (45690) covalent geometry : angle 0.55794 / 0.27 (62145) hydrogen bonds : bond 0.03188 / 2.07 ( 1710) hydrogen bonds : angle 3.78060 / 2.59 ( 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 974 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 871 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8856 (ptp-110) cc_final: 0.8595 (ptp-110) REVERT: C 53 ASP cc_start: 0.8863 (t0) cc_final: 0.8507 (t0) REVERT: C 143 ARG cc_start: 0.7624 (pmt170) cc_final: 0.7133 (ptt-90) REVERT: C 150 LYS cc_start: 0.8601 (mtmm) cc_final: 0.7774 (mttp) REVERT: C 332 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9167 (tp) REVERT: C 371 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7620 (mtp180) REVERT: A 123 MET cc_start: 0.6655 (mtm) cc_final: 0.6390 (ptp) REVERT: A 143 ARG cc_start: 0.7738 (pmt170) cc_final: 0.7449 (ptt-90) REVERT: A 256 ASP cc_start: 0.8372 (t70) cc_final: 0.8022 (t70) REVERT: A 280 MET cc_start: 0.9088 (mmt) cc_final: 0.8803 (mmm) REVERT: A 304 GLN cc_start: 0.8049 (mt0) cc_final: 0.7696 (mm-40) REVERT: A 367 GLU cc_start: 0.8271 (tt0) cc_final: 0.7982 (tt0) REVERT: A 371 ARG cc_start: 0.7913 (mtp180) cc_final: 0.7566 (mtp180) REVERT: D 143 ARG cc_start: 0.7712 (pmt170) cc_final: 0.7212 (ptt-90) REVERT: D 150 LYS cc_start: 0.8867 (mtmm) cc_final: 0.8257 (mttt) REVERT: D 212 GLU cc_start: 0.8768 (pt0) cc_final: 0.8545 (pt0) REVERT: G 156 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7526 (tm-30) REVERT: G 201 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: G 371 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7730 (mtp180) REVERT: I 53 ASP cc_start: 0.8743 (t0) cc_final: 0.8522 (t0) REVERT: I 57 ARG cc_start: 0.8267 (ptp-110) cc_final: 0.8056 (ttp-170) REVERT: I 143 ARG cc_start: 0.7836 (pmt170) cc_final: 0.7515 (ptt-90) REVERT: I 159 ASP cc_start: 0.8196 (p0) cc_final: 0.7820 (p0) REVERT: I 201 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: I 256 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8228 (t70) REVERT: I 271 LEU cc_start: 0.8812 (mt) cc_final: 0.8564 (mt) REVERT: K 5 LEU cc_start: 0.8848 (mm) cc_final: 0.8629 (mm) REVERT: K 53 ASP cc_start: 0.8814 (t0) cc_final: 0.8555 (t0) REVERT: K 57 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8015 (ttp-170) REVERT: K 102 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8259 (pp) REVERT: K 150 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8364 (mtpt) REVERT: K 159 ASP cc_start: 0.8289 (p0) cc_final: 0.7970 (p0) REVERT: K 201 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7734 (mt0) REVERT: K 209 PHE cc_start: 0.8230 (m-10) cc_final: 0.7978 (m-10) REVERT: K 227 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8581 (tp) REVERT: M 102 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8358 (pp) REVERT: M 103 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8282 (mt-10) REVERT: M 143 ARG cc_start: 0.7849 (pmt170) cc_final: 0.7406 (ptt-90) REVERT: M 156 GLU cc_start: 0.7675 (tm-30) cc_final: 0.6716 (tm-30) REVERT: M 371 ARG cc_start: 0.7893 (mtp180) cc_final: 0.7434 (mtp180) REVERT: O 6 ARG cc_start: 0.8543 (ptp90) cc_final: 0.8288 (ttp-110) REVERT: O 53 ASP cc_start: 0.8806 (t0) cc_final: 0.8542 (t0) REVERT: O 54 ARG cc_start: 0.8370 (mmp80) cc_final: 0.7978 (mmp80) REVERT: O 82 GLU cc_start: 0.8426 (tt0) cc_final: 0.8185 (mt-10) REVERT: O 93 ASP cc_start: 0.7674 (p0) cc_final: 0.7392 (t70) REVERT: O 100 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8361 (tmm160) REVERT: O 143 ARG cc_start: 0.7641 (pmt170) cc_final: 0.7218 (ptt-90) REVERT: O 371 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7518 (mtp180) REVERT: Q 53 ASP cc_start: 0.8773 (t0) cc_final: 0.8469 (t0) REVERT: Q 57 ARG cc_start: 0.8463 (ptm160) cc_final: 0.8181 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7652 (pmt170) cc_final: 0.6895 (ptm-80) REVERT: Q 158 GLN cc_start: 0.8422 (mp10) cc_final: 0.8154 (mp10) REVERT: Q 213 ARG cc_start: 0.8238 (mtp-110) cc_final: 0.7897 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7892 (m-30) cc_final: 0.7521 (m-30) REVERT: Q 351 ASN cc_start: 0.8808 (t0) cc_final: 0.8559 (t0) REVERT: S 111 GLN cc_start: 0.8482 (tp40) cc_final: 0.7916 (tp40) REVERT: S 143 ARG cc_start: 0.7330 (ptt-90) cc_final: 0.6296 (ttp-110) REVERT: S 150 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8029 (mttm) REVERT: S 228 SER cc_start: 0.8957 (p) cc_final: 0.8701 (m) REVERT: S 371 ARG cc_start: 0.7799 (mtp180) cc_final: 0.7446 (mtp180) REVERT: U 143 ARG cc_start: 0.7678 (pmt170) cc_final: 0.6911 (ttp-110) REVERT: U 201 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: U 227 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8621 (tp) REVERT: U 258 ASP cc_start: 0.8992 (t70) cc_final: 0.8783 (t0) REVERT: W 31 ILE cc_start: 0.9038 (tp) cc_final: 0.8828 (tp) REVERT: W 111 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7826 (tp40) REVERT: W 143 ARG cc_start: 0.7637 (pmt170) cc_final: 0.6657 (ptm-80) REVERT: W 164 ASN cc_start: 0.8906 (t0) cc_final: 0.8682 (m-40) REVERT: W 225 GLU cc_start: 0.8650 (tt0) cc_final: 0.8445 (tt0) REVERT: W 371 ARG cc_start: 0.7906 (mtp180) cc_final: 0.7452 (mtp180) REVERT: Y 6 ARG cc_start: 0.8544 (ptp90) cc_final: 0.8128 (mtm110) REVERT: Y 55 LEU cc_start: 0.8790 (tp) cc_final: 0.8588 (mt) REVERT: Y 123 MET cc_start: 0.6092 (mtm) cc_final: 0.5703 (mtp) REVERT: Y 126 GLU cc_start: 0.7797 (tm-30) cc_final: 0.6959 (tt0) REVERT: Y 225 GLU cc_start: 0.8647 (tt0) cc_final: 0.8332 (tt0) REVERT: Y 301 ASN cc_start: 0.8334 (m110) cc_final: 0.8060 (m-40) REVERT: Y 371 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7395 (mtp180) REVERT: 0 53 ASP cc_start: 0.9065 (t0) cc_final: 0.8824 (t0) REVERT: 0 123 MET cc_start: 0.7238 (mtp) cc_final: 0.6911 (mtp) REVERT: 0 201 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: 0 209 PHE cc_start: 0.8201 (m-10) cc_final: 0.7966 (m-80) REVERT: 0 313 MET cc_start: 0.8830 (ptp) cc_final: 0.8574 (ptm) REVERT: 0 371 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7379 (mtp180) REVERT: 2 53 ASP cc_start: 0.9103 (t0) cc_final: 0.8788 (t0) REVERT: 2 54 ARG cc_start: 0.8236 (mmp80) cc_final: 0.7856 (mmt-90) REVERT: 2 102 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8387 (pp) REVERT: 2 201 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: 2 209 PHE cc_start: 0.7867 (m-10) cc_final: 0.7593 (m-10) REVERT: 2 258 ASP cc_start: 0.9083 (t70) cc_final: 0.8818 (t0) REVERT: 2 274 LYS cc_start: 0.8967 (tttp) cc_final: 0.8734 (ttmt) REVERT: 2 317 GLU cc_start: 0.6004 (tm-30) cc_final: 0.5253 (tm-30) REVERT: 2 371 ARG cc_start: 0.7728 (mtp180) cc_final: 0.7355 (mtp180) outliers start: 103 outliers final: 59 residues processed: 950 average time/residue: 0.2982 time to fit residues: 451.4078 Evaluate side-chains 879 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 805 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 332 LEU 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 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 367 GLU 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 201 GLN 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 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 5 LEU 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 186 ASP 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 186 ASP Chi-restraints excluded: chain U residue 98 SER 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 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 259 THR 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 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP 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 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 65 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 339 optimal weight: 0.9980 chunk 538 optimal weight: 8.9990 chunk 410 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 263 optimal weight: 20.0000 chunk 520 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 HIS C 246 ASN C 304 GLN A 33 HIS 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 33 HIS ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 HIS Q 33 HIS Q 164 ASN ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 304 GLN S 33 HIS S 322 ASN U 33 HIS U 304 GLN U 322 ASN W 33 HIS W 322 ASN Y 33 HIS Y 304 GLN 0 33 HIS 2 89 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.107530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.089962 restraints weight = 68841.326| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.09 r_work: 0.2848 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 45690 Z= 0.182 Angle : 0.608 9.506 62145 Z= 0.297 Chirality : 0.048 0.248 7110 Planarity : 0.004 0.034 7650 Dihedral : 8.340 77.801 6960 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 2.60 % Allowed : 12.22 % Favored : 85.18 % 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 are not related in a simple way. whole: -0.66 (0.12), residues: 5355 helix: 0.31 (0.10), residues: 3075 sheet: -1.82 (0.25), residues: 390 loop : -1.24 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 90 TYR 0.020 0.002 TYR Q 303 PHE 0.012 0.002 PHE S 209 TRP 0.005 0.001 TRP O 146 HIS 0.005 0.001 HIS W 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (45690) covalent geometry : angle 0.60801 / 0.30 (62145) hydrogen bonds : bond 0.03290 / 2.14 ( 1710) hydrogen bonds : angle 3.87367 / 2.65 ( 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 957 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 836 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8877 (ptp-110) cc_final: 0.8632 (ptp-110) REVERT: C 53 ASP cc_start: 0.8889 (t0) cc_final: 0.8553 (t0) REVERT: C 93 ASP cc_start: 0.8066 (p0) cc_final: 0.7859 (p0) REVERT: C 143 ARG cc_start: 0.7632 (pmt170) cc_final: 0.7109 (ptt-90) REVERT: C 213 ARG cc_start: 0.8048 (mtp-110) cc_final: 0.7827 (ttm-80) REVERT: C 332 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9216 (tp) REVERT: C 371 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7639 (mtp180) REVERT: A 143 ARG cc_start: 0.7721 (pmt170) cc_final: 0.7296 (ptt-90) REVERT: A 212 GLU cc_start: 0.8858 (pt0) cc_final: 0.8601 (pt0) REVERT: A 256 ASP cc_start: 0.8523 (t70) cc_final: 0.8162 (t70) REVERT: A 280 MET cc_start: 0.9114 (mmt) cc_final: 0.8829 (mmm) REVERT: A 304 GLN cc_start: 0.8103 (mt0) cc_final: 0.7747 (mm-40) REVERT: A 367 GLU cc_start: 0.8303 (tt0) cc_final: 0.8000 (tt0) REVERT: A 371 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7473 (mtp180) REVERT: D 143 ARG cc_start: 0.7742 (pmt170) cc_final: 0.7225 (ptt-90) REVERT: D 150 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8350 (mttt) REVERT: G 156 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7549 (tm-30) REVERT: G 201 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7950 (mt0) REVERT: G 371 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7822 (mtp180) REVERT: I 53 ASP cc_start: 0.8772 (t0) cc_final: 0.8545 (t0) REVERT: I 57 ARG cc_start: 0.8333 (ptp-110) cc_final: 0.8046 (ttp-170) REVERT: I 143 ARG cc_start: 0.7905 (pmt170) cc_final: 0.7571 (ptt-90) REVERT: I 159 ASP cc_start: 0.8240 (p0) cc_final: 0.7922 (p0) REVERT: I 201 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: I 271 LEU cc_start: 0.8862 (mt) cc_final: 0.8578 (mt) REVERT: I 371 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7753 (mtp180) REVERT: K 53 ASP cc_start: 0.8885 (t0) cc_final: 0.8655 (t0) REVERT: K 102 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8459 (pp) REVERT: K 150 LYS cc_start: 0.8873 (mtmm) cc_final: 0.8397 (mtpt) REVERT: K 159 ASP cc_start: 0.8340 (p0) cc_final: 0.8014 (p0) REVERT: K 201 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: M 102 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8521 (pp) REVERT: M 143 ARG cc_start: 0.7891 (pmt170) cc_final: 0.7436 (ptt-90) REVERT: M 156 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7359 (tm-30) REVERT: M 308 GLU cc_start: 0.8540 (pm20) cc_final: 0.8206 (pt0) REVERT: M 371 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7404 (mtp180) REVERT: O 6 ARG cc_start: 0.8552 (ptp90) cc_final: 0.8311 (ttp-110) REVERT: O 53 ASP cc_start: 0.8804 (t0) cc_final: 0.8426 (t0) REVERT: O 54 ARG cc_start: 0.8410 (mmp80) cc_final: 0.7912 (mmp80) REVERT: O 82 GLU cc_start: 0.8475 (tt0) cc_final: 0.8234 (mt-10) REVERT: O 93 ASP cc_start: 0.7756 (p0) cc_final: 0.7467 (t70) REVERT: O 100 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8437 (tmm160) REVERT: O 143 ARG cc_start: 0.7656 (pmt170) cc_final: 0.7211 (ptt-90) REVERT: O 371 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7516 (mtp180) REVERT: Q 53 ASP cc_start: 0.8856 (t0) cc_final: 0.8575 (t0) REVERT: Q 143 ARG cc_start: 0.7587 (pmt170) cc_final: 0.6768 (ptm-80) REVERT: Q 158 GLN cc_start: 0.8439 (mp10) cc_final: 0.8234 (mp10) REVERT: Q 213 ARG cc_start: 0.8280 (mtp-110) cc_final: 0.7963 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7961 (m-30) cc_final: 0.7631 (m-30) REVERT: Q 351 ASN cc_start: 0.8830 (t0) cc_final: 0.8571 (t0) REVERT: S 111 GLN cc_start: 0.8449 (tp40) cc_final: 0.7907 (tp40) REVERT: S 150 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8075 (mttt) REVERT: S 228 SER cc_start: 0.8959 (p) cc_final: 0.8726 (m) REVERT: S 371 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7485 (mtp180) REVERT: U 103 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8249 (mt-10) REVERT: U 143 ARG cc_start: 0.7676 (pmt170) cc_final: 0.6862 (ttp-110) REVERT: U 201 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: U 209 PHE cc_start: 0.8290 (m-10) cc_final: 0.8026 (m-10) REVERT: U 256 ASP cc_start: 0.8951 (t70) cc_final: 0.8261 (t0) REVERT: U 371 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7460 (mtp180) REVERT: W 31 ILE cc_start: 0.9012 (tp) cc_final: 0.8767 (tp) REVERT: W 111 GLN cc_start: 0.8469 (tp-100) cc_final: 0.7898 (tp40) REVERT: W 123 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5464 (mtm) REVERT: W 143 ARG cc_start: 0.7705 (pmt170) cc_final: 0.6681 (ptm-80) REVERT: W 225 GLU cc_start: 0.8671 (tt0) cc_final: 0.8469 (tt0) REVERT: W 371 ARG cc_start: 0.7859 (mtp180) cc_final: 0.7401 (mtp180) REVERT: Y 6 ARG cc_start: 0.8580 (ptp90) cc_final: 0.8119 (mtm110) REVERT: Y 123 MET cc_start: 0.6028 (mtm) cc_final: 0.5573 (mtp) REVERT: Y 126 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7559 (tt0) REVERT: Y 150 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7934 (mttt) REVERT: Y 225 GLU cc_start: 0.8647 (tt0) cc_final: 0.8389 (tt0) REVERT: Y 301 ASN cc_start: 0.8336 (m110) cc_final: 0.8030 (m-40) REVERT: Y 371 ARG cc_start: 0.7954 (mtp180) cc_final: 0.7433 (mtp180) REVERT: 0 53 ASP cc_start: 0.9111 (t0) cc_final: 0.8852 (t0) REVERT: 0 123 MET cc_start: 0.7145 (mtp) cc_final: 0.6826 (mtp) REVERT: 0 201 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: 0 351 ASN cc_start: 0.8785 (t0) cc_final: 0.8562 (t0) REVERT: 0 371 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7414 (mtp180) REVERT: 2 102 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8454 (pp) REVERT: 2 201 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8420 (mt0) REVERT: 2 209 PHE cc_start: 0.8057 (m-10) cc_final: 0.7736 (m-10) REVERT: 2 256 ASP cc_start: 0.9036 (t70) cc_final: 0.8372 (t0) REVERT: 2 274 LYS cc_start: 0.8991 (tttp) cc_final: 0.8742 (ttmt) REVERT: 2 317 GLU cc_start: 0.6191 (tm-30) cc_final: 0.4339 (tm-30) REVERT: 2 371 ARG cc_start: 0.7782 (mtp180) cc_final: 0.7270 (mtp180) outliers start: 121 outliers final: 78 residues processed: 932 average time/residue: 0.2991 time to fit residues: 444.5438 Evaluate side-chains 884 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 793 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain C residue 332 LEU 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 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 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 35 ILE Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 228 SER 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 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 102 LEU Chi-restraints excluded: chain O residue 165 MET 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 91 ILE Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER 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 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 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 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 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 228 SER Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 2 residue 10 LEU 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 355 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 76 optimal weight: 9.9990 chunk 150 optimal weight: 0.0170 chunk 423 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 451 optimal weight: 9.9990 chunk 250 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 528 optimal weight: 2.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 HIS C 304 GLN G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 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 Q 164 ASN ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 HIS U 304 GLN U 322 ASN W 33 HIS W 322 ASN Y 33 HIS Y 304 GLN 0 33 HIS 0 304 GLN 2 89 GLN 2 304 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.110272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.092937 restraints weight = 67952.110| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.06 r_work: 0.2925 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45690 Z= 0.132 Angle : 0.576 9.670 62145 Z= 0.283 Chirality : 0.046 0.241 7110 Planarity : 0.003 0.036 7650 Dihedral : 8.230 80.622 6960 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.01 % Favored : 96.86 % Rotamer: Outliers : 2.65 % Allowed : 12.92 % Favored : 84.43 % 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 are not related in a simple way. whole: -0.53 (0.12), residues: 5355 helix: 0.42 (0.10), residues: 3060 sheet: -1.83 (0.25), residues: 390 loop : -1.17 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 143 TYR 0.020 0.001 TYR D 303 PHE 0.015 0.001 PHE Y 209 TRP 0.006 0.001 TRP W 333 HIS 0.006 0.001 HIS G 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (45690) covalent geometry : angle 0.57567 / 0.28 (62145) hydrogen bonds : bond 0.03165 / 2.05 ( 1710) hydrogen bonds : angle 3.76433 / 2.58 ( 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 944 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 821 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8871 (ptp-110) cc_final: 0.8648 (ptp-110) REVERT: C 53 ASP cc_start: 0.8900 (t0) cc_final: 0.8586 (t0) REVERT: C 55 LEU cc_start: 0.9045 (tp) cc_final: 0.8723 (mt) REVERT: C 93 ASP cc_start: 0.8016 (p0) cc_final: 0.7810 (p0) REVERT: C 143 ARG cc_start: 0.7602 (pmt170) cc_final: 0.7103 (ptt-90) REVERT: C 150 LYS cc_start: 0.8637 (mtmm) cc_final: 0.7920 (mttp) REVERT: C 332 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9214 (tp) REVERT: C 371 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7635 (mtp180) REVERT: A 143 ARG cc_start: 0.7703 (pmt170) cc_final: 0.7273 (ptt-90) REVERT: A 150 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8126 (mttt) REVERT: A 156 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 212 GLU cc_start: 0.8827 (pt0) cc_final: 0.8418 (pt0) REVERT: A 280 MET cc_start: 0.9114 (mmt) cc_final: 0.8826 (mmm) REVERT: A 304 GLN cc_start: 0.8028 (mt0) cc_final: 0.7699 (mm-40) REVERT: A 367 GLU cc_start: 0.8312 (tt0) cc_final: 0.8011 (tt0) REVERT: A 371 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7473 (mtp180) REVERT: D 143 ARG cc_start: 0.7725 (pmt170) cc_final: 0.7229 (ptt-90) REVERT: D 150 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8382 (mttt) REVERT: D 212 GLU cc_start: 0.8803 (pt0) cc_final: 0.8451 (pt0) REVERT: G 150 LYS cc_start: 0.8677 (ptpp) cc_final: 0.7933 (mttp) REVERT: G 156 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7559 (tm-30) REVERT: G 201 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: I 53 ASP cc_start: 0.8773 (t0) cc_final: 0.8529 (t0) REVERT: I 57 ARG cc_start: 0.8320 (ptp-110) cc_final: 0.8038 (ttp-170) REVERT: I 143 ARG cc_start: 0.7895 (pmt170) cc_final: 0.7568 (ptt-90) REVERT: I 156 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7666 (tm-30) REVERT: I 159 ASP cc_start: 0.8226 (p0) cc_final: 0.7928 (p0) REVERT: I 201 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: I 271 LEU cc_start: 0.8822 (mt) cc_final: 0.8544 (mt) REVERT: K 5 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8610 (mm) REVERT: K 53 ASP cc_start: 0.8886 (t0) cc_final: 0.8621 (t0) REVERT: K 57 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8013 (ttp-170) REVERT: K 102 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8351 (pp) REVERT: K 150 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8312 (mttt) REVERT: K 159 ASP cc_start: 0.8335 (p0) cc_final: 0.8013 (p0) REVERT: K 201 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.7714 (mt0) REVERT: K 256 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8086 (t0) REVERT: M 102 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8480 (pp) REVERT: M 143 ARG cc_start: 0.7862 (pmt170) cc_final: 0.7415 (ptt-90) REVERT: M 156 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7308 (tm-30) REVERT: M 371 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7394 (mtp180) REVERT: O 6 ARG cc_start: 0.8550 (ptp90) cc_final: 0.8343 (ttp-110) REVERT: O 53 ASP cc_start: 0.8800 (t0) cc_final: 0.8432 (t0) REVERT: O 54 ARG cc_start: 0.8412 (mmp80) cc_final: 0.7926 (mmp80) REVERT: O 82 GLU cc_start: 0.8462 (tt0) cc_final: 0.8228 (mt-10) REVERT: O 93 ASP cc_start: 0.7724 (p0) cc_final: 0.7476 (t70) REVERT: O 100 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8436 (tmm160) REVERT: O 143 ARG cc_start: 0.7600 (pmt170) cc_final: 0.7157 (ptt-90) REVERT: Q 53 ASP cc_start: 0.8849 (t0) cc_final: 0.8575 (t0) REVERT: Q 143 ARG cc_start: 0.7584 (pmt170) cc_final: 0.6767 (ptm-80) REVERT: Q 212 GLU cc_start: 0.8794 (pt0) cc_final: 0.8485 (pt0) REVERT: Q 213 ARG cc_start: 0.8250 (mtp-110) cc_final: 0.7912 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7910 (m-30) cc_final: 0.7572 (m-30) REVERT: S 111 GLN cc_start: 0.8429 (tp40) cc_final: 0.7901 (tp40) REVERT: S 143 ARG cc_start: 0.7446 (ptt-90) cc_final: 0.6681 (ptm-80) REVERT: S 150 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8323 (mtpt) REVERT: S 161 GLU cc_start: 0.7965 (pt0) cc_final: 0.7713 (pt0) REVERT: S 212 GLU cc_start: 0.8737 (pt0) cc_final: 0.8513 (pt0) REVERT: S 225 GLU cc_start: 0.8623 (tt0) cc_final: 0.8324 (tt0) REVERT: S 228 SER cc_start: 0.8969 (p) cc_final: 0.8739 (m) REVERT: S 371 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7501 (mtp180) REVERT: U 103 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8275 (mt-10) REVERT: U 143 ARG cc_start: 0.7656 (pmt170) cc_final: 0.6860 (ttp-110) REVERT: U 201 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: U 209 PHE cc_start: 0.8261 (m-10) cc_final: 0.7989 (m-10) REVERT: U 253 MET cc_start: 0.9010 (ttm) cc_final: 0.8795 (ttp) REVERT: U 371 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7460 (mtp180) REVERT: W 31 ILE cc_start: 0.9007 (tp) cc_final: 0.8784 (tp) REVERT: W 111 GLN cc_start: 0.8403 (tp-100) cc_final: 0.7845 (tp40) REVERT: W 143 ARG cc_start: 0.7682 (pmt170) cc_final: 0.6702 (ptm-80) REVERT: W 371 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7333 (mtp180) REVERT: Y 6 ARG cc_start: 0.8527 (ptp90) cc_final: 0.8134 (mtm110) REVERT: Y 15 LYS cc_start: 0.8807 (ptmm) cc_final: 0.8514 (ptmm) REVERT: Y 123 MET cc_start: 0.6035 (mtm) cc_final: 0.5597 (mtp) REVERT: Y 126 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7611 (tt0) REVERT: Y 150 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8030 (mtpt) REVERT: Y 201 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8691 (mp10) REVERT: Y 225 GLU cc_start: 0.8624 (tt0) cc_final: 0.8421 (tt0) REVERT: Y 304 GLN cc_start: 0.8690 (tt0) cc_final: 0.8461 (mt0) REVERT: Y 371 ARG cc_start: 0.7941 (mtp180) cc_final: 0.7489 (mtp180) REVERT: 0 29 ARG cc_start: 0.8810 (ptp90) cc_final: 0.8357 (ptp90) REVERT: 0 53 ASP cc_start: 0.9099 (t0) cc_final: 0.8846 (t0) REVERT: 0 123 MET cc_start: 0.7164 (mtp) cc_final: 0.6851 (mtp) REVERT: 0 201 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: 0 225 GLU cc_start: 0.8639 (tt0) cc_final: 0.8326 (tt0) REVERT: 0 325 SER cc_start: 0.9331 (t) cc_final: 0.9008 (p) REVERT: 0 371 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7431 (mtp180) REVERT: 2 102 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8451 (pp) REVERT: 2 201 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8380 (mt0) REVERT: 2 209 PHE cc_start: 0.7851 (m-10) cc_final: 0.7408 (m-80) REVERT: 2 212 GLU cc_start: 0.8441 (pt0) cc_final: 0.8005 (pt0) REVERT: 2 256 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8323 (t0) REVERT: 2 274 LYS cc_start: 0.8968 (tttp) cc_final: 0.8738 (ttmt) REVERT: 2 317 GLU cc_start: 0.6165 (tm-30) cc_final: 0.4231 (tm-30) REVERT: 2 371 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7468 (mtp180) outliers start: 123 outliers final: 82 residues processed: 909 average time/residue: 0.3010 time to fit residues: 436.0568 Evaluate side-chains 877 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 778 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 256 ASP Chi-restraints excluded: chain C residue 332 LEU 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 182 VAL 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 5 LEU 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 G residue 14 ASN 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 201 GLN Chi-restraints excluded: chain I residue 228 SER 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 5 LEU 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 228 SER Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 165 MET 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 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 S residue 337 MET Chi-restraints excluded: chain U residue 34 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 228 SER Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 186 ASP Chi-restraints excluded: chain W residue 228 SER Chi-restraints excluded: chain W residue 259 THR 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 129 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 262 optimal weight: 7.9990 chunk 352 optimal weight: 6.9990 chunk 289 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 510 optimal weight: 0.0970 chunk 477 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 486 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 HIS C 304 GLN G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS I 246 ASN K 33 HIS ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS O 304 GLN Q 33 HIS Q 164 ASN ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 304 GLN ** 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 0 33 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.107471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.089955 restraints weight = 68673.067| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.08 r_work: 0.2843 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 45690 Z= 0.177 Angle : 0.608 9.184 62145 Z= 0.299 Chirality : 0.048 0.255 7110 Planarity : 0.004 0.037 7650 Dihedral : 8.243 85.578 6960 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 2.73 % Allowed : 13.05 % Favored : 84.22 % 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 are not related in a simple way. whole: -0.54 (0.12), residues: 5355 helix: 0.41 (0.10), residues: 3060 sheet: -1.84 (0.25), residues: 390 loop : -1.15 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 249 TYR 0.024 0.002 TYR D 303 PHE 0.024 0.001 PHE 0 209 TRP 0.007 0.001 TRP O 146 HIS 0.007 0.001 HIS G 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (45690) covalent geometry : angle 0.60841 / 0.30 (62145) hydrogen bonds : bond 0.03218 / 2.10 ( 1710) hydrogen bonds : angle 3.82739 / 2.62 ( 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 950 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 823 time to evaluate : 1.796 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: 0.8898 (t0) cc_final: 0.8681 (t0) REVERT: C 93 ASP cc_start: 0.8040 (p0) cc_final: 0.7823 (p0) REVERT: C 143 ARG cc_start: 0.7577 (pmt170) cc_final: 0.7032 (ptt-90) REVERT: C 201 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7588 (mp10) REVERT: C 332 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9219 (tp) REVERT: C 371 ARG cc_start: 0.7965 (mtp180) cc_final: 0.7697 (mtp180) REVERT: A 143 ARG cc_start: 0.7724 (pmt170) cc_final: 0.7281 (ptt-90) REVERT: A 150 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8223 (mttt) REVERT: A 156 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 201 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7680 (mp10) REVERT: A 212 GLU cc_start: 0.8870 (pt0) cc_final: 0.8305 (pt0) REVERT: A 256 ASP cc_start: 0.8551 (t70) cc_final: 0.8197 (t70) REVERT: A 280 MET cc_start: 0.9127 (mmt) cc_final: 0.8838 (mmm) REVERT: A 304 GLN cc_start: 0.8067 (mt0) cc_final: 0.7683 (mm-40) REVERT: A 367 GLU cc_start: 0.8391 (tt0) cc_final: 0.8052 (tt0) REVERT: A 371 ARG cc_start: 0.7834 (mtp180) cc_final: 0.7410 (mtp180) REVERT: D 143 ARG cc_start: 0.7758 (pmt170) cc_final: 0.7244 (ptt-90) REVERT: D 150 LYS cc_start: 0.8875 (mtmm) cc_final: 0.8398 (mttt) REVERT: D 304 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8310 (mm-40) REVERT: G 5 LEU cc_start: 0.9002 (mm) cc_final: 0.8687 (mm) REVERT: G 150 LYS cc_start: 0.8684 (ptpp) cc_final: 0.7961 (mttp) REVERT: G 156 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7557 (tm-30) REVERT: G 201 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8600 (mt0) REVERT: I 53 ASP cc_start: 0.8782 (t0) cc_final: 0.8573 (t0) REVERT: I 57 ARG cc_start: 0.8359 (ptp-110) cc_final: 0.8023 (ttp-170) REVERT: I 143 ARG cc_start: 0.7867 (pmt170) cc_final: 0.7535 (ptt-90) REVERT: I 156 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7758 (tm-30) REVERT: I 159 ASP cc_start: 0.8252 (p0) cc_final: 0.7954 (p0) REVERT: I 201 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: I 271 LEU cc_start: 0.8843 (mt) cc_final: 0.8566 (mt) REVERT: I 304 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8443 (mm-40) REVERT: K 5 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8604 (mm) REVERT: K 57 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8005 (ttp-170) REVERT: K 102 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8425 (pp) REVERT: K 150 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8324 (mttt) REVERT: K 159 ASP cc_start: 0.8346 (p0) cc_final: 0.8029 (p0) REVERT: K 201 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.7728 (mt0) REVERT: K 371 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7665 (mtp180) REVERT: M 102 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8531 (pp) REVERT: M 143 ARG cc_start: 0.7815 (pmt170) cc_final: 0.7363 (ptt-90) REVERT: M 371 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7546 (mtp180) REVERT: O 6 ARG cc_start: 0.8598 (ptp90) cc_final: 0.8352 (ttp80) REVERT: O 53 ASP cc_start: 0.8843 (t0) cc_final: 0.8473 (t0) REVERT: O 54 ARG cc_start: 0.8417 (mmp80) cc_final: 0.7902 (mmp80) REVERT: O 82 GLU cc_start: 0.8496 (tt0) cc_final: 0.8246 (mt-10) REVERT: O 93 ASP cc_start: 0.7755 (p0) cc_final: 0.7497 (t70) REVERT: O 100 ARG cc_start: 0.8728 (ttp80) cc_final: 0.8458 (tmm160) REVERT: O 143 ARG cc_start: 0.7546 (pmt170) cc_final: 0.7083 (ptt-90) REVERT: O 301 ASN cc_start: 0.8318 (m110) cc_final: 0.8113 (m-40) REVERT: O 371 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7604 (mtp180) REVERT: Q 53 ASP cc_start: 0.8886 (t0) cc_final: 0.8605 (t0) REVERT: Q 143 ARG cc_start: 0.7579 (pmt170) cc_final: 0.6769 (ptm-80) REVERT: Q 212 GLU cc_start: 0.8815 (pt0) cc_final: 0.8485 (pt0) REVERT: Q 213 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7953 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7950 (m-30) cc_final: 0.7615 (m-30) REVERT: S 150 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8285 (mtpt) REVERT: S 161 GLU cc_start: 0.8030 (pt0) cc_final: 0.7760 (pt0) REVERT: S 212 GLU cc_start: 0.8756 (pt0) cc_final: 0.8504 (pt0) REVERT: S 228 SER cc_start: 0.8951 (p) cc_final: 0.8735 (m) REVERT: S 371 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7510 (mtp180) REVERT: U 143 ARG cc_start: 0.7625 (pmt170) cc_final: 0.6793 (ttp-110) REVERT: U 201 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: U 209 PHE cc_start: 0.8378 (m-10) cc_final: 0.8112 (m-10) REVERT: U 212 GLU cc_start: 0.8651 (pt0) cc_final: 0.8321 (pt0) REVERT: U 253 MET cc_start: 0.8967 (ttm) cc_final: 0.8751 (ttp) REVERT: U 371 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7488 (mtp180) REVERT: W 31 ILE cc_start: 0.9008 (tp) cc_final: 0.8774 (tp) REVERT: W 111 GLN cc_start: 0.8433 (tp-100) cc_final: 0.7853 (tp40) REVERT: W 143 ARG cc_start: 0.7670 (pmt170) cc_final: 0.6659 (ptm-80) REVERT: W 371 ARG cc_start: 0.7782 (mtp180) cc_final: 0.7358 (mtp180) REVERT: Y 6 ARG cc_start: 0.8514 (ptp90) cc_final: 0.8114 (mtm110) REVERT: Y 123 MET cc_start: 0.5998 (mtm) cc_final: 0.5515 (mtp) REVERT: Y 126 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7640 (tt0) REVERT: Y 150 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8039 (mtpt) REVERT: Y 201 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: Y 225 GLU cc_start: 0.8631 (tt0) cc_final: 0.8412 (tt0) REVERT: Y 304 GLN cc_start: 0.8720 (tt0) cc_final: 0.8458 (mt0) REVERT: Y 371 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7413 (mtp180) REVERT: 0 15 LYS cc_start: 0.8784 (ptmm) cc_final: 0.8528 (ptmm) REVERT: 0 123 MET cc_start: 0.7172 (mtp) cc_final: 0.6786 (mtp) REVERT: 0 201 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: 0 225 GLU cc_start: 0.8647 (tt0) cc_final: 0.8358 (tt0) REVERT: 0 371 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7442 (mtp180) REVERT: 2 102 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8488 (pp) REVERT: 2 201 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8426 (mt0) REVERT: 2 209 PHE cc_start: 0.8049 (m-10) cc_final: 0.7732 (m-10) REVERT: 2 274 LYS cc_start: 0.8981 (tttp) cc_final: 0.8737 (ttmt) REVERT: 2 317 GLU cc_start: 0.6255 (tm-30) cc_final: 0.4682 (tm-30) REVERT: 2 371 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7562 (mtp180) outliers start: 127 outliers final: 92 residues processed: 917 average time/residue: 0.3040 time to fit residues: 444.3524 Evaluate side-chains 903 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 792 time to evaluate : 1.731 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 332 LEU 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 182 VAL 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 5 LEU 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 304 GLN Chi-restraints excluded: chain G residue 14 ASN Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 35 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 35 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 5 LEU 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 103 GLU Chi-restraints excluded: chain M residue 164 ASN Chi-restraints excluded: chain M residue 228 SER Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 165 MET 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 91 ILE Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER 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 337 MET 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 129 GLN 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 228 SER Chi-restraints excluded: chain U residue 237 ILE 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 186 ASP Chi-restraints excluded: chain W residue 228 SER Chi-restraints excluded: chain W residue 304 GLN 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 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 55 LEU 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 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 256 ASP Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 508 optimal weight: 0.6980 chunk 313 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 457 optimal weight: 0.8980 chunk 277 optimal weight: 0.9990 chunk 183 optimal weight: 0.3980 chunk 149 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 437 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 HIS C 304 GLN G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN K 33 HIS ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 322 ASN M 33 HIS O 33 HIS Q 33 HIS Q 164 ASN ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 304 GLN U 322 ASN W 33 HIS W 246 ASN Y 33 HIS Y 246 ASN 0 33 HIS 2 304 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105976 restraints weight = 65166.298| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.95 r_work: 0.3014 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.3619 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= 0.102 Angle : 0.559 8.911 62145 Z= 0.277 Chirality : 0.045 0.268 7110 Planarity : 0.003 0.040 7650 Dihedral : 8.062 87.796 6960 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 2.02 % Allowed : 14.15 % Favored : 83.83 % 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 are not related in a simple way. whole: -0.36 (0.12), residues: 5355 helix: 0.55 (0.10), residues: 3060 sheet: -1.87 (0.24), residues: 390 loop : -1.05 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 249 TYR 0.018 0.001 TYR D 303 PHE 0.020 0.001 PHE 0 209 TRP 0.009 0.001 TRP A 175 HIS 0.007 0.001 HIS G 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (45690) covalent geometry : angle 0.55925 / 0.28 (62145) hydrogen bonds : bond 0.03000 / 1.96 ( 1710) hydrogen bonds : angle 3.64126 / 2.49 ( 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 957 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 863 time to evaluate : 1.722 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 6 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7789 (ttm110) REVERT: C 53 ASP cc_start: 0.8909 (t0) cc_final: 0.8596 (t0) REVERT: C 143 ARG cc_start: 0.7536 (pmt170) cc_final: 0.7005 (ptt-90) REVERT: C 150 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8207 (mmmt) REVERT: C 332 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9245 (tp) REVERT: C 371 ARG cc_start: 0.7884 (mtp180) cc_final: 0.7627 (mtp180) REVERT: A 143 ARG cc_start: 0.7656 (pmt170) cc_final: 0.7240 (ptt-90) REVERT: A 212 GLU cc_start: 0.8795 (pt0) cc_final: 0.8354 (pt0) REVERT: A 280 MET cc_start: 0.9104 (mmt) cc_final: 0.8851 (mmm) REVERT: A 304 GLN cc_start: 0.7987 (mt0) cc_final: 0.7653 (mm-40) REVERT: A 367 GLU cc_start: 0.8384 (tt0) cc_final: 0.8082 (tt0) REVERT: A 371 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7461 (mtp180) REVERT: D 123 MET cc_start: 0.6075 (ptt) cc_final: 0.5743 (ptp) REVERT: D 143 ARG cc_start: 0.7687 (pmt170) cc_final: 0.7197 (ptt-90) REVERT: D 150 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8499 (mttt) REVERT: D 212 GLU cc_start: 0.8791 (pt0) cc_final: 0.8488 (pt0) REVERT: D 304 GLN cc_start: 0.8596 (pt0) cc_final: 0.8265 (mm-40) REVERT: G 5 LEU cc_start: 0.9041 (mm) cc_final: 0.8730 (mm) REVERT: G 150 LYS cc_start: 0.8602 (ptpp) cc_final: 0.8018 (mttp) REVERT: G 156 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7649 (tm-30) REVERT: G 201 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: G 256 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8021 (t0) REVERT: G 258 ASP cc_start: 0.9005 (t70) cc_final: 0.8733 (t0) REVERT: I 53 ASP cc_start: 0.8728 (t0) cc_final: 0.8450 (t0) REVERT: I 57 ARG cc_start: 0.8261 (ptp-110) cc_final: 0.8009 (ttp-170) REVERT: I 103 GLU cc_start: 0.8303 (mp0) cc_final: 0.8093 (mp0) REVERT: I 143 ARG cc_start: 0.7898 (pmt170) cc_final: 0.7566 (ptt-90) REVERT: I 150 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8432 (mttt) REVERT: I 156 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7805 (tm-30) REVERT: I 159 ASP cc_start: 0.8192 (p0) cc_final: 0.7885 (p0) REVERT: I 271 LEU cc_start: 0.8765 (mt) cc_final: 0.8525 (mt) REVERT: I 304 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8417 (mm-40) REVERT: K 5 LEU cc_start: 0.8954 (mm) cc_final: 0.8630 (mm) REVERT: K 57 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8060 (ttp-170) REVERT: K 102 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8291 (pp) REVERT: K 150 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8445 (mttt) REVERT: K 159 ASP cc_start: 0.8237 (p0) cc_final: 0.7922 (p0) REVERT: K 201 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7493 (mt0) REVERT: K 256 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8055 (t0) REVERT: M 102 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8397 (pp) REVERT: M 143 ARG cc_start: 0.7759 (pmt170) cc_final: 0.7323 (ptt-90) REVERT: M 150 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8175 (mmtm) REVERT: M 156 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7437 (tm-30) REVERT: M 325 SER cc_start: 0.9302 (t) cc_final: 0.9062 (p) REVERT: M 371 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7383 (mtp180) REVERT: O 53 ASP cc_start: 0.8760 (t0) cc_final: 0.8405 (t0) REVERT: O 54 ARG cc_start: 0.8340 (mmp80) cc_final: 0.7864 (mmp80) REVERT: O 82 GLU cc_start: 0.8432 (tt0) cc_final: 0.8210 (mt-10) REVERT: O 93 ASP cc_start: 0.7739 (p0) cc_final: 0.7460 (t70) REVERT: O 100 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8384 (tmm160) REVERT: O 143 ARG cc_start: 0.7458 (pmt170) cc_final: 0.7014 (ptt-90) REVERT: O 150 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8024 (mmtm) REVERT: O 201 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: Q 53 ASP cc_start: 0.8809 (t0) cc_final: 0.8526 (t0) REVERT: Q 143 ARG cc_start: 0.7502 (pmt170) cc_final: 0.6653 (ttp-110) REVERT: Q 201 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: Q 212 GLU cc_start: 0.8757 (pt0) cc_final: 0.8482 (pt0) REVERT: Q 213 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7890 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7851 (m-30) cc_final: 0.7489 (m-30) REVERT: Q 256 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8121 (t0) REVERT: Q 325 SER cc_start: 0.9255 (t) cc_final: 0.8878 (p) REVERT: S 143 ARG cc_start: 0.7464 (ptt-90) cc_final: 0.6499 (ttp-110) REVERT: S 150 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8225 (mttt) REVERT: S 161 GLU cc_start: 0.7940 (pt0) cc_final: 0.7712 (pt0) REVERT: S 212 GLU cc_start: 0.8647 (pt0) cc_final: 0.8370 (pt0) REVERT: S 228 SER cc_start: 0.8938 (p) cc_final: 0.8714 (m) REVERT: S 371 ARG cc_start: 0.7764 (mtp180) cc_final: 0.7498 (mtp180) REVERT: U 31 ILE cc_start: 0.9001 (tp) cc_final: 0.8778 (tp) REVERT: U 103 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8285 (mt-10) REVERT: U 143 ARG cc_start: 0.7564 (pmt170) cc_final: 0.6760 (ttp-110) REVERT: U 201 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.7655 (mt0) REVERT: U 212 GLU cc_start: 0.8615 (pt0) cc_final: 0.8328 (pt0) REVERT: U 256 ASP cc_start: 0.8831 (t70) cc_final: 0.7974 (t0) REVERT: U 371 ARG cc_start: 0.7744 (mtp180) cc_final: 0.7427 (mtp180) REVERT: W 111 GLN cc_start: 0.8272 (tp-100) cc_final: 0.7737 (tp40) REVERT: W 143 ARG cc_start: 0.7613 (pmt170) cc_final: 0.6665 (ptm-80) REVERT: W 371 ARG cc_start: 0.7702 (mtp180) cc_final: 0.7345 (mtp180) REVERT: Y 6 ARG cc_start: 0.8458 (ptp90) cc_final: 0.8090 (mtm110) REVERT: Y 123 MET cc_start: 0.6133 (mtm) cc_final: 0.5667 (mtp) REVERT: Y 126 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7695 (tt0) REVERT: Y 201 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8663 (mp10) REVERT: Y 209 PHE cc_start: 0.8328 (m-10) cc_final: 0.8115 (m-10) REVERT: Y 371 ARG cc_start: 0.7737 (mtp180) cc_final: 0.7321 (mtp180) REVERT: 0 15 LYS cc_start: 0.8733 (ptmm) cc_final: 0.8520 (ptmm) REVERT: 0 123 MET cc_start: 0.7241 (mtp) cc_final: 0.6947 (mtp) REVERT: 0 201 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: 0 225 GLU cc_start: 0.8592 (tt0) cc_final: 0.8323 (tt0) REVERT: 0 313 MET cc_start: 0.8542 (ptp) cc_final: 0.8285 (ptm) REVERT: 0 325 SER cc_start: 0.9299 (t) cc_final: 0.8985 (p) REVERT: 0 371 ARG cc_start: 0.7855 (mtp180) cc_final: 0.7436 (mtp180) REVERT: 2 53 ASP cc_start: 0.9060 (t0) cc_final: 0.8785 (t0) REVERT: 2 54 ARG cc_start: 0.8239 (mmp80) cc_final: 0.8032 (mmt-90) REVERT: 2 102 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8381 (pp) REVERT: 2 161 GLU cc_start: 0.8201 (pt0) cc_final: 0.7899 (pt0) REVERT: 2 201 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8343 (mt0) REVERT: 2 209 PHE cc_start: 0.7574 (m-10) cc_final: 0.7079 (m-80) REVERT: 2 256 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8227 (t0) REVERT: 2 274 LYS cc_start: 0.8967 (tttp) cc_final: 0.8746 (ttmt) REVERT: 2 317 GLU cc_start: 0.6180 (tm-30) cc_final: 0.4161 (tm-30) REVERT: 2 371 ARG cc_start: 0.7821 (mtp180) cc_final: 0.7021 (mtp180) outliers start: 94 outliers final: 60 residues processed: 928 average time/residue: 0.2959 time to fit residues: 436.8128 Evaluate side-chains 885 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 805 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 332 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 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 14 ASN 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 I residue 14 ASN Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 228 SER 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 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 103 GLU Chi-restraints excluded: chain M residue 228 SER Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 165 MET 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 91 ILE Chi-restraints excluded: chain Q residue 201 GLN Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 256 ASP Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain S residue 29 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 S residue 256 ASP Chi-restraints excluded: chain S residue 337 MET Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 228 SER Chi-restraints excluded: chain U residue 237 ILE Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain W residue 186 ASP Chi-restraints excluded: chain W residue 228 SER 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 355 SER Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 129 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 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 237 ILE Chi-restraints excluded: chain 2 residue 256 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 471 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 512 optimal weight: 0.1980 chunk 136 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 422 optimal weight: 0.4980 chunk 368 optimal weight: 0.9980 chunk 454 optimal weight: 4.9990 chunk 474 optimal weight: 0.0000 chunk 235 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 HIS A 33 HIS G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 33 HIS K 304 GLN K 322 ASN M 33 HIS O 33 HIS Q 33 HIS Q 246 ASN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 ASN W 33 HIS Y 33 HIS Y 246 ASN 0 33 HIS 2 86 GLN 2 304 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099722 restraints weight = 67350.723| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.06 r_work: 0.3070 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 45690 Z= 0.097 Angle : 0.551 9.123 62145 Z= 0.273 Chirality : 0.044 0.234 7110 Planarity : 0.003 0.039 7650 Dihedral : 7.718 79.504 6960 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.70 % Allowed : 15.05 % Favored : 83.25 % 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 are not related in a simple way. whole: -0.21 (0.12), residues: 5355 helix: 0.64 (0.10), residues: 3090 sheet: -1.74 (0.24), residues: 390 loop : -0.97 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 249 TYR 0.019 0.001 TYR D 303 PHE 0.022 0.001 PHE 0 209 TRP 0.008 0.001 TRP O 333 HIS 0.007 0.001 HIS U 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (45690) covalent geometry : angle 0.55080 / 0.27 (62145) hydrogen bonds : bond 0.02856 / 1.87 ( 1710) hydrogen bonds : angle 3.53642 / 2.42 ( 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 998 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 919 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7738 (ttm110) REVERT: C 53 ASP cc_start: 0.8915 (t0) cc_final: 0.8600 (t0) REVERT: C 143 ARG cc_start: 0.7459 (pmt170) cc_final: 0.6926 (ptt-90) REVERT: C 150 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8214 (mmmt) REVERT: C 332 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9197 (tp) REVERT: C 371 ARG cc_start: 0.7927 (mtp180) cc_final: 0.7717 (mtp180) REVERT: A 143 ARG cc_start: 0.7605 (pmt170) cc_final: 0.7190 (ptt-90) REVERT: A 201 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: A 280 MET cc_start: 0.9084 (mmt) cc_final: 0.8855 (mmm) REVERT: A 304 GLN cc_start: 0.7955 (mt0) cc_final: 0.7595 (mm-40) REVERT: A 367 GLU cc_start: 0.8370 (tt0) cc_final: 0.8073 (tt0) REVERT: A 371 ARG cc_start: 0.7819 (mtp180) cc_final: 0.7470 (mtp180) REVERT: D 21 THR cc_start: 0.7579 (p) cc_final: 0.7285 (p) REVERT: D 57 ARG cc_start: 0.8343 (ptp-110) cc_final: 0.8051 (ttp-170) REVERT: D 123 MET cc_start: 0.6118 (ptt) cc_final: 0.5879 (ptp) REVERT: D 143 ARG cc_start: 0.7696 (pmt170) cc_final: 0.7201 (ptt-90) REVERT: D 150 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8498 (mmtt) REVERT: D 212 GLU cc_start: 0.8708 (pt0) cc_final: 0.8440 (pt0) REVERT: G 5 LEU cc_start: 0.9002 (mm) cc_final: 0.8688 (mm) REVERT: G 103 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8134 (mt-10) REVERT: G 123 MET cc_start: 0.5898 (ptt) cc_final: 0.5573 (ptp) REVERT: G 150 LYS cc_start: 0.8591 (ptpp) cc_final: 0.8075 (mttp) REVERT: G 156 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7691 (tm-30) REVERT: G 159 ASP cc_start: 0.8022 (p0) cc_final: 0.7755 (p0) REVERT: G 201 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: G 258 ASP cc_start: 0.8959 (t70) cc_final: 0.8588 (t0) REVERT: G 351 ASN cc_start: 0.8889 (t0) cc_final: 0.8609 (t0) REVERT: I 53 ASP cc_start: 0.8764 (t0) cc_final: 0.8474 (t0) REVERT: I 143 ARG cc_start: 0.7868 (pmt170) cc_final: 0.7543 (ptt-90) REVERT: I 150 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8334 (mmtt) REVERT: I 156 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7808 (tm-30) REVERT: I 159 ASP cc_start: 0.8088 (p0) cc_final: 0.7635 (p0) REVERT: I 304 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8443 (mm-40) REVERT: K 5 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8635 (mm) REVERT: K 57 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8133 (ttp-170) REVERT: K 102 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8084 (pp) REVERT: K 150 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8464 (mmmt) REVERT: K 159 ASP cc_start: 0.8158 (p0) cc_final: 0.7902 (p0) REVERT: K 201 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: M 102 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8316 (pp) REVERT: M 143 ARG cc_start: 0.7726 (pmt170) cc_final: 0.7288 (ptt-90) REVERT: M 150 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8327 (mmtm) REVERT: M 156 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7446 (tm-30) REVERT: M 213 ARG cc_start: 0.8269 (mtp-110) cc_final: 0.8001 (ttm-80) REVERT: M 325 SER cc_start: 0.9318 (t) cc_final: 0.9022 (p) REVERT: M 371 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7375 (mtp180) REVERT: O 53 ASP cc_start: 0.8756 (t0) cc_final: 0.8446 (t0) REVERT: O 54 ARG cc_start: 0.8211 (mmp80) cc_final: 0.7706 (mmp80) REVERT: O 82 GLU cc_start: 0.8412 (tt0) cc_final: 0.8198 (mt-10) REVERT: O 93 ASP cc_start: 0.7728 (p0) cc_final: 0.7457 (t70) REVERT: O 100 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8249 (tmm160) REVERT: O 143 ARG cc_start: 0.7414 (pmt170) cc_final: 0.6959 (ptt-90) REVERT: O 150 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8095 (mmtm) REVERT: O 201 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: O 280 MET cc_start: 0.8994 (mmm) cc_final: 0.8783 (mmm) REVERT: O 301 ASN cc_start: 0.8199 (m110) cc_final: 0.7928 (m110) REVERT: Q 53 ASP cc_start: 0.8821 (t0) cc_final: 0.8507 (t0) REVERT: Q 143 ARG cc_start: 0.7548 (pmt170) cc_final: 0.6678 (ttp-110) REVERT: Q 201 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: Q 212 GLU cc_start: 0.8745 (pt0) cc_final: 0.8511 (pt0) REVERT: Q 213 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7913 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7867 (m-30) cc_final: 0.7520 (m-30) REVERT: Q 256 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8244 (t0) REVERT: Q 301 ASN cc_start: 0.8178 (m-40) cc_final: 0.7973 (m-40) REVERT: Q 325 SER cc_start: 0.9248 (t) cc_final: 0.8814 (p) REVERT: S 143 ARG cc_start: 0.7431 (ptt-90) cc_final: 0.6435 (ttp-110) REVERT: S 161 GLU cc_start: 0.7894 (pt0) cc_final: 0.7645 (pt0) REVERT: S 212 GLU cc_start: 0.8627 (pt0) cc_final: 0.8142 (pt0) REVERT: S 213 ARG cc_start: 0.8219 (mtp-110) cc_final: 0.7736 (ttt180) REVERT: U 31 ILE cc_start: 0.8952 (tp) cc_final: 0.8750 (tp) REVERT: U 54 ARG cc_start: 0.8285 (mmt-90) cc_final: 0.7900 (mmt-90) REVERT: U 143 ARG cc_start: 0.7558 (pmt170) cc_final: 0.6713 (ttp-110) REVERT: U 150 LYS cc_start: 0.8336 (ptpp) cc_final: 0.7936 (mttt) REVERT: U 201 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: U 212 GLU cc_start: 0.8601 (pt0) cc_final: 0.8164 (pt0) REVERT: U 371 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7486 (mtp180) REVERT: W 54 ARG cc_start: 0.8287 (mmt-90) cc_final: 0.8051 (mmt-90) REVERT: W 111 GLN cc_start: 0.8310 (tp-100) cc_final: 0.7756 (tp40) REVERT: W 143 ARG cc_start: 0.7617 (pmt170) cc_final: 0.6666 (ptm-80) REVERT: W 325 SER cc_start: 0.9359 (t) cc_final: 0.9036 (p) REVERT: W 371 ARG cc_start: 0.7787 (mtp180) cc_final: 0.7357 (mtp180) REVERT: Y 6 ARG cc_start: 0.8439 (ptp90) cc_final: 0.8091 (mtm110) REVERT: Y 123 MET cc_start: 0.6053 (mtm) cc_final: 0.5575 (mtp) REVERT: Y 201 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8679 (mp10) REVERT: Y 209 PHE cc_start: 0.8221 (m-10) cc_final: 0.7969 (m-10) REVERT: Y 371 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7342 (mtp180) REVERT: 0 15 LYS cc_start: 0.8752 (ptmm) cc_final: 0.8440 (ptmm) REVERT: 0 123 MET cc_start: 0.7222 (mtp) cc_final: 0.6915 (mtp) REVERT: 0 201 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: 0 225 GLU cc_start: 0.8627 (tt0) cc_final: 0.8266 (tt0) REVERT: 0 325 SER cc_start: 0.9258 (t) cc_final: 0.8921 (p) REVERT: 0 371 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7484 (mtp180) REVERT: 2 53 ASP cc_start: 0.9063 (t0) cc_final: 0.8777 (t0) REVERT: 2 102 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8286 (pp) REVERT: 2 150 LYS cc_start: 0.8474 (ptpp) cc_final: 0.7880 (mttm) REVERT: 2 161 GLU cc_start: 0.8230 (pt0) cc_final: 0.7925 (pt0) REVERT: 2 201 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: 2 209 PHE cc_start: 0.7509 (m-10) cc_final: 0.7086 (m-80) REVERT: 2 274 LYS cc_start: 0.8950 (tttp) cc_final: 0.8720 (ttmt) REVERT: 2 317 GLU cc_start: 0.6161 (tm-30) cc_final: 0.4493 (tm-30) REVERT: 2 371 ARG cc_start: 0.7787 (mtp180) cc_final: 0.6999 (mtp180) outliers start: 79 outliers final: 51 residues processed: 976 average time/residue: 0.3020 time to fit residues: 468.4409 Evaluate side-chains 904 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 835 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 332 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 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 367 GLU Chi-restraints excluded: chain G residue 14 ASN 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 228 SER Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 5 LEU 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 164 ASN 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 91 ILE Chi-restraints excluded: chain Q residue 201 GLN Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 256 ASP Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain S residue 91 ILE Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 102 LEU 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 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 201 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 129 GLN Chi-restraints excluded: chain 0 residue 201 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 480 optimal weight: 0.2980 chunk 182 optimal weight: 10.0000 chunk 491 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 474 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 502 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 398 optimal weight: 10.0000 chunk 470 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 HIS A 33 HIS G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 33 HIS ** K 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN M 322 ASN O 33 HIS O 301 ASN Q 33 HIS Q 304 GLN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 ASN U 33 HIS U 322 ASN W 33 HIS W 322 ASN Y 33 HIS Y 322 ASN 0 33 HIS 0 246 ASN 2 86 GLN 2 89 GLN ** 2 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.097176 restraints weight = 67681.976| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.07 r_work: 0.3014 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 45690 Z= 0.120 Angle : 0.562 8.923 62145 Z= 0.279 Chirality : 0.045 0.220 7110 Planarity : 0.004 0.044 7650 Dihedral : 7.724 76.043 6960 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.74 % Allowed : 15.91 % Favored : 82.34 % 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 are not related in a simple way. whole: -0.19 (0.12), residues: 5355 helix: 0.65 (0.10), residues: 3090 sheet: -1.68 (0.25), residues: 390 loop : -0.94 (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 D 303 PHE 0.023 0.001 PHE 0 209 TRP 0.007 0.001 TRP Y 333 HIS 0.007 0.001 HIS M 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (45690) covalent geometry : angle 0.56156 / 0.28 (62145) hydrogen bonds : bond 0.02900 / 1.89 ( 1710) hydrogen bonds : angle 3.57017 / 2.45 ( 4950) =============================================================================== Job complete usr+sys time: 12794.90 seconds wall clock time: 219 minutes 22.95 seconds (13162.95 seconds total)