Starting phenix.real_space_refine on Thu Dec 26 06:44:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h5s_0142/12_2024/6h5s_0142.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h5s_0142/12_2024/6h5s_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_0142/12_2024/6h5s_0142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h5s_0142/12_2024/6h5s_0142.map" model { file = "/net/cci-nas-00/data/ceres_data/6h5s_0142/12_2024/6h5s_0142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h5s_0142/12_2024/6h5s_0142.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44700 Number of models: 1 Model: "" Number of chains: 2 Chain: "0" 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: "1" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Restraints were copied for chains: 2, A, C, D, G, I, K, M, O, Q, S, U, W, Y, 3, B, E, F, H, J, L, N, P, R, T, V, X, Z Time building chain proxies: 11.02, per 1000 atoms: 0.25 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: 10.41 Conformation dependent library (CDL) restraints added in 5.4 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: 14.90 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: 18.35 Time building geometry restraints manager: 11.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 13815 1.33 - 1.45: 6865 1.45 - 1.57: 24515 1.57 - 1.69: 150 1.69 - 1.80: 345 Bond restraints: 45690 Sorted by residual: bond pdb=" CB VAL Q 314 " pdb=" CG1 VAL Q 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB VAL 2 314 " pdb=" CG1 VAL 2 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB VAL G 314 " pdb=" CG1 VAL G 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CB VAL A 314 " pdb=" CG1 VAL A 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CB VAL K 314 " pdb=" CG1 VAL K 314 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.13e+00 ... (remaining 45685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 60016 2.63 - 5.25: 1878 5.25 - 7.88: 161 7.88 - 10.50: 75 10.50 - 13.13: 15 Bond angle restraints: 62145 Sorted by residual: angle pdb=" N ILE M 28 " pdb=" CA ILE M 28 " pdb=" C ILE M 28 " ideal model delta sigma weight residual 113.71 106.84 6.87 9.50e-01 1.11e+00 5.22e+01 angle pdb=" N ILE 0 28 " pdb=" CA ILE 0 28 " pdb=" C ILE 0 28 " ideal model delta sigma weight residual 113.71 106.86 6.85 9.50e-01 1.11e+00 5.21e+01 angle pdb=" N ILE U 28 " pdb=" CA ILE U 28 " pdb=" C ILE U 28 " ideal model delta sigma weight residual 113.71 106.86 6.85 9.50e-01 1.11e+00 5.20e+01 angle pdb=" N ILE Y 28 " pdb=" CA ILE Y 28 " pdb=" C ILE Y 28 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.19e+01 angle pdb=" N ILE I 28 " pdb=" CA ILE I 28 " pdb=" C ILE I 28 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.19e+01 ... (remaining 62140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 25486 15.16 - 30.32: 1664 30.32 - 45.47: 330 45.47 - 60.63: 90 60.63 - 75.79: 75 Dihedral angle restraints: 27645 sinusoidal: 12075 harmonic: 15570 Sorted by residual: dihedral pdb=" CA LYS Q 150 " pdb=" C LYS Q 150 " pdb=" N GLU Q 151 " pdb=" CA GLU Q 151 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS K 150 " pdb=" C LYS K 150 " pdb=" N GLU K 151 " pdb=" CA GLU K 151 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS 2 150 " pdb=" C LYS 2 150 " pdb=" N GLU 2 151 " pdb=" CA GLU 2 151 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 27642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5739 0.075 - 0.151: 1221 0.151 - 0.226: 120 0.226 - 0.302: 15 0.302 - 0.377: 15 Chirality restraints: 7110 Sorted by residual: chirality pdb=" CA ASP O 42 " pdb=" N ASP O 42 " pdb=" C ASP O 42 " pdb=" CB ASP O 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ASP I 42 " pdb=" N ASP I 42 " pdb=" C ASP I 42 " pdb=" CB ASP I 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ASP Y 42 " pdb=" N ASP Y 42 " pdb=" C ASP Y 42 " pdb=" CB ASP Y 42 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 7107 not shown) Planarity restraints: 7650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 281 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO S 282 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO S 282 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 282 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 0 281 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO 0 282 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO 0 282 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 0 282 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 281 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO A 282 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " -0.031 5.00e-02 4.00e+02 ... (remaining 7647 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 155 2.43 - 3.05: 26374 3.05 - 3.67: 70678 3.67 - 4.28: 108487 4.28 - 4.90: 175372 Nonbonded interactions: 381066 Sorted by model distance: nonbonded pdb=" O GLY A 23 " pdb=" OE2 GLU 0 342 " model vdw 1.817 3.040 nonbonded pdb=" O GLY D 23 " pdb=" OE2 GLU 2 342 " model vdw 1.817 3.040 nonbonded pdb=" OG SER Y 334 " pdb=" O PHE Y 357 " model vdw 2.272 3.040 nonbonded pdb=" OG SER S 334 " pdb=" O PHE S 357 " model vdw 2.272 3.040 nonbonded pdb=" OG SER W 334 " pdb=" O PHE W 357 " model vdw 2.272 3.040 ... (remaining 381061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain 'A' selection = chain 'C' 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' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'B' selection = chain 'E' 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' } 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.780 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 88.720 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.440 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: 0.020 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.060 45690 Z= 0.619 Angle : 1.118 13.127 62145 Z= 0.607 Chirality : 0.063 0.377 7110 Planarity : 0.007 0.056 7650 Dihedral : 11.844 75.788 17625 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.65 % Allowed : 4.19 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.003 TRP Y 215 HIS 0.004 0.001 HIS O 287 PHE 0.020 0.004 PHE G 324 TYR 0.029 0.005 TYR O 281 ARG 0.011 0.001 ARG D 370 *********************** 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 : 4.986 Fit side-chains revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8344 (ptp-110) cc_final: 0.8029 (ptp-110) REVERT: C 143 ARG cc_start: 0.7223 (pmt170) cc_final: 0.6689 (ptm-80) REVERT: C 166 ILE cc_start: 0.9019 (mm) cc_final: 0.8814 (mt) REVERT: C 256 ASP cc_start: 0.8847 (t70) cc_final: 0.8252 (t0) REVERT: C 306 MET cc_start: 0.8949 (mtp) cc_final: 0.8705 (mtp) REVERT: A 143 ARG cc_start: 0.7317 (pmt170) cc_final: 0.6829 (ttp-110) REVERT: A 156 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6601 (tm-30) REVERT: A 320 ILE cc_start: 0.9108 (tt) cc_final: 0.8776 (tt) REVERT: A 367 GLU cc_start: 0.7353 (tt0) cc_final: 0.7031 (tt0) REVERT: D 29 ARG cc_start: 0.8407 (ptp-110) cc_final: 0.8067 (ptp-110) REVERT: D 53 ASP cc_start: 0.8341 (t0) cc_final: 0.7861 (t0) REVERT: D 76 ILE cc_start: 0.8588 (pt) cc_final: 0.8245 (pt) REVERT: D 143 ARG cc_start: 0.7375 (pmt170) cc_final: 0.6961 (ptt-90) REVERT: D 297 GLU cc_start: 0.7808 (tt0) cc_final: 0.7576 (tt0) REVERT: D 320 ILE cc_start: 0.9164 (tt) cc_final: 0.8869 (tt) REVERT: G 13 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7156 (mtm110) REVERT: G 156 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6656 (tm-30) REVERT: G 297 GLU cc_start: 0.7905 (tt0) cc_final: 0.7629 (tt0) REVERT: G 306 MET cc_start: 0.8946 (mtp) cc_final: 0.8675 (mtp) REVERT: I 53 ASP cc_start: 0.8188 (t0) cc_final: 0.7979 (t0) REVERT: I 57 ARG cc_start: 0.8188 (ptp-110) cc_final: 0.7927 (ttp-170) REVERT: I 123 MET cc_start: 0.6115 (mtm) cc_final: 0.5910 (ptt) REVERT: I 143 ARG cc_start: 0.7443 (pmt170) cc_final: 0.7143 (ptt-90) REVERT: I 159 ASP cc_start: 0.8641 (p0) cc_final: 0.8378 (p0) REVERT: I 297 GLU cc_start: 0.7796 (tt0) cc_final: 0.7552 (tt0) REVERT: I 320 ILE cc_start: 0.9104 (tt) cc_final: 0.8855 (tt) REVERT: K 156 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6555 (tm-30) REVERT: K 158 GLN cc_start: 0.7966 (mp10) cc_final: 0.7602 (mm-40) REVERT: K 252 GLU cc_start: 0.8119 (tp30) cc_final: 0.7818 (tp30) REVERT: K 297 GLU cc_start: 0.7735 (tt0) cc_final: 0.7442 (tt0) REVERT: K 320 ILE cc_start: 0.9068 (tt) cc_final: 0.8827 (tt) REVERT: M 3 THR cc_start: 0.8878 (t) cc_final: 0.8632 (m) REVERT: M 29 ARG cc_start: 0.8372 (ptp-110) cc_final: 0.8148 (ptp-110) REVERT: M 53 ASP cc_start: 0.8202 (t0) cc_final: 0.7989 (t0) REVERT: M 143 ARG cc_start: 0.7485 (pmt170) cc_final: 0.7110 (ptt-90) REVERT: M 156 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6144 (tm-30) REVERT: M 158 GLN cc_start: 0.8036 (mp10) cc_final: 0.7767 (mm-40) REVERT: M 166 ILE cc_start: 0.8987 (mm) cc_final: 0.8775 (mt) REVERT: M 263 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7850 (mt-10) REVERT: M 320 ILE cc_start: 0.9049 (tt) cc_final: 0.8748 (tt) REVERT: M 371 ARG cc_start: 0.7307 (mtp180) cc_final: 0.7087 (mtp180) REVERT: O 29 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.7938 (ptp-110) REVERT: O 53 ASP cc_start: 0.8342 (t0) cc_final: 0.8057 (t0) REVERT: O 143 ARG cc_start: 0.7331 (pmt170) cc_final: 0.6889 (ptm-80) REVERT: O 217 ASP cc_start: 0.7574 (m-30) cc_final: 0.7208 (m-30) REVERT: O 320 ILE cc_start: 0.9103 (tt) cc_final: 0.8842 (tt) REVERT: O 371 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6871 (mtp180) REVERT: Q 10 LEU cc_start: 0.9043 (mt) cc_final: 0.8803 (mp) REVERT: Q 29 ARG cc_start: 0.8393 (ptp-110) cc_final: 0.8060 (ptp-110) REVERT: Q 53 ASP cc_start: 0.8358 (t0) cc_final: 0.7935 (t0) REVERT: Q 109 GLN cc_start: 0.7236 (tm-30) cc_final: 0.7035 (tm-30) REVERT: Q 143 ARG cc_start: 0.7297 (pmt170) cc_final: 0.7038 (ptm-80) REVERT: Q 217 ASP cc_start: 0.7541 (m-30) cc_final: 0.7083 (m-30) REVERT: Q 253 MET cc_start: 0.8187 (ttm) cc_final: 0.7968 (ttp) REVERT: Q 371 ARG cc_start: 0.7311 (mtp180) cc_final: 0.7043 (mtp180) REVERT: S 13 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.7053 (mtm110) REVERT: S 166 ILE cc_start: 0.9061 (mm) cc_final: 0.8836 (mt) REVERT: S 256 ASP cc_start: 0.8764 (t70) cc_final: 0.8106 (t0) REVERT: S 304 GLN cc_start: 0.7935 (pt0) cc_final: 0.7710 (pt0) REVERT: U 29 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.8148 (ptp-110) REVERT: U 143 ARG cc_start: 0.7374 (pmt170) cc_final: 0.6980 (mtp-110) REVERT: U 159 ASP cc_start: 0.8672 (p0) cc_final: 0.8409 (p0) REVERT: U 166 ILE cc_start: 0.9116 (mm) cc_final: 0.8890 (mt) REVERT: U 256 ASP cc_start: 0.8707 (t70) cc_final: 0.7959 (t0) REVERT: U 306 MET cc_start: 0.8921 (mtp) cc_final: 0.8670 (mtm) REVERT: U 371 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6899 (mtp180) REVERT: W 5 LEU cc_start: 0.8707 (mm) cc_final: 0.8507 (mm) REVERT: W 10 LEU cc_start: 0.8950 (mt) cc_final: 0.8666 (mt) REVERT: W 111 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7538 (tp40) REVERT: W 143 ARG cc_start: 0.7218 (pmt170) cc_final: 0.6645 (ptm-80) REVERT: W 367 GLU cc_start: 0.7472 (tt0) cc_final: 0.7271 (tt0) REVERT: W 371 ARG cc_start: 0.7317 (mtp180) cc_final: 0.7066 (mtp180) REVERT: Y 31 ILE cc_start: 0.8835 (tp) cc_final: 0.8571 (tp) REVERT: Y 53 ASP cc_start: 0.8570 (t0) cc_final: 0.8333 (t0) REVERT: Y 123 MET cc_start: 0.5922 (mtm) cc_final: 0.5454 (mtp) REVERT: Y 166 ILE cc_start: 0.9054 (mm) cc_final: 0.8814 (mt) REVERT: Y 209 PHE cc_start: 0.8582 (m-10) cc_final: 0.8320 (m-80) REVERT: Y 337 MET cc_start: 0.8494 (mmp) cc_final: 0.8275 (mmp) REVERT: Y 367 GLU cc_start: 0.7488 (tt0) cc_final: 0.7262 (tt0) REVERT: Y 371 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6934 (mtp180) REVERT: 0 53 ASP cc_start: 0.8687 (t0) cc_final: 0.8300 (t0) REVERT: 0 337 MET cc_start: 0.8589 (mmp) cc_final: 0.8310 (mmp) REVERT: 0 371 ARG cc_start: 0.7213 (mtp180) cc_final: 0.6742 (mtp180) REVERT: 2 3 THR cc_start: 0.8554 (t) cc_final: 0.8256 (m) REVERT: 2 10 LEU cc_start: 0.9044 (mt) cc_final: 0.8808 (mt) REVERT: 2 29 ARG cc_start: 0.8365 (ptp-110) cc_final: 0.7918 (ptp90) REVERT: 2 256 ASP cc_start: 0.8711 (t70) cc_final: 0.8005 (t0) REVERT: 2 274 LYS cc_start: 0.8670 (tttp) cc_final: 0.8439 (ttmt) REVERT: 2 320 ILE cc_start: 0.9108 (tt) cc_final: 0.8887 (tt) REVERT: 2 371 ARG cc_start: 0.7273 (mtp180) cc_final: 0.6887 (mtp180) outliers start: 30 outliers final: 7 residues processed: 1267 average time/residue: 0.6730 time to fit residues: 1353.6718 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 : 5.270 ------------------------------------------------------------------------------- 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 455 optimal weight: 0.9980 chunk 409 optimal weight: 0.9990 chunk 227 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 276 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 423 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 chunk 315 optimal weight: 3.9990 chunk 490 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 33 HIS C 61 ASN C 164 ASN C 202 GLN C 351 ASN A 33 HIS A 61 ASN A 304 GLN A 351 ASN D 61 ASN D 246 ASN D 322 ASN D 351 ASN G 33 HIS G 61 ASN G 246 ASN G 351 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN I 351 ASN K 33 HIS K 61 ASN K 149 ASN K 164 ASN K 246 ASN K 322 ASN K 351 ASN M 33 HIS M 61 ASN M 149 ASN M 202 GLN M 246 ASN M 351 ASN O 33 HIS O 61 ASN O 164 ASN O 246 ASN O 304 GLN O 351 ASN ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS Q 61 ASN Q 246 ASN Q 322 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 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 351 ASN 0 14 ASN 0 33 HIS 0 61 ASN 0 164 ASN ** 0 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 14 ASN 2 33 HIS 2 61 ASN 2 164 ASN 2 351 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2103 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= 0.178 Angle : 0.634 9.244 62145 Z= 0.331 Chirality : 0.044 0.238 7110 Planarity : 0.005 0.047 7650 Dihedral : 10.959 73.542 7184 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.22 % Allowed : 8.84 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP M 333 HIS 0.005 0.001 HIS S 33 PHE 0.015 0.002 PHE K 324 TYR 0.012 0.001 TYR 0 361 ARG 0.007 0.001 ARG M 231 *********************** 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 1048 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 945 time to evaluate : 5.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8416 (ptp-110) cc_final: 0.8104 (ptp-110) REVERT: C 53 ASP cc_start: 0.8391 (t0) cc_final: 0.7984 (t0) REVERT: C 143 ARG cc_start: 0.7305 (pmt170) cc_final: 0.6660 (ptm-80) REVERT: C 209 PHE cc_start: 0.8756 (m-10) cc_final: 0.8502 (m-10) REVERT: C 371 ARG cc_start: 0.7100 (mtp180) cc_final: 0.6843 (mtp180) REVERT: D 143 ARG cc_start: 0.7470 (pmt170) cc_final: 0.7143 (ptt-90) REVERT: D 320 ILE cc_start: 0.9116 (tt) cc_final: 0.8916 (tt) REVERT: D 344 GLU cc_start: 0.7918 (mp0) cc_final: 0.7636 (mp0) REVERT: G 53 ASP cc_start: 0.8421 (t0) cc_final: 0.8205 (t0) REVERT: G 165 MET cc_start: 0.8433 (tpt) cc_final: 0.8214 (tpt) REVERT: G 306 MET cc_start: 0.8779 (mtp) cc_final: 0.8488 (mtp) REVERT: G 337 MET cc_start: 0.8439 (mmp) cc_final: 0.8157 (mmp) REVERT: I 53 ASP cc_start: 0.8226 (t0) cc_final: 0.7998 (t0) REVERT: I 57 ARG cc_start: 0.8178 (ptp-110) cc_final: 0.7934 (ttp-170) REVERT: I 129 GLN cc_start: 0.8238 (mp10) cc_final: 0.7987 (mp10) REVERT: I 143 ARG cc_start: 0.7539 (pmt170) cc_final: 0.7113 (ptt-90) REVERT: K 13 ARG cc_start: 0.7535 (mtp180) cc_final: 0.7157 (mtm110) REVERT: K 29 ARG cc_start: 0.8436 (ptp-110) cc_final: 0.8113 (ptp90) REVERT: K 156 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6527 (tm-30) REVERT: K 159 ASP cc_start: 0.8222 (p0) cc_final: 0.7859 (p0) REVERT: K 227 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8335 (tp) REVERT: K 256 ASP cc_start: 0.8606 (t70) cc_final: 0.8138 (t0) REVERT: K 320 ILE cc_start: 0.9064 (tt) cc_final: 0.8777 (tt) REVERT: K 344 GLU cc_start: 0.7800 (mp0) cc_final: 0.7512 (mm-30) REVERT: K 371 ARG cc_start: 0.7374 (mtp180) cc_final: 0.7071 (mtp180) REVERT: M 143 ARG cc_start: 0.7532 (pmt170) cc_final: 0.6918 (ptt-90) REVERT: M 156 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6228 (tm-30) REVERT: M 158 GLN cc_start: 0.8118 (mp10) cc_final: 0.7859 (mm-40) REVERT: M 217 ASP cc_start: 0.7232 (m-30) cc_final: 0.6647 (m-30) REVERT: M 263 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7805 (mt-10) REVERT: M 371 ARG cc_start: 0.7217 (mtp180) cc_final: 0.6728 (mtp180) REVERT: O 6 ARG cc_start: 0.8016 (ptp90) cc_final: 0.7605 (ttp-110) REVERT: O 82 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: O 86 GLN cc_start: 0.8469 (pt0) cc_final: 0.8240 (pt0) REVERT: O 100 ARG cc_start: 0.8338 (ttp80) cc_final: 0.8116 (tmm160) REVERT: O 143 ARG cc_start: 0.7340 (pmt170) cc_final: 0.6894 (ptm-80) REVERT: O 212 GLU cc_start: 0.8168 (pt0) cc_final: 0.7965 (pt0) REVERT: O 217 ASP cc_start: 0.7360 (m-30) cc_final: 0.6882 (m-30) REVERT: O 367 GLU cc_start: 0.7628 (tt0) cc_final: 0.7120 (tt0) REVERT: O 371 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6788 (mtp180) REVERT: Q 53 ASP cc_start: 0.8375 (t0) cc_final: 0.8069 (t0) REVERT: Q 57 ARG cc_start: 0.8291 (ptp-110) cc_final: 0.8031 (ptm160) REVERT: Q 109 GLN cc_start: 0.7152 (tm-30) cc_final: 0.6940 (tm-30) REVERT: Q 143 ARG cc_start: 0.7280 (pmt170) cc_final: 0.6923 (ptm-80) REVERT: Q 213 ARG cc_start: 0.7656 (mtp-110) cc_final: 0.7297 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7236 (m-30) cc_final: 0.6840 (m-30) REVERT: Q 371 ARG cc_start: 0.7220 (mtp180) cc_final: 0.6888 (mtp180) REVERT: S 143 ARG cc_start: 0.7155 (ptt-90) cc_final: 0.6344 (ttp-110) REVERT: S 280 MET cc_start: 0.8340 (mmm) cc_final: 0.7885 (mmt) REVERT: S 371 ARG cc_start: 0.7031 (mtp180) cc_final: 0.6784 (mtp180) REVERT: U 143 ARG cc_start: 0.7397 (pmt170) cc_final: 0.6897 (mtp-110) REVERT: U 371 ARG cc_start: 0.7139 (mtp180) cc_final: 0.6770 (mtp180) REVERT: W 111 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7635 (tp40) REVERT: W 143 ARG cc_start: 0.7214 (pmt170) cc_final: 0.6603 (ptm-80) REVERT: W 371 ARG cc_start: 0.7242 (mtp180) cc_final: 0.6908 (mtp180) REVERT: Y 6 ARG cc_start: 0.8183 (ptp90) cc_final: 0.7819 (mtm110) REVERT: Y 100 ARG cc_start: 0.7804 (ttp-110) cc_final: 0.7476 (tmm160) REVERT: Y 123 MET cc_start: 0.5844 (mtm) cc_final: 0.5450 (mtp) REVERT: Y 164 ASN cc_start: 0.8706 (t0) cc_final: 0.8492 (t0) REVERT: Y 258 ASP cc_start: 0.8758 (t70) cc_final: 0.8434 (t0) REVERT: Y 371 ARG cc_start: 0.7180 (mtp180) cc_final: 0.6932 (mtp180) REVERT: 0 53 ASP cc_start: 0.8667 (t0) cc_final: 0.8413 (t0) REVERT: 0 123 MET cc_start: 0.6773 (mtp) cc_final: 0.6369 (mtp) REVERT: 0 225 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: 0 371 ARG cc_start: 0.7155 (mtp180) cc_final: 0.6639 (mtp180) REVERT: 2 10 LEU cc_start: 0.9019 (mt) cc_final: 0.8731 (mm) REVERT: 2 53 ASP cc_start: 0.8676 (t0) cc_final: 0.8304 (t0) REVERT: 2 258 ASP cc_start: 0.8681 (t70) cc_final: 0.8441 (t0) REVERT: 2 274 LYS cc_start: 0.8603 (tttp) cc_final: 0.8377 (ttmt) REVERT: 2 317 GLU cc_start: 0.5640 (tm-30) cc_final: 0.4960 (tm-30) REVERT: 2 371 ARG cc_start: 0.7214 (mtp180) cc_final: 0.6766 (mtp180) outliers start: 103 outliers final: 54 residues processed: 1023 average time/residue: 0.6865 time to fit residues: 1091.1224 Evaluate side-chains 893 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 836 time to evaluate : 4.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 150 LYS Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 150 LYS Chi-restraints excluded: chain K residue 225 GLU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 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 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 272 optimal weight: 8.9990 chunk 152 optimal weight: 0.0870 chunk 408 optimal weight: 9.9990 chunk 333 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 491 optimal weight: 0.5980 chunk 530 optimal weight: 9.9990 chunk 437 optimal weight: 0.7980 chunk 487 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 394 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN A 33 HIS A 304 GLN D 33 HIS D 246 ASN ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 33 HIS G 246 ASN G 322 ASN I 33 HIS I 301 ASN I 322 ASN K 33 HIS K 202 GLN K 246 ASN 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 Y 33 HIS 0 33 HIS 2 33 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 45690 Z= 0.153 Angle : 0.545 8.004 62145 Z= 0.283 Chirality : 0.043 0.184 7110 Planarity : 0.004 0.036 7650 Dihedral : 10.604 73.514 7170 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.06 % Allowed : 10.06 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.11), residues: 5355 helix: -0.64 (0.09), residues: 3075 sheet: -1.66 (0.26), residues: 390 loop : -1.66 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 333 HIS 0.004 0.001 HIS S 33 PHE 0.013 0.001 PHE U 163 TYR 0.011 0.001 TYR G 303 ARG 0.007 0.000 ARG S 100 *********************** 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 1031 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 935 time to evaluate : 5.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8466 (ptp-110) cc_final: 0.8100 (ptp-110) REVERT: C 53 ASP cc_start: 0.8478 (t0) cc_final: 0.8055 (t0) REVERT: C 143 ARG cc_start: 0.7262 (pmt170) cc_final: 0.6618 (ptm-80) REVERT: C 371 ARG cc_start: 0.7111 (mtp180) cc_final: 0.6862 (mtp180) REVERT: A 13 ARG cc_start: 0.7538 (ttp-110) cc_final: 0.6941 (mtm110) REVERT: A 156 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6702 (tm-30) REVERT: A 158 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8009 (mm-40) REVERT: A 258 ASP cc_start: 0.8734 (t70) cc_final: 0.8533 (t0) REVERT: A 280 MET cc_start: 0.8401 (mmt) cc_final: 0.8123 (mmm) REVERT: A 297 GLU cc_start: 0.6831 (tt0) cc_final: 0.6580 (tt0) REVERT: A 371 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6671 (mtp180) REVERT: D 143 ARG cc_start: 0.7442 (pmt170) cc_final: 0.7006 (ptt-90) REVERT: D 150 LYS cc_start: 0.8652 (ptpp) cc_final: 0.7986 (mtpt) REVERT: D 249 ARG cc_start: 0.8369 (ttt-90) cc_final: 0.8165 (ttt-90) REVERT: D 320 ILE cc_start: 0.9064 (tt) cc_final: 0.8784 (tt) REVERT: D 344 GLU cc_start: 0.7950 (mp0) cc_final: 0.7546 (mp0) REVERT: G 13 ARG cc_start: 0.7480 (mtm-85) cc_final: 0.7238 (mtm110) REVERT: G 53 ASP cc_start: 0.8478 (t0) cc_final: 0.8178 (t0) REVERT: G 201 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7340 (mt0) REVERT: I 57 ARG cc_start: 0.8141 (ptp-110) cc_final: 0.7934 (ttp-170) REVERT: I 129 GLN cc_start: 0.8183 (mp10) cc_final: 0.7954 (mp10) REVERT: I 143 ARG cc_start: 0.7551 (pmt170) cc_final: 0.7259 (ptt-90) REVERT: I 159 ASP cc_start: 0.8067 (p0) cc_final: 0.7764 (p0) REVERT: I 201 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7423 (mt0) REVERT: I 227 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8456 (tp) REVERT: I 271 LEU cc_start: 0.8599 (mt) cc_final: 0.8323 (mt) REVERT: K 5 LEU cc_start: 0.8680 (mm) cc_final: 0.8472 (mm) REVERT: K 29 ARG cc_start: 0.8385 (ptp-110) cc_final: 0.8034 (ptp90) REVERT: K 57 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7824 (ttp-170) REVERT: K 102 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8060 (pp) REVERT: K 159 ASP cc_start: 0.8156 (p0) cc_final: 0.7796 (p0) REVERT: K 201 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: K 227 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8323 (tp) REVERT: K 320 ILE cc_start: 0.9039 (tt) cc_final: 0.8728 (tt) REVERT: K 371 ARG cc_start: 0.7314 (mtp180) cc_final: 0.7054 (mtp180) REVERT: M 53 ASP cc_start: 0.8165 (t0) cc_final: 0.7932 (t0) REVERT: M 143 ARG cc_start: 0.7540 (pmt170) cc_final: 0.7115 (ptt-90) REVERT: M 156 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6270 (tm-30) REVERT: M 158 GLN cc_start: 0.8181 (mp10) cc_final: 0.7892 (mm-40) REVERT: M 217 ASP cc_start: 0.7156 (m-30) cc_final: 0.6563 (m-30) REVERT: M 263 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7747 (mt-10) REVERT: M 371 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6937 (mtp180) REVERT: O 6 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7671 (ttp-110) REVERT: O 53 ASP cc_start: 0.8289 (t0) cc_final: 0.7946 (t0) REVERT: O 82 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: O 86 GLN cc_start: 0.8409 (pt0) cc_final: 0.8187 (pt0) REVERT: O 100 ARG cc_start: 0.8269 (ttp80) cc_final: 0.8025 (tmm160) REVERT: O 143 ARG cc_start: 0.7353 (pmt170) cc_final: 0.6978 (ptt-90) REVERT: O 150 LYS cc_start: 0.8692 (mtmm) cc_final: 0.7957 (mttm) REVERT: O 217 ASP cc_start: 0.7274 (m-30) cc_final: 0.6824 (m-30) REVERT: O 280 MET cc_start: 0.8547 (mmt) cc_final: 0.8325 (mmm) REVERT: O 371 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6823 (mtp180) REVERT: Q 53 ASP cc_start: 0.8349 (t0) cc_final: 0.8077 (t0) REVERT: Q 57 ARG cc_start: 0.8339 (ptp-110) cc_final: 0.8063 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7297 (pmt170) cc_final: 0.6905 (ptm-80) REVERT: Q 213 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.7233 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7323 (m-30) cc_final: 0.6908 (m-30) REVERT: Q 371 ARG cc_start: 0.7237 (mtp180) cc_final: 0.6917 (mtp180) REVERT: S 143 ARG cc_start: 0.7132 (ptt-90) cc_final: 0.6553 (ptm-80) REVERT: S 280 MET cc_start: 0.8356 (mmm) cc_final: 0.7969 (mmt) REVERT: S 371 ARG cc_start: 0.7031 (mtp180) cc_final: 0.6659 (mtp180) REVERT: U 10 LEU cc_start: 0.8926 (mp) cc_final: 0.8353 (mp) REVERT: U 143 ARG cc_start: 0.7435 (pmt170) cc_final: 0.6972 (ttp-110) REVERT: U 201 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: U 227 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8354 (tp) REVERT: U 258 ASP cc_start: 0.8756 (t70) cc_final: 0.8443 (t0) REVERT: W 10 LEU cc_start: 0.8974 (mt) cc_final: 0.8665 (mm) REVERT: W 93 ASP cc_start: 0.7426 (p0) cc_final: 0.7180 (p0) REVERT: W 111 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7640 (tp40) REVERT: W 143 ARG cc_start: 0.7277 (pmt170) cc_final: 0.6633 (ptm-80) REVERT: W 371 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6761 (mtp180) REVERT: Y 6 ARG cc_start: 0.8230 (ptp90) cc_final: 0.7690 (mtm110) REVERT: Y 10 LEU cc_start: 0.8764 (mt) cc_final: 0.8530 (mt) REVERT: Y 123 MET cc_start: 0.5922 (mtm) cc_final: 0.5556 (mtp) REVERT: Y 126 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6674 (tt0) REVERT: Y 164 ASN cc_start: 0.8734 (t0) cc_final: 0.8497 (t0) REVERT: Y 225 GLU cc_start: 0.7903 (tt0) cc_final: 0.7515 (tt0) REVERT: Y 258 ASP cc_start: 0.8732 (t70) cc_final: 0.8526 (t0) REVERT: Y 301 ASN cc_start: 0.7923 (m110) cc_final: 0.7515 (m-40) REVERT: Y 371 ARG cc_start: 0.7221 (mtp180) cc_final: 0.6663 (mtp180) REVERT: 0 53 ASP cc_start: 0.8670 (t0) cc_final: 0.8449 (t0) REVERT: 0 123 MET cc_start: 0.6703 (mtp) cc_final: 0.6288 (mtp) REVERT: 0 165 MET cc_start: 0.8141 (tpp) cc_final: 0.7903 (mmt) REVERT: 0 371 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6611 (mtp180) REVERT: 2 10 LEU cc_start: 0.9015 (mt) cc_final: 0.8749 (mm) REVERT: 2 53 ASP cc_start: 0.8731 (t0) cc_final: 0.8440 (t0) REVERT: 2 161 GLU cc_start: 0.7858 (pt0) cc_final: 0.7647 (pt0) REVERT: 2 274 LYS cc_start: 0.8597 (tttp) cc_final: 0.8384 (ttmt) REVERT: 2 317 GLU cc_start: 0.5711 (tm-30) cc_final: 0.4971 (tm-30) REVERT: 2 371 ARG cc_start: 0.7190 (mtp180) cc_final: 0.6820 (mtp180) outliers start: 96 outliers final: 39 residues processed: 1006 average time/residue: 0.6839 time to fit residues: 1071.6989 Evaluate side-chains 851 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 802 time to evaluate : 5.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU 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 355 SER 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 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S 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 U residue 367 GLU Chi-restraints excluded: chain W residue 86 GLN 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 129 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 259 THR Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 259 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 4.9990 chunk 369 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 329 optimal weight: 2.9990 chunk 493 optimal weight: 6.9990 chunk 521 optimal weight: 0.0020 chunk 257 optimal weight: 3.9990 chunk 467 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 HIS A 304 GLN D 33 HIS D 246 ASN ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 ASN K 33 HIS K 164 ASN K 246 ASN M 33 HIS M 246 ASN O 14 ASN O 33 HIS O 164 ASN O 246 ASN O 322 ASN Q 33 HIS Q 164 ASN ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 33 HIS U 33 HIS U 164 ASN U 322 ASN W 33 HIS W 304 GLN Y 33 HIS 0 33 HIS ** 0 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 45690 Z= 0.239 Angle : 0.558 8.064 62145 Z= 0.287 Chirality : 0.044 0.170 7110 Planarity : 0.004 0.037 7650 Dihedral : 10.459 73.559 7170 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 2.32 % Allowed : 10.11 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.12), residues: 5355 helix: -0.09 (0.10), residues: 3075 sheet: -1.54 (0.27), residues: 390 loop : -1.43 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 333 HIS 0.006 0.001 HIS I 33 PHE 0.016 0.002 PHE 0 209 TYR 0.017 0.001 TYR D 303 ARG 0.007 0.000 ARG 0 213 *********************** 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 976 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 868 time to evaluate : 4.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 LEU cc_start: 0.9017 (mp) cc_final: 0.8786 (mm) REVERT: C 29 ARG cc_start: 0.8521 (ptp-110) cc_final: 0.8200 (ptp-110) REVERT: C 53 ASP cc_start: 0.8516 (t0) cc_final: 0.8113 (t0) REVERT: C 93 ASP cc_start: 0.7599 (p0) cc_final: 0.7377 (p0) REVERT: C 143 ARG cc_start: 0.7355 (pmt170) cc_final: 0.6846 (ptt-90) REVERT: C 271 LEU cc_start: 0.8662 (mt) cc_final: 0.8436 (mt) REVERT: C 371 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6771 (mtp180) REVERT: A 156 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6983 (tm-30) REVERT: A 256 ASP cc_start: 0.8316 (t70) cc_final: 0.7874 (t70) REVERT: A 280 MET cc_start: 0.8415 (mmt) cc_final: 0.8040 (mmm) REVERT: A 297 GLU cc_start: 0.6756 (tt0) cc_final: 0.6535 (tt0) REVERT: A 371 ARG cc_start: 0.7334 (mtp180) cc_final: 0.6917 (mtp180) REVERT: D 143 ARG cc_start: 0.7428 (pmt170) cc_final: 0.7013 (ptt-90) REVERT: D 150 LYS cc_start: 0.8621 (ptpp) cc_final: 0.8086 (mtpt) REVERT: D 367 GLU cc_start: 0.7545 (tt0) cc_final: 0.7318 (tt0) REVERT: G 201 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: I 53 ASP cc_start: 0.8213 (t0) cc_final: 0.7965 (t0) REVERT: I 57 ARG cc_start: 0.8140 (ptp-110) cc_final: 0.7922 (ttp-170) REVERT: I 143 ARG cc_start: 0.7531 (pmt170) cc_final: 0.7232 (ptt-90) REVERT: I 159 ASP cc_start: 0.8043 (p0) cc_final: 0.7758 (p0) REVERT: I 201 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: I 271 LEU cc_start: 0.8593 (mt) cc_final: 0.8292 (mt) REVERT: I 371 ARG cc_start: 0.7341 (mtp180) cc_final: 0.7035 (mtp180) REVERT: K 5 LEU cc_start: 0.8715 (mm) cc_final: 0.8490 (mm) REVERT: K 29 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.7933 (ptp90) REVERT: K 102 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8285 (pp) REVERT: K 159 ASP cc_start: 0.8173 (p0) cc_final: 0.7856 (p0) REVERT: K 201 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7409 (mt0) REVERT: K 320 ILE cc_start: 0.9097 (tt) cc_final: 0.8771 (tt) REVERT: K 371 ARG cc_start: 0.7285 (mtp180) cc_final: 0.7029 (mtp180) REVERT: M 53 ASP cc_start: 0.8275 (t0) cc_final: 0.8019 (t0) REVERT: M 102 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8293 (pp) REVERT: M 143 ARG cc_start: 0.7567 (pmt170) cc_final: 0.7139 (ptt-90) REVERT: M 156 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6991 (tm-30) REVERT: M 263 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7828 (mt-10) REVERT: M 371 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6831 (mtp180) REVERT: O 6 ARG cc_start: 0.8043 (ptp90) cc_final: 0.7637 (ttp-110) REVERT: O 53 ASP cc_start: 0.8480 (t0) cc_final: 0.8175 (t0) REVERT: O 82 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: O 93 ASP cc_start: 0.7446 (p0) cc_final: 0.7180 (t70) REVERT: O 100 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8054 (tmm160) REVERT: O 143 ARG cc_start: 0.7362 (pmt170) cc_final: 0.6978 (ptt-90) REVERT: O 212 GLU cc_start: 0.8275 (pt0) cc_final: 0.7948 (pt0) REVERT: O 280 MET cc_start: 0.8534 (mmt) cc_final: 0.8206 (mmt) REVERT: O 371 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6962 (mtp180) REVERT: Q 53 ASP cc_start: 0.8392 (t0) cc_final: 0.8111 (t0) REVERT: Q 57 ARG cc_start: 0.8289 (ptp-110) cc_final: 0.8017 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7255 (pmt170) cc_final: 0.6815 (ptm-80) REVERT: Q 213 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7339 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7268 (m-30) cc_final: 0.6899 (m-30) REVERT: Q 371 ARG cc_start: 0.7323 (mtp180) cc_final: 0.6987 (mtp180) REVERT: S 6 ARG cc_start: 0.8121 (ttp-170) cc_final: 0.7909 (ttp-110) REVERT: S 143 ARG cc_start: 0.7140 (ptt-90) cc_final: 0.6516 (ptm-80) REVERT: S 228 SER cc_start: 0.8830 (p) cc_final: 0.8569 (m) REVERT: S 371 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6720 (mtp180) REVERT: U 143 ARG cc_start: 0.7416 (pmt170) cc_final: 0.6924 (ttp-110) REVERT: U 201 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7415 (mt0) REVERT: U 227 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8523 (tp) REVERT: U 253 MET cc_start: 0.8230 (ttm) cc_final: 0.7991 (ttp) REVERT: U 258 ASP cc_start: 0.8772 (t70) cc_final: 0.8516 (t0) REVERT: W 10 LEU cc_start: 0.8912 (mt) cc_final: 0.8690 (mm) REVERT: W 31 ILE cc_start: 0.8972 (tp) cc_final: 0.8758 (tp) REVERT: W 93 ASP cc_start: 0.7431 (p0) cc_final: 0.7202 (p0) REVERT: W 111 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7681 (tp40) REVERT: W 143 ARG cc_start: 0.7349 (pmt170) cc_final: 0.6618 (ptm-80) REVERT: W 225 GLU cc_start: 0.7985 (tt0) cc_final: 0.7727 (tt0) REVERT: W 371 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6764 (mtp180) REVERT: Y 6 ARG cc_start: 0.8178 (ptp90) cc_final: 0.7704 (mtm110) REVERT: Y 123 MET cc_start: 0.5857 (mtm) cc_final: 0.5547 (mtp) REVERT: Y 126 GLU cc_start: 0.7597 (tm-30) cc_final: 0.6758 (tt0) REVERT: Y 164 ASN cc_start: 0.8786 (t0) cc_final: 0.8530 (t0) REVERT: Y 225 GLU cc_start: 0.8012 (tt0) cc_final: 0.7642 (tt0) REVERT: Y 301 ASN cc_start: 0.7928 (m110) cc_final: 0.7708 (m-40) REVERT: Y 371 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6795 (mtp180) REVERT: 0 53 ASP cc_start: 0.8732 (t0) cc_final: 0.8503 (t0) REVERT: 0 165 MET cc_start: 0.8151 (tpp) cc_final: 0.7937 (mmt) REVERT: 0 317 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7128 (mm-30) REVERT: 0 371 ARG cc_start: 0.7217 (mtp180) cc_final: 0.6712 (mtp180) REVERT: 2 10 LEU cc_start: 0.8976 (mt) cc_final: 0.8750 (mm) REVERT: 2 102 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8310 (pp) REVERT: 2 201 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: 2 212 GLU cc_start: 0.8119 (pt0) cc_final: 0.7811 (pt0) REVERT: 2 274 LYS cc_start: 0.8614 (tttp) cc_final: 0.8405 (ttmt) REVERT: 2 317 GLU cc_start: 0.5497 (tm-30) cc_final: 0.4660 (tm-30) REVERT: 2 371 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6832 (mtp180) outliers start: 108 outliers final: 63 residues processed: 947 average time/residue: 0.6662 time to fit residues: 993.9937 Evaluate side-chains 865 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 792 time to evaluate : 5.276 ------------------------------------------------------------------------------- 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 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 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 G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 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 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 82 GLU 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 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 U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 341 VAL 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 91 ILE Chi-restraints excluded: chain Y residue 129 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 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 355 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 0.9990 chunk 296 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 445 optimal weight: 0.0470 chunk 360 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 468 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 33 HIS D 33 HIS ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS I 301 ASN I 322 ASN K 33 HIS K 164 ASN M 33 HIS M 246 ASN O 33 HIS ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 304 GLN S 33 HIS S 304 GLN U 33 HIS U 164 ASN U 304 GLN U 322 ASN W 33 HIS Y 33 HIS 0 33 HIS 0 322 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3041 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= 0.241 Angle : 0.554 9.343 62145 Z= 0.284 Chirality : 0.044 0.154 7110 Planarity : 0.004 0.043 7650 Dihedral : 10.453 73.551 7170 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 2.24 % Allowed : 11.57 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.12), residues: 5355 helix: 0.11 (0.10), residues: 3120 sheet: -1.74 (0.26), residues: 390 loop : -1.32 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 333 HIS 0.004 0.001 HIS S 33 PHE 0.015 0.001 PHE 0 209 TYR 0.021 0.001 TYR D 303 ARG 0.007 0.000 ARG G 143 *********************** 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 938 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 834 time to evaluate : 5.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 LEU cc_start: 0.9002 (mp) cc_final: 0.8757 (mm) REVERT: C 29 ARG cc_start: 0.8523 (ptp-110) cc_final: 0.8226 (ptp-110) REVERT: C 53 ASP cc_start: 0.8552 (t0) cc_final: 0.8151 (t0) REVERT: C 55 LEU cc_start: 0.8674 (tp) cc_final: 0.8386 (mt) REVERT: C 93 ASP cc_start: 0.7610 (p0) cc_final: 0.7397 (p0) REVERT: C 143 ARG cc_start: 0.7303 (pmt170) cc_final: 0.6806 (ptt-90) REVERT: C 213 ARG cc_start: 0.7306 (ttm-80) cc_final: 0.7101 (mtp-110) REVERT: C 271 LEU cc_start: 0.8631 (mt) cc_final: 0.8427 (mt) REVERT: C 371 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6811 (mtp180) REVERT: A 82 GLU cc_start: 0.3839 (mp0) cc_final: 0.3625 (mp0) REVERT: A 256 ASP cc_start: 0.8278 (t70) cc_final: 0.7816 (t70) REVERT: A 280 MET cc_start: 0.8424 (mmt) cc_final: 0.8052 (mmm) REVERT: A 297 GLU cc_start: 0.6826 (tt0) cc_final: 0.6602 (tt0) REVERT: A 323 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8657 (ttmm) REVERT: A 371 ARG cc_start: 0.7331 (mtp180) cc_final: 0.6897 (mtp180) REVERT: D 143 ARG cc_start: 0.7444 (pmt170) cc_final: 0.7019 (ptt-90) REVERT: D 150 LYS cc_start: 0.8616 (ptpp) cc_final: 0.8075 (mttm) REVERT: G 201 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: I 53 ASP cc_start: 0.8295 (t0) cc_final: 0.7995 (t0) REVERT: I 57 ARG cc_start: 0.8187 (ptp-110) cc_final: 0.7944 (ttp-170) REVERT: I 143 ARG cc_start: 0.7533 (pmt170) cc_final: 0.7238 (ptt-90) REVERT: I 159 ASP cc_start: 0.8050 (p0) cc_final: 0.7736 (p0) REVERT: I 201 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: I 271 LEU cc_start: 0.8578 (mt) cc_final: 0.8287 (mt) REVERT: I 371 ARG cc_start: 0.7419 (mtp180) cc_final: 0.7030 (mtp180) REVERT: K 5 LEU cc_start: 0.8811 (mm) cc_final: 0.8558 (mm) REVERT: K 53 ASP cc_start: 0.8450 (t0) cc_final: 0.8231 (t0) REVERT: K 102 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8280 (pp) REVERT: K 159 ASP cc_start: 0.8143 (p0) cc_final: 0.7798 (p0) REVERT: K 201 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: M 53 ASP cc_start: 0.8352 (t0) cc_final: 0.8136 (t0) REVERT: M 102 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8301 (pp) REVERT: M 143 ARG cc_start: 0.7564 (pmt170) cc_final: 0.7132 (ptt-90) REVERT: M 156 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6405 (tm-30) REVERT: M 212 GLU cc_start: 0.8327 (pt0) cc_final: 0.8097 (pt0) REVERT: M 263 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7850 (mt-10) REVERT: M 308 GLU cc_start: 0.8107 (pm20) cc_final: 0.7801 (pt0) REVERT: M 371 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6795 (mtp180) REVERT: O 6 ARG cc_start: 0.8037 (ptp90) cc_final: 0.7733 (ttp-110) REVERT: O 82 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: O 93 ASP cc_start: 0.7458 (p0) cc_final: 0.7196 (t70) REVERT: O 100 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8084 (tmm160) REVERT: O 143 ARG cc_start: 0.7349 (pmt170) cc_final: 0.6957 (ptt-90) REVERT: O 212 GLU cc_start: 0.8233 (pt0) cc_final: 0.7943 (pt0) REVERT: O 280 MET cc_start: 0.8565 (mmt) cc_final: 0.8261 (mmt) REVERT: Q 53 ASP cc_start: 0.8397 (t0) cc_final: 0.8132 (t0) REVERT: Q 57 ARG cc_start: 0.8268 (ptp-110) cc_final: 0.8017 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7250 (pmt170) cc_final: 0.6740 (ptm-80) REVERT: Q 213 ARG cc_start: 0.7630 (mtp-110) cc_final: 0.7366 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7310 (m-30) cc_final: 0.6960 (m-30) REVERT: S 6 ARG cc_start: 0.8166 (ttp-170) cc_final: 0.7928 (ttp-110) REVERT: S 111 GLN cc_start: 0.8363 (tp40) cc_final: 0.7807 (tp40) REVERT: S 150 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7990 (mttm) REVERT: S 212 GLU cc_start: 0.8284 (pt0) cc_final: 0.7886 (pt0) REVERT: S 228 SER cc_start: 0.8847 (p) cc_final: 0.8617 (m) REVERT: S 371 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6687 (mtp180) REVERT: U 143 ARG cc_start: 0.7381 (pmt170) cc_final: 0.6836 (ttp-110) REVERT: U 201 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.7442 (mt0) REVERT: U 227 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8501 (tp) REVERT: U 253 MET cc_start: 0.8238 (ttm) cc_final: 0.8015 (ttp) REVERT: U 258 ASP cc_start: 0.8790 (t70) cc_final: 0.8553 (t0) REVERT: U 371 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6704 (mtp180) REVERT: W 31 ILE cc_start: 0.8969 (tp) cc_final: 0.8745 (tp) REVERT: W 111 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7692 (tp40) REVERT: W 143 ARG cc_start: 0.7368 (pmt170) cc_final: 0.6628 (ptm-80) REVERT: W 225 GLU cc_start: 0.7995 (tt0) cc_final: 0.7767 (tt0) REVERT: W 371 ARG cc_start: 0.7184 (mtp180) cc_final: 0.6810 (mtp180) REVERT: Y 6 ARG cc_start: 0.8196 (ptp90) cc_final: 0.7746 (mtm110) REVERT: Y 123 MET cc_start: 0.5839 (mtm) cc_final: 0.5487 (mtp) REVERT: Y 126 GLU cc_start: 0.7680 (tm-30) cc_final: 0.6777 (tt0) REVERT: Y 225 GLU cc_start: 0.8026 (tt0) cc_final: 0.7704 (tt0) REVERT: Y 301 ASN cc_start: 0.7890 (m110) cc_final: 0.7666 (m-40) REVERT: Y 371 ARG cc_start: 0.7332 (mtp180) cc_final: 0.6812 (mtp180) REVERT: 0 53 ASP cc_start: 0.8753 (t0) cc_final: 0.8536 (t0) REVERT: 0 123 MET cc_start: 0.6781 (mtp) cc_final: 0.6436 (mtp) REVERT: 0 165 MET cc_start: 0.8139 (tpp) cc_final: 0.7899 (mmt) REVERT: 0 371 ARG cc_start: 0.7205 (mtp180) cc_final: 0.6780 (mtp180) REVERT: 2 102 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8314 (pp) REVERT: 2 201 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: 2 256 ASP cc_start: 0.8778 (t70) cc_final: 0.8042 (t0) REVERT: 2 274 LYS cc_start: 0.8649 (tttp) cc_final: 0.8437 (ttmt) REVERT: 2 317 GLU cc_start: 0.5512 (tm-30) cc_final: 0.3869 (tm-30) REVERT: 2 371 ARG cc_start: 0.7181 (mtp180) cc_final: 0.6861 (mtp180) outliers start: 104 outliers final: 69 residues processed: 910 average time/residue: 0.6738 time to fit residues: 959.5312 Evaluate side-chains 870 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 789 time to evaluate : 5.046 ------------------------------------------------------------------------------- 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 355 SER Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 GLU 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 G residue 34 ILE 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 91 ILE Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 259 THR 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 82 GLU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain 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 186 ASP Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 129 GLN 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 3 THR 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 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 259 THR Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 6.9990 chunk 470 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 522 optimal weight: 2.9990 chunk 433 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN A 33 HIS D 33 HIS G 33 HIS G 164 ASN G 246 ASN I 322 ASN K 164 ASN ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS O 246 ASN Q 33 HIS ** 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 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 322 ASN Y 33 HIS Y 304 GLN ** Y 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 322 ASN 2 89 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45690 Z= 0.214 Angle : 0.540 8.486 62145 Z= 0.276 Chirality : 0.043 0.130 7110 Planarity : 0.003 0.037 7650 Dihedral : 10.453 73.512 7170 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.45 % Favored : 96.41 % Rotamer: Outliers : 2.88 % Allowed : 11.59 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 5355 helix: 0.21 (0.10), residues: 3150 sheet: -1.81 (0.25), residues: 390 loop : -1.21 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 333 HIS 0.005 0.001 HIS S 33 PHE 0.018 0.001 PHE 0 209 TYR 0.021 0.001 TYR D 303 ARG 0.007 0.000 ARG S 143 *********************** 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 970 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 836 time to evaluate : 4.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 LEU cc_start: 0.9010 (mp) cc_final: 0.8784 (mm) REVERT: C 29 ARG cc_start: 0.8509 (ptp-110) cc_final: 0.8236 (ptp-110) REVERT: C 53 ASP cc_start: 0.8553 (t0) cc_final: 0.8171 (t0) REVERT: C 55 LEU cc_start: 0.8674 (tp) cc_final: 0.8420 (mt) REVERT: C 93 ASP cc_start: 0.7609 (p0) cc_final: 0.7405 (p0) REVERT: C 143 ARG cc_start: 0.7286 (pmt170) cc_final: 0.6787 (ptt-90) REVERT: C 201 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7394 (mp10) REVERT: C 213 ARG cc_start: 0.7345 (ttm-80) cc_final: 0.7132 (mtp-110) REVERT: C 256 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8056 (t0) REVERT: C 371 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6919 (mtp180) REVERT: A 201 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: A 212 GLU cc_start: 0.8424 (pt0) cc_final: 0.8055 (pt0) REVERT: A 280 MET cc_start: 0.8448 (mmt) cc_final: 0.8122 (mmm) REVERT: A 297 GLU cc_start: 0.6834 (tt0) cc_final: 0.6633 (tt0) REVERT: A 323 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8672 (ttmm) REVERT: A 371 ARG cc_start: 0.7321 (mtp180) cc_final: 0.6908 (mtp180) REVERT: D 143 ARG cc_start: 0.7436 (pmt170) cc_final: 0.7008 (ptt-90) REVERT: D 150 LYS cc_start: 0.8572 (ptpp) cc_final: 0.8109 (mttt) REVERT: D 201 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: G 201 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7442 (mt0) REVERT: I 53 ASP cc_start: 0.8322 (t0) cc_final: 0.8029 (t0) REVERT: I 57 ARG cc_start: 0.8181 (ptp-110) cc_final: 0.7937 (ttp-170) REVERT: I 143 ARG cc_start: 0.7532 (pmt170) cc_final: 0.7246 (ptt-90) REVERT: I 159 ASP cc_start: 0.8029 (p0) cc_final: 0.7704 (p0) REVERT: I 201 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7341 (mt0) REVERT: I 271 LEU cc_start: 0.8560 (mt) cc_final: 0.8264 (mt) REVERT: I 371 ARG cc_start: 0.7322 (mtp180) cc_final: 0.7081 (mtp180) REVERT: K 53 ASP cc_start: 0.8492 (t0) cc_final: 0.8200 (t0) REVERT: K 57 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7883 (ttp-170) REVERT: K 102 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8256 (pp) REVERT: K 150 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8398 (mtpt) REVERT: K 159 ASP cc_start: 0.8153 (p0) cc_final: 0.7818 (p0) REVERT: K 201 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: M 53 ASP cc_start: 0.8382 (t0) cc_final: 0.8158 (t0) REVERT: M 102 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8324 (pp) REVERT: M 103 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7684 (mt-10) REVERT: M 143 ARG cc_start: 0.7541 (pmt170) cc_final: 0.7113 (ptt-90) REVERT: M 201 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: M 263 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7851 (mt-10) REVERT: M 371 ARG cc_start: 0.7129 (mtp180) cc_final: 0.6690 (mtp180) REVERT: O 6 ARG cc_start: 0.8020 (ptp90) cc_final: 0.7776 (ttp-110) REVERT: O 53 ASP cc_start: 0.8416 (t0) cc_final: 0.8066 (t0) REVERT: O 54 ARG cc_start: 0.8139 (mmp80) cc_final: 0.7773 (mmp80) REVERT: O 82 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: O 93 ASP cc_start: 0.7428 (p0) cc_final: 0.7184 (t70) REVERT: O 100 ARG cc_start: 0.8390 (ttp80) cc_final: 0.8081 (tmm160) REVERT: O 143 ARG cc_start: 0.7320 (pmt170) cc_final: 0.6921 (ptt-90) REVERT: O 201 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: O 212 GLU cc_start: 0.8204 (pt0) cc_final: 0.7951 (pt0) REVERT: O 280 MET cc_start: 0.8561 (mmt) cc_final: 0.8302 (mmt) REVERT: Q 53 ASP cc_start: 0.8406 (t0) cc_final: 0.8134 (t0) REVERT: Q 57 ARG cc_start: 0.8269 (ptp-110) cc_final: 0.8006 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7231 (pmt170) cc_final: 0.6719 (ptm-80) REVERT: Q 213 ARG cc_start: 0.7635 (mtp-110) cc_final: 0.7373 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7302 (m-30) cc_final: 0.6955 (m-30) REVERT: S 6 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7987 (ttp-110) REVERT: S 111 GLN cc_start: 0.8334 (tp40) cc_final: 0.7793 (tp40) REVERT: S 143 ARG cc_start: 0.7239 (ptt-90) cc_final: 0.6663 (ptm-80) REVERT: S 150 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8087 (mttm) REVERT: S 161 GLU cc_start: 0.7503 (pt0) cc_final: 0.7240 (pt0) REVERT: S 201 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: S 212 GLU cc_start: 0.8286 (pt0) cc_final: 0.7828 (pt0) REVERT: S 228 SER cc_start: 0.8827 (p) cc_final: 0.8589 (m) REVERT: S 371 ARG cc_start: 0.7082 (mtp180) cc_final: 0.6749 (mtp180) REVERT: U 143 ARG cc_start: 0.7341 (pmt170) cc_final: 0.6800 (ttp-110) REVERT: U 201 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7395 (mt0) REVERT: U 209 PHE cc_start: 0.7964 (m-10) cc_final: 0.7758 (m-10) REVERT: U 253 MET cc_start: 0.8203 (ttm) cc_final: 0.7982 (ttp) REVERT: U 258 ASP cc_start: 0.8816 (t70) cc_final: 0.8593 (t0) REVERT: U 371 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6711 (mtp180) REVERT: W 31 ILE cc_start: 0.8918 (tp) cc_final: 0.8702 (tp) REVERT: W 111 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7689 (tp40) REVERT: W 143 ARG cc_start: 0.7362 (pmt170) cc_final: 0.6623 (ptm-80) REVERT: W 323 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8899 (ttmm) REVERT: W 371 ARG cc_start: 0.7136 (mtp180) cc_final: 0.6718 (mtp180) REVERT: Y 6 ARG cc_start: 0.8199 (ptp90) cc_final: 0.7733 (mtm110) REVERT: Y 123 MET cc_start: 0.5854 (mtm) cc_final: 0.5455 (mtp) REVERT: Y 126 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7448 (tt0) REVERT: Y 150 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8004 (mtpt) REVERT: Y 201 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: Y 225 GLU cc_start: 0.8003 (tt0) cc_final: 0.7772 (tt0) REVERT: Y 301 ASN cc_start: 0.7865 (m110) cc_final: 0.7526 (m-40) REVERT: Y 371 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6856 (mtp180) REVERT: 0 53 ASP cc_start: 0.8761 (t0) cc_final: 0.8549 (t0) REVERT: 0 165 MET cc_start: 0.8134 (tpp) cc_final: 0.7888 (mmt) REVERT: 0 201 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: 0 225 GLU cc_start: 0.8060 (tt0) cc_final: 0.7696 (tt0) REVERT: 0 292 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: 0 371 ARG cc_start: 0.7223 (mtp180) cc_final: 0.6816 (mtp180) REVERT: 2 55 LEU cc_start: 0.8368 (tp) cc_final: 0.8104 (mt) REVERT: 2 201 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: 2 209 PHE cc_start: 0.7941 (m-10) cc_final: 0.7658 (m-80) REVERT: 2 274 LYS cc_start: 0.8653 (tttp) cc_final: 0.8416 (ttmt) REVERT: 2 317 GLU cc_start: 0.5514 (tm-30) cc_final: 0.3673 (tm-30) REVERT: 2 371 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6990 (mtp180) outliers start: 134 outliers final: 88 residues processed: 937 average time/residue: 0.6754 time to fit residues: 990.7531 Evaluate side-chains 898 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 787 time to evaluate : 5.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 GLU 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 201 GLN Chi-restraints excluded: chain D residue 227 LEU 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 227 LEU Chi-restraints excluded: chain I residue 228 SER 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 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 201 GLN 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 82 GLU 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 201 GLN Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 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 201 GLN Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 102 LEU 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 237 ILE Chi-restraints excluded: chain U residue 341 VAL 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 304 GLN Chi-restraints excluded: chain W residue 323 LYS Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 5 LEU 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 129 GLN 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 Y residue 367 GLU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 55 LEU Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 129 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 228 SER Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 0 residue 292 GLU Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 256 ASP Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 0.9990 chunk 58 optimal weight: 0.0570 chunk 297 optimal weight: 10.0000 chunk 381 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 439 optimal weight: 3.9990 chunk 291 optimal weight: 8.9990 chunk 520 optimal weight: 0.9980 chunk 325 optimal weight: 4.9990 chunk 317 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 246 ASN C 304 GLN A 14 ASN A 33 HIS D 33 HIS D 322 ASN G 33 HIS ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 322 ASN M 33 HIS M 246 ASN O 33 HIS Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 304 GLN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 304 GLN U 322 ASN W 33 HIS Y 33 HIS Y 164 ASN Y 304 GLN Y 322 ASN 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 89 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45690 Z= 0.180 Angle : 0.528 7.722 62145 Z= 0.270 Chirality : 0.043 0.127 7110 Planarity : 0.003 0.038 7650 Dihedral : 10.412 73.463 7170 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.06 % Favored : 96.79 % Rotamer: Outliers : 2.77 % Allowed : 12.43 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.12), residues: 5355 helix: 0.31 (0.10), residues: 3150 sheet: -1.82 (0.25), residues: 390 loop : -1.13 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 333 HIS 0.007 0.001 HIS U 33 PHE 0.019 0.001 PHE 0 209 TYR 0.021 0.001 TYR D 303 ARG 0.007 0.000 ARG A 249 *********************** 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 961 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 832 time to evaluate : 5.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 LEU cc_start: 0.9024 (mp) cc_final: 0.8792 (mm) REVERT: C 53 ASP cc_start: 0.8569 (t0) cc_final: 0.8197 (t0) REVERT: C 55 LEU cc_start: 0.8633 (tp) cc_final: 0.8369 (mt) REVERT: C 93 ASP cc_start: 0.7633 (p0) cc_final: 0.7419 (p0) REVERT: C 143 ARG cc_start: 0.7269 (pmt170) cc_final: 0.6782 (ptt-90) REVERT: C 150 LYS cc_start: 0.8656 (mtmm) cc_final: 0.7984 (mttp) REVERT: C 201 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: C 213 ARG cc_start: 0.7353 (ttm-80) cc_final: 0.7138 (mtp-110) REVERT: C 371 ARG cc_start: 0.7186 (mtp180) cc_final: 0.6929 (mtp180) REVERT: A 14 ASN cc_start: 0.8026 (m-40) cc_final: 0.7398 (m110) REVERT: A 150 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8192 (mttt) REVERT: A 201 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7283 (mp10) REVERT: A 212 GLU cc_start: 0.8421 (pt0) cc_final: 0.7835 (pt0) REVERT: A 256 ASP cc_start: 0.8277 (t70) cc_final: 0.7794 (t70) REVERT: A 280 MET cc_start: 0.8463 (mmt) cc_final: 0.8128 (mmm) REVERT: A 371 ARG cc_start: 0.7297 (mtp180) cc_final: 0.6898 (mtp180) REVERT: D 143 ARG cc_start: 0.7443 (pmt170) cc_final: 0.7023 (ptt-90) REVERT: D 150 LYS cc_start: 0.8536 (ptpp) cc_final: 0.8198 (mtpt) REVERT: D 201 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: D 212 GLU cc_start: 0.8297 (pt0) cc_final: 0.7966 (pt0) REVERT: D 256 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.7811 (t0) REVERT: G 201 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: G 256 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.7802 (t0) REVERT: G 371 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7256 (mtp180) REVERT: I 53 ASP cc_start: 0.8300 (t0) cc_final: 0.8016 (t0) REVERT: I 57 ARG cc_start: 0.8160 (ptp-110) cc_final: 0.7937 (ttp-170) REVERT: I 143 ARG cc_start: 0.7545 (pmt170) cc_final: 0.7246 (ptt-90) REVERT: I 159 ASP cc_start: 0.8002 (p0) cc_final: 0.7672 (p0) REVERT: I 201 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7248 (mt0) REVERT: I 256 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8085 (t70) REVERT: I 271 LEU cc_start: 0.8554 (mt) cc_final: 0.8267 (mt) REVERT: I 371 ARG cc_start: 0.7359 (mtp180) cc_final: 0.7065 (mtp180) REVERT: K 53 ASP cc_start: 0.8524 (t0) cc_final: 0.8215 (t0) REVERT: K 57 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7944 (ttp-170) REVERT: K 102 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8187 (pp) REVERT: K 150 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8341 (mttt) REVERT: K 159 ASP cc_start: 0.8136 (p0) cc_final: 0.7817 (p0) REVERT: K 201 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7343 (mt0) REVERT: M 53 ASP cc_start: 0.8401 (t0) cc_final: 0.8172 (t0) REVERT: M 102 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8261 (pp) REVERT: M 103 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7669 (mt-10) REVERT: M 143 ARG cc_start: 0.7529 (pmt170) cc_final: 0.7107 (ptt-90) REVERT: M 201 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: M 212 GLU cc_start: 0.8313 (pt0) cc_final: 0.8047 (pt0) REVERT: M 263 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7825 (mt-10) REVERT: M 371 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6677 (mtp180) REVERT: O 6 ARG cc_start: 0.8003 (ptp90) cc_final: 0.7793 (ttp-110) REVERT: O 53 ASP cc_start: 0.8419 (t0) cc_final: 0.8151 (t0) REVERT: O 82 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: O 86 GLN cc_start: 0.8442 (pt0) cc_final: 0.8118 (pt0) REVERT: O 93 ASP cc_start: 0.7432 (p0) cc_final: 0.7213 (t70) REVERT: O 100 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8047 (tmm160) REVERT: O 143 ARG cc_start: 0.7310 (pmt170) cc_final: 0.6907 (ptt-90) REVERT: O 201 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: O 280 MET cc_start: 0.8545 (mmt) cc_final: 0.8287 (mmt) REVERT: Q 53 ASP cc_start: 0.8409 (t0) cc_final: 0.8152 (t0) REVERT: Q 57 ARG cc_start: 0.8267 (ptp-110) cc_final: 0.8027 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7232 (pmt170) cc_final: 0.6719 (ptm-80) REVERT: Q 201 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: Q 213 ARG cc_start: 0.7620 (mtp-110) cc_final: 0.7340 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7309 (m-30) cc_final: 0.6932 (m-30) REVERT: S 111 GLN cc_start: 0.8321 (tp40) cc_final: 0.7789 (tp40) REVERT: S 150 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8293 (mtpt) REVERT: S 161 GLU cc_start: 0.7540 (pt0) cc_final: 0.7268 (pt0) REVERT: S 201 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: S 212 GLU cc_start: 0.8245 (pt0) cc_final: 0.7859 (pt0) REVERT: S 228 SER cc_start: 0.8825 (p) cc_final: 0.8574 (m) REVERT: S 371 ARG cc_start: 0.7095 (mtp180) cc_final: 0.6784 (mtp180) REVERT: U 31 ILE cc_start: 0.8868 (tp) cc_final: 0.8662 (tp) REVERT: U 103 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7749 (mt-10) REVERT: U 143 ARG cc_start: 0.7330 (pmt170) cc_final: 0.6784 (ttp-110) REVERT: U 201 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: U 209 PHE cc_start: 0.7896 (m-10) cc_final: 0.7686 (m-10) REVERT: U 256 ASP cc_start: 0.8551 (t70) cc_final: 0.7758 (t0) REVERT: U 371 ARG cc_start: 0.7034 (mtp180) cc_final: 0.6718 (mtp180) REVERT: W 10 LEU cc_start: 0.8883 (mm) cc_final: 0.8475 (mp) REVERT: W 31 ILE cc_start: 0.8919 (tp) cc_final: 0.8718 (tp) REVERT: W 111 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7686 (tp40) REVERT: W 143 ARG cc_start: 0.7334 (pmt170) cc_final: 0.6630 (ptm-80) REVERT: W 258 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8565 (t0) REVERT: W 323 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8865 (ttmm) REVERT: W 371 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6677 (mtp180) REVERT: Y 6 ARG cc_start: 0.8174 (ptp90) cc_final: 0.7738 (mtm110) REVERT: Y 123 MET cc_start: 0.5833 (mtm) cc_final: 0.5409 (mtp) REVERT: Y 126 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7475 (tt0) REVERT: Y 150 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8015 (mttt) REVERT: Y 201 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: Y 301 ASN cc_start: 0.7874 (m110) cc_final: 0.7585 (m-40) REVERT: Y 371 ARG cc_start: 0.7390 (mtp180) cc_final: 0.6945 (mtp180) REVERT: 0 123 MET cc_start: 0.6834 (mtp) cc_final: 0.6460 (mtp) REVERT: 0 201 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: 0 225 GLU cc_start: 0.8029 (tt0) cc_final: 0.7717 (tt0) REVERT: 0 371 ARG cc_start: 0.7234 (mtp180) cc_final: 0.6839 (mtp180) REVERT: 2 201 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: 2 209 PHE cc_start: 0.7910 (m-10) cc_final: 0.7568 (m-80) REVERT: 2 256 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8031 (t0) REVERT: 2 274 LYS cc_start: 0.8642 (tttp) cc_final: 0.8423 (ttmt) REVERT: 2 317 GLU cc_start: 0.5377 (tm-30) cc_final: 0.3499 (tm-30) REVERT: 2 371 ARG cc_start: 0.7215 (mtp180) cc_final: 0.6472 (mtp180) outliers start: 129 outliers final: 85 residues processed: 929 average time/residue: 0.7069 time to fit residues: 1034.4106 Evaluate side-chains 887 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 776 time to evaluate : 5.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 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 367 GLU 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 201 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 256 ASP Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 SER 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 K residue 259 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 201 GLN 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 82 GLU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 186 ASP 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 35 ILE Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 201 GLN Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 57 ARG Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 201 GLN 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 237 ILE 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 123 MET Chi-restraints excluded: chain W residue 186 ASP Chi-restraints excluded: chain W residue 258 ASP Chi-restraints excluded: chain W residue 323 LYS 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 129 GLN 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 Y residue 367 GLU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 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 35 ILE Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 256 ASP Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 310 optimal weight: 0.9980 chunk 156 optimal weight: 0.3980 chunk 102 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 330 optimal weight: 7.9990 chunk 354 optimal weight: 8.9990 chunk 257 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 409 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN A 33 HIS D 33 HIS G 33 HIS I 246 ASN ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 322 ASN M 33 HIS M 246 ASN O 33 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** U 304 GLN U 322 ASN W 33 HIS Y 33 HIS 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.003 0.042 45690 Z= 0.189 Angle : 0.533 7.225 62145 Z= 0.273 Chirality : 0.043 0.122 7110 Planarity : 0.003 0.040 7650 Dihedral : 10.381 73.444 7170 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 2.69 % Allowed : 13.14 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 5355 helix: 0.38 (0.10), residues: 3135 sheet: -1.83 (0.25), residues: 390 loop : -1.02 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 333 HIS 0.006 0.001 HIS U 33 PHE 0.022 0.001 PHE 0 209 TYR 0.021 0.001 TYR D 303 ARG 0.010 0.000 ARG A 249 *********************** 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 952 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 827 time to evaluate : 5.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 LEU cc_start: 0.9005 (mp) cc_final: 0.8781 (mm) REVERT: C 53 ASP cc_start: 0.8566 (t0) cc_final: 0.8186 (t0) REVERT: C 93 ASP cc_start: 0.7576 (p0) cc_final: 0.7352 (p0) REVERT: C 143 ARG cc_start: 0.7254 (pmt170) cc_final: 0.6766 (ptt-90) REVERT: C 150 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8043 (mttp) REVERT: C 201 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7413 (mp10) REVERT: C 213 ARG cc_start: 0.7328 (ttm-80) cc_final: 0.7101 (mtp-110) REVERT: C 371 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6952 (mtp180) REVERT: A 150 LYS cc_start: 0.8479 (mtmm) cc_final: 0.8142 (mttt) REVERT: A 201 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: A 212 GLU cc_start: 0.8434 (pt0) cc_final: 0.7715 (pt0) REVERT: A 256 ASP cc_start: 0.8279 (t70) cc_final: 0.7792 (t70) REVERT: A 280 MET cc_start: 0.8485 (mmt) cc_final: 0.8203 (mmm) REVERT: A 323 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8708 (ttmm) REVERT: A 371 ARG cc_start: 0.7285 (mtp180) cc_final: 0.6897 (mtp180) REVERT: D 143 ARG cc_start: 0.7445 (pmt170) cc_final: 0.7022 (ptt-90) REVERT: D 150 LYS cc_start: 0.8523 (ptpp) cc_final: 0.8199 (mtpt) REVERT: D 201 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: D 212 GLU cc_start: 0.8295 (pt0) cc_final: 0.7953 (pt0) REVERT: D 256 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.7932 (t0) REVERT: G 150 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8101 (mttp) REVERT: G 201 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: G 256 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8144 (t70) REVERT: G 371 ARG cc_start: 0.7497 (mtp180) cc_final: 0.7250 (mtp180) REVERT: I 53 ASP cc_start: 0.8298 (t0) cc_final: 0.8020 (t0) REVERT: I 57 ARG cc_start: 0.8154 (ptp-110) cc_final: 0.7923 (ttp-170) REVERT: I 143 ARG cc_start: 0.7569 (pmt170) cc_final: 0.7267 (ptt-90) REVERT: I 159 ASP cc_start: 0.7996 (p0) cc_final: 0.7584 (p0) REVERT: I 271 LEU cc_start: 0.8539 (mt) cc_final: 0.8274 (mt) REVERT: K 53 ASP cc_start: 0.8533 (t0) cc_final: 0.8223 (t0) REVERT: K 57 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7952 (ttp-170) REVERT: K 102 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8170 (pp) REVERT: K 150 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8326 (mttt) REVERT: K 159 ASP cc_start: 0.8123 (p0) cc_final: 0.7808 (p0) REVERT: K 201 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: K 256 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8039 (t0) REVERT: K 371 ARG cc_start: 0.7284 (mtp180) cc_final: 0.6941 (mtp180) REVERT: M 53 ASP cc_start: 0.8428 (t0) cc_final: 0.8202 (t0) REVERT: M 102 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8269 (pp) REVERT: M 103 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7688 (mt-10) REVERT: M 143 ARG cc_start: 0.7500 (pmt170) cc_final: 0.7074 (ptt-90) REVERT: M 201 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: M 212 GLU cc_start: 0.8314 (pt0) cc_final: 0.8040 (pt0) REVERT: M 263 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7826 (mt-10) REVERT: M 371 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6760 (mtp180) REVERT: O 53 ASP cc_start: 0.8468 (t0) cc_final: 0.8142 (t0) REVERT: O 54 ARG cc_start: 0.8088 (mmp80) cc_final: 0.7767 (mmp80) REVERT: O 82 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: O 86 GLN cc_start: 0.8434 (pt0) cc_final: 0.8132 (pt0) REVERT: O 93 ASP cc_start: 0.7428 (p0) cc_final: 0.7210 (t70) REVERT: O 100 ARG cc_start: 0.8328 (ttp80) cc_final: 0.8013 (tmm160) REVERT: O 143 ARG cc_start: 0.7289 (pmt170) cc_final: 0.6889 (ptt-90) REVERT: O 201 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: O 212 GLU cc_start: 0.8275 (pt0) cc_final: 0.7883 (pt0) REVERT: O 280 MET cc_start: 0.8541 (mmt) cc_final: 0.8275 (mmt) REVERT: Q 53 ASP cc_start: 0.8429 (t0) cc_final: 0.8150 (t0) REVERT: Q 57 ARG cc_start: 0.8290 (ptp-110) cc_final: 0.8084 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7223 (pmt170) cc_final: 0.6729 (ptm-80) REVERT: Q 201 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: Q 212 GLU cc_start: 0.8307 (pt0) cc_final: 0.7904 (pt0) REVERT: Q 213 ARG cc_start: 0.7632 (mtp-110) cc_final: 0.7297 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7269 (m-30) cc_final: 0.6869 (m-30) REVERT: Q 280 MET cc_start: 0.8212 (mmm) cc_final: 0.7951 (mmm) REVERT: Q 301 ASN cc_start: 0.7800 (m-40) cc_final: 0.7503 (m-40) REVERT: S 111 GLN cc_start: 0.8319 (tp40) cc_final: 0.7798 (tp40) REVERT: S 143 ARG cc_start: 0.7229 (ptt-90) cc_final: 0.6584 (ptm-80) REVERT: S 150 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8321 (mtpt) REVERT: S 161 GLU cc_start: 0.7538 (pt0) cc_final: 0.7265 (pt0) REVERT: S 201 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7379 (mp10) REVERT: S 228 SER cc_start: 0.8782 (p) cc_final: 0.8563 (m) REVERT: S 371 ARG cc_start: 0.7101 (mtp180) cc_final: 0.6799 (mtp180) REVERT: U 31 ILE cc_start: 0.8885 (tp) cc_final: 0.8673 (tp) REVERT: U 103 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7762 (mt-10) REVERT: U 143 ARG cc_start: 0.7338 (pmt170) cc_final: 0.6749 (ttp-110) REVERT: U 201 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: U 209 PHE cc_start: 0.7872 (m-10) cc_final: 0.7664 (m-10) REVERT: U 256 ASP cc_start: 0.8560 (t70) cc_final: 0.7734 (t0) REVERT: U 371 ARG cc_start: 0.7045 (mtp180) cc_final: 0.6744 (mtp180) REVERT: W 31 ILE cc_start: 0.8924 (tp) cc_final: 0.8721 (tp) REVERT: W 111 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7670 (tp40) REVERT: W 143 ARG cc_start: 0.7353 (pmt170) cc_final: 0.6590 (ptm-80) REVERT: W 201 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: W 323 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8860 (ttmm) REVERT: W 371 ARG cc_start: 0.7096 (mtp180) cc_final: 0.6729 (mtp180) REVERT: Y 6 ARG cc_start: 0.8159 (ptp90) cc_final: 0.7749 (mtm110) REVERT: Y 123 MET cc_start: 0.5827 (mtm) cc_final: 0.5417 (mtp) REVERT: Y 126 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7467 (tt0) REVERT: Y 150 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8131 (mtpt) REVERT: Y 201 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: Y 301 ASN cc_start: 0.7904 (m110) cc_final: 0.7648 (m-40) REVERT: Y 323 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8745 (ttmm) REVERT: Y 371 ARG cc_start: 0.7362 (mtp180) cc_final: 0.6872 (mtp180) REVERT: 0 123 MET cc_start: 0.6794 (mtp) cc_final: 0.6462 (mtp) REVERT: 0 201 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: 0 225 GLU cc_start: 0.8037 (tt0) cc_final: 0.7750 (tt0) REVERT: 0 371 ARG cc_start: 0.7255 (mtp180) cc_final: 0.6874 (mtp180) REVERT: 2 201 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: 2 256 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8047 (t0) REVERT: 2 274 LYS cc_start: 0.8641 (tttp) cc_final: 0.8427 (ttmt) REVERT: 2 317 GLU cc_start: 0.5420 (tm-30) cc_final: 0.3528 (tm-30) REVERT: 2 371 ARG cc_start: 0.7301 (mtp180) cc_final: 0.6575 (mtp180) outliers start: 125 outliers final: 87 residues processed: 926 average time/residue: 0.6527 time to fit residues: 953.6362 Evaluate side-chains 916 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 802 time to evaluate : 5.186 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE 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 323 LYS Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 256 ASP Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 227 LEU 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 102 LEU Chi-restraints excluded: chain M residue 201 GLN 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 82 GLU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 186 ASP 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 35 ILE Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 201 GLN Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 29 ARG 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 201 GLN Chi-restraints excluded: chain S residue 237 ILE Chi-restraints excluded: chain S residue 256 ASP Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 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 237 ILE Chi-restraints excluded: chain U residue 341 VAL 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 201 GLN Chi-restraints excluded: chain W residue 323 LYS Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 5 LEU 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 323 LYS Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain Y residue 367 GLU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 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 35 ILE Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 256 ASP Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 0.9990 chunk 498 optimal weight: 1.9990 chunk 454 optimal weight: 5.9990 chunk 485 optimal weight: 0.0870 chunk 291 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 380 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 438 optimal weight: 0.3980 chunk 458 optimal weight: 2.9990 chunk 483 optimal weight: 4.9990 overall best weight: 1.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN A 33 HIS G 33 HIS K 164 ASN ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 322 ASN M 33 HIS O 33 HIS Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 ASN W 33 HIS Y 33 HIS ** Y 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45690 Z= 0.175 Angle : 0.530 9.058 62145 Z= 0.271 Chirality : 0.042 0.137 7110 Planarity : 0.003 0.039 7650 Dihedral : 10.329 73.426 7170 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 2.73 % Allowed : 13.48 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 5355 helix: 0.43 (0.10), residues: 3150 sheet: -1.87 (0.25), residues: 390 loop : -0.97 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 333 HIS 0.007 0.001 HIS U 33 PHE 0.022 0.001 PHE 0 209 TYR 0.021 0.001 TYR D 303 ARG 0.009 0.000 ARG A 249 *********************** 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 978 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 851 time to evaluate : 4.977 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 10 LEU cc_start: 0.8972 (mp) cc_final: 0.8740 (mm) REVERT: C 53 ASP cc_start: 0.8575 (t0) cc_final: 0.8244 (t0) REVERT: C 143 ARG cc_start: 0.7223 (pmt170) cc_final: 0.6716 (ptt-90) REVERT: C 150 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8144 (mmmt) REVERT: C 201 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: C 213 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.7102 (mtp-110) REVERT: C 308 GLU cc_start: 0.8016 (pm20) cc_final: 0.7453 (pm20) REVERT: C 371 ARG cc_start: 0.7257 (mtp180) cc_final: 0.7048 (mtp180) REVERT: A 150 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8184 (mmmt) REVERT: A 201 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: A 212 GLU cc_start: 0.8416 (pt0) cc_final: 0.7790 (pt0) REVERT: A 280 MET cc_start: 0.8501 (mmt) cc_final: 0.8221 (mmm) REVERT: A 323 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8668 (ttmm) REVERT: A 371 ARG cc_start: 0.7326 (mtp180) cc_final: 0.6932 (mtp180) REVERT: D 143 ARG cc_start: 0.7440 (pmt170) cc_final: 0.7012 (ptt-90) REVERT: D 150 LYS cc_start: 0.8490 (ptpp) cc_final: 0.8193 (mtpt) REVERT: D 201 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: D 212 GLU cc_start: 0.8285 (pt0) cc_final: 0.7939 (pt0) REVERT: G 14 ASN cc_start: 0.7741 (m-40) cc_final: 0.7520 (t0) REVERT: G 150 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8144 (mttp) REVERT: G 201 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: G 371 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7285 (mtp180) REVERT: I 53 ASP cc_start: 0.8273 (t0) cc_final: 0.8007 (t0) REVERT: I 57 ARG cc_start: 0.8155 (ptp-110) cc_final: 0.7955 (ttp-170) REVERT: I 143 ARG cc_start: 0.7566 (pmt170) cc_final: 0.7264 (ptt-90) REVERT: I 159 ASP cc_start: 0.7943 (p0) cc_final: 0.7524 (p0) REVERT: I 256 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8036 (t70) REVERT: I 271 LEU cc_start: 0.8528 (mt) cc_final: 0.8259 (mt) REVERT: I 304 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7324 (mm-40) REVERT: K 5 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8435 (mm) REVERT: K 53 ASP cc_start: 0.8541 (t0) cc_final: 0.8222 (t0) REVERT: K 57 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7996 (ttp-170) REVERT: K 102 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8142 (pp) REVERT: K 150 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8351 (mttt) REVERT: K 159 ASP cc_start: 0.8096 (p0) cc_final: 0.7799 (p0) REVERT: K 201 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7247 (mt0) REVERT: K 256 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8016 (t0) REVERT: M 53 ASP cc_start: 0.8423 (t0) cc_final: 0.8206 (t0) REVERT: M 102 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8242 (pp) REVERT: M 103 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7702 (mt-10) REVERT: M 143 ARG cc_start: 0.7489 (pmt170) cc_final: 0.7072 (ptt-90) REVERT: M 201 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: M 212 GLU cc_start: 0.8273 (pt0) cc_final: 0.8052 (pt0) REVERT: M 371 ARG cc_start: 0.7145 (mtp180) cc_final: 0.6747 (mtp180) REVERT: O 53 ASP cc_start: 0.8459 (t0) cc_final: 0.8121 (t0) REVERT: O 54 ARG cc_start: 0.8073 (mmp80) cc_final: 0.7745 (mmp80) REVERT: O 82 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: O 86 GLN cc_start: 0.8409 (pt0) cc_final: 0.8112 (pt0) REVERT: O 93 ASP cc_start: 0.7394 (p0) cc_final: 0.7174 (t70) REVERT: O 100 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7999 (tmm160) REVERT: O 143 ARG cc_start: 0.7204 (pmt170) cc_final: 0.6797 (ptt-90) REVERT: O 150 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8175 (mmmt) REVERT: O 201 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: O 212 GLU cc_start: 0.8245 (pt0) cc_final: 0.7606 (pt0) REVERT: O 258 ASP cc_start: 0.8774 (t70) cc_final: 0.8544 (t0) REVERT: O 280 MET cc_start: 0.8527 (mmt) cc_final: 0.8283 (mmt) REVERT: Q 53 ASP cc_start: 0.8439 (t0) cc_final: 0.8157 (t0) REVERT: Q 57 ARG cc_start: 0.8295 (ptp-110) cc_final: 0.8079 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7268 (pmt170) cc_final: 0.6696 (ttp-110) REVERT: Q 201 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.6982 (mp10) REVERT: Q 212 GLU cc_start: 0.8317 (pt0) cc_final: 0.7921 (pt0) REVERT: Q 213 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.7319 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7276 (m-30) cc_final: 0.6879 (m-30) REVERT: Q 256 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8058 (t0) REVERT: Q 301 ASN cc_start: 0.7829 (m-40) cc_final: 0.7556 (m-40) REVERT: S 143 ARG cc_start: 0.7200 (ptt-90) cc_final: 0.6565 (ptm-80) REVERT: S 150 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8190 (mttt) REVERT: S 161 GLU cc_start: 0.7543 (pt0) cc_final: 0.7278 (pt0) REVERT: S 201 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: S 212 GLU cc_start: 0.8128 (pt0) cc_final: 0.7808 (pt0) REVERT: S 228 SER cc_start: 0.8778 (p) cc_final: 0.8558 (m) REVERT: S 256 ASP cc_start: 0.8637 (t70) cc_final: 0.7883 (t0) REVERT: S 371 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6879 (mtp180) REVERT: U 10 LEU cc_start: 0.8649 (mp) cc_final: 0.8405 (mm) REVERT: U 103 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7764 (mt-10) REVERT: U 143 ARG cc_start: 0.7328 (pmt170) cc_final: 0.6736 (ttp-110) REVERT: U 201 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: U 209 PHE cc_start: 0.7819 (m-10) cc_final: 0.7597 (m-10) REVERT: U 256 ASP cc_start: 0.8545 (t70) cc_final: 0.7692 (t0) REVERT: U 280 MET cc_start: 0.8264 (mmm) cc_final: 0.8037 (mmm) REVERT: U 301 ASN cc_start: 0.8132 (m110) cc_final: 0.7900 (m-40) REVERT: U 371 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6833 (mtp180) REVERT: W 111 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7688 (tp40) REVERT: W 143 ARG cc_start: 0.7327 (pmt170) cc_final: 0.6620 (ptm-80) REVERT: W 201 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: W 371 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6736 (mtp180) REVERT: Y 6 ARG cc_start: 0.8151 (ptp90) cc_final: 0.7702 (mtm110) REVERT: Y 15 LYS cc_start: 0.8747 (ptmm) cc_final: 0.8486 (ptmm) REVERT: Y 123 MET cc_start: 0.5842 (mtm) cc_final: 0.5434 (mtp) REVERT: Y 126 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7507 (tt0) REVERT: Y 150 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8143 (mtpt) REVERT: Y 201 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: Y 301 ASN cc_start: 0.7890 (m110) cc_final: 0.7684 (m-40) REVERT: Y 323 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8719 (ttmm) REVERT: Y 371 ARG cc_start: 0.7275 (mtp180) cc_final: 0.6874 (mtp180) REVERT: 0 123 MET cc_start: 0.6824 (mtp) cc_final: 0.6514 (mtp) REVERT: 0 201 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: 0 225 GLU cc_start: 0.8018 (tt0) cc_final: 0.7660 (tt0) REVERT: 0 371 ARG cc_start: 0.7252 (mtp180) cc_final: 0.6867 (mtp180) REVERT: 2 150 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7875 (mttm) REVERT: 2 201 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: 2 212 GLU cc_start: 0.8038 (pt0) cc_final: 0.7616 (pt0) REVERT: 2 256 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8033 (t0) REVERT: 2 274 LYS cc_start: 0.8641 (tttp) cc_final: 0.8440 (ttmt) REVERT: 2 317 GLU cc_start: 0.5544 (tm-30) cc_final: 0.4029 (tm-30) REVERT: 2 371 ARG cc_start: 0.7291 (mtp180) cc_final: 0.6582 (mtp180) outliers start: 127 outliers final: 91 residues processed: 949 average time/residue: 0.6590 time to fit residues: 981.0434 Evaluate side-chains 940 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 821 time to evaluate : 4.711 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE 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 323 LYS Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 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 227 LEU Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 256 ASP 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 34 ILE 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 201 GLN Chi-restraints excluded: chain M residue 228 SER Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 186 ASP 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 35 ILE Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 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 Q residue 367 GLU Chi-restraints excluded: chain S residue 29 ARG 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 201 GLN Chi-restraints excluded: chain S residue 237 ILE 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 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 341 VAL 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 201 GLN Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 5 LEU 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 323 LYS Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain Y residue 367 GLU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 228 SER Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 91 ILE Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 256 ASP Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 0.5980 chunk 512 optimal weight: 0.9980 chunk 313 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 356 optimal weight: 7.9990 chunk 537 optimal weight: 2.9990 chunk 495 optimal weight: 0.9990 chunk 428 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 330 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN A 33 HIS G 33 HIS ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS O 33 HIS Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 ASN W 33 HIS Y 33 HIS ** Y 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 ASN 0 33 HIS 0 202 GLN ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 HIS 2 86 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3652 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= 0.157 Angle : 0.525 9.399 62145 Z= 0.269 Chirality : 0.042 0.145 7110 Planarity : 0.003 0.041 7650 Dihedral : 10.288 73.397 7170 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 2.54 % Allowed : 14.02 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.12), residues: 5355 helix: 0.48 (0.10), residues: 3150 sheet: -1.83 (0.25), residues: 390 loop : -0.92 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 175 HIS 0.008 0.001 HIS U 33 PHE 0.024 0.001 PHE 0 209 TYR 0.020 0.001 TYR D 303 ARG 0.010 0.000 ARG A 249 ********************** 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 1000 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 882 time to evaluate : 4.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 LEU cc_start: 0.8966 (mp) cc_final: 0.8735 (mm) REVERT: C 53 ASP cc_start: 0.8590 (t0) cc_final: 0.8338 (t0) REVERT: C 103 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7864 (mt-10) REVERT: C 143 ARG cc_start: 0.7205 (pmt170) cc_final: 0.6700 (ptt-90) REVERT: C 150 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8213 (mmmt) REVERT: C 201 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7398 (mp10) REVERT: C 213 ARG cc_start: 0.7330 (ttm-80) cc_final: 0.7099 (mtp-110) REVERT: C 308 GLU cc_start: 0.7985 (pm20) cc_final: 0.7426 (pm20) REVERT: A 201 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: A 212 GLU cc_start: 0.8388 (pt0) cc_final: 0.7727 (pt0) REVERT: A 280 MET cc_start: 0.8479 (mmt) cc_final: 0.8207 (mmm) REVERT: A 317 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7106 (mm-30) REVERT: A 323 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8620 (ttmm) REVERT: A 371 ARG cc_start: 0.7320 (mtp180) cc_final: 0.6932 (mtp180) REVERT: D 57 ARG cc_start: 0.8212 (ptp-110) cc_final: 0.7919 (ttp-170) REVERT: D 123 MET cc_start: 0.6014 (ptt) cc_final: 0.5679 (ptp) REVERT: D 143 ARG cc_start: 0.7425 (pmt170) cc_final: 0.6999 (ptt-90) REVERT: D 150 LYS cc_start: 0.8471 (ptpp) cc_final: 0.8226 (mttt) REVERT: D 201 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7136 (mp10) REVERT: D 212 GLU cc_start: 0.8244 (pt0) cc_final: 0.7835 (pt0) REVERT: G 150 LYS cc_start: 0.8772 (mtmm) cc_final: 0.8163 (mmtm) REVERT: G 201 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: G 256 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8107 (t0) REVERT: G 371 ARG cc_start: 0.7518 (mtp180) cc_final: 0.7282 (mtp180) REVERT: I 53 ASP cc_start: 0.8283 (t0) cc_final: 0.8015 (t0) REVERT: I 103 GLU cc_start: 0.7704 (mp0) cc_final: 0.7467 (mp0) REVERT: I 143 ARG cc_start: 0.7554 (pmt170) cc_final: 0.7264 (ptt-90) REVERT: I 150 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8305 (mmtt) REVERT: I 159 ASP cc_start: 0.7888 (p0) cc_final: 0.7475 (p0) REVERT: I 227 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8443 (tp) REVERT: I 256 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.7908 (t70) REVERT: I 271 LEU cc_start: 0.8505 (mt) cc_final: 0.8248 (mt) REVERT: I 304 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7389 (mm-40) REVERT: K 5 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8429 (mm) REVERT: K 53 ASP cc_start: 0.8545 (t0) cc_final: 0.8237 (t0) REVERT: K 57 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8016 (ttp-170) REVERT: K 102 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8076 (pp) REVERT: K 150 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8391 (mttt) REVERT: K 159 ASP cc_start: 0.8075 (p0) cc_final: 0.7811 (p0) REVERT: K 201 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7141 (mt0) REVERT: K 256 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.7980 (t0) REVERT: M 53 ASP cc_start: 0.8423 (t0) cc_final: 0.8219 (t0) REVERT: M 102 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8199 (pp) REVERT: M 103 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7703 (mt-10) REVERT: M 143 ARG cc_start: 0.7491 (pmt170) cc_final: 0.7074 (ptt-90) REVERT: M 263 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7564 (mt-10) REVERT: M 325 SER cc_start: 0.9069 (t) cc_final: 0.8861 (p) REVERT: M 371 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6786 (mtp180) REVERT: O 53 ASP cc_start: 0.8424 (t0) cc_final: 0.8062 (t0) REVERT: O 54 ARG cc_start: 0.8021 (mmp80) cc_final: 0.7671 (mmp80) REVERT: O 82 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: O 93 ASP cc_start: 0.7408 (p0) cc_final: 0.7202 (t70) REVERT: O 100 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7969 (tmm160) REVERT: O 143 ARG cc_start: 0.7177 (pmt170) cc_final: 0.6782 (ptt-90) REVERT: O 150 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8142 (mmtm) REVERT: O 159 ASP cc_start: 0.7923 (p0) cc_final: 0.7525 (p0) REVERT: O 201 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: O 212 GLU cc_start: 0.8209 (pt0) cc_final: 0.7741 (pt0) REVERT: O 256 ASP cc_start: 0.8722 (t70) cc_final: 0.7877 (t0) REVERT: O 280 MET cc_start: 0.8532 (mmt) cc_final: 0.8214 (mmm) REVERT: Q 53 ASP cc_start: 0.8440 (t0) cc_final: 0.8152 (t0) REVERT: Q 57 ARG cc_start: 0.8284 (ptp-110) cc_final: 0.8008 (ttp-170) REVERT: Q 143 ARG cc_start: 0.7247 (pmt170) cc_final: 0.6673 (ttp-110) REVERT: Q 201 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: Q 212 GLU cc_start: 0.8299 (pt0) cc_final: 0.7946 (pt0) REVERT: Q 213 ARG cc_start: 0.7620 (mtp-110) cc_final: 0.7304 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7251 (m-30) cc_final: 0.6879 (m-30) REVERT: Q 256 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8049 (t0) REVERT: S 143 ARG cc_start: 0.7153 (ptt-90) cc_final: 0.6336 (ttp-110) REVERT: S 150 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8281 (mttt) REVERT: S 161 GLU cc_start: 0.7580 (pt0) cc_final: 0.7320 (pt0) REVERT: S 201 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: S 212 GLU cc_start: 0.8123 (pt0) cc_final: 0.7732 (pt0) REVERT: S 213 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.7124 (ttt180) REVERT: S 228 SER cc_start: 0.8779 (p) cc_final: 0.8553 (m) REVERT: U 10 LEU cc_start: 0.8628 (mp) cc_final: 0.8377 (mm) REVERT: U 54 ARG cc_start: 0.8161 (mmt-90) cc_final: 0.7610 (mmt-90) REVERT: U 103 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7753 (mt-10) REVERT: U 143 ARG cc_start: 0.7309 (pmt170) cc_final: 0.6716 (ttp-110) REVERT: U 201 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7370 (mt0) REVERT: U 256 ASP cc_start: 0.8520 (t70) cc_final: 0.7661 (t0) REVERT: U 280 MET cc_start: 0.8261 (mmm) cc_final: 0.8038 (mmm) REVERT: U 301 ASN cc_start: 0.8133 (m110) cc_final: 0.7900 (m-40) REVERT: U 371 ARG cc_start: 0.7106 (mtp180) cc_final: 0.6825 (mtp180) REVERT: W 54 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7881 (mmt-90) REVERT: W 111 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7656 (tp40) REVERT: W 143 ARG cc_start: 0.7313 (pmt170) cc_final: 0.6612 (ptm-80) REVERT: W 201 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: W 258 ASP cc_start: 0.8782 (t70) cc_final: 0.8569 (t0) REVERT: W 325 SER cc_start: 0.9172 (t) cc_final: 0.8844 (p) REVERT: W 371 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6730 (mtp180) REVERT: Y 6 ARG cc_start: 0.8100 (ptp90) cc_final: 0.7715 (mtm110) REVERT: Y 15 LYS cc_start: 0.8714 (ptmm) cc_final: 0.8468 (ptmm) REVERT: Y 201 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: Y 323 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8719 (ttmm) REVERT: Y 371 ARG cc_start: 0.7205 (mtp180) cc_final: 0.6837 (mtp180) REVERT: 0 123 MET cc_start: 0.6816 (mtp) cc_final: 0.6557 (mtp) REVERT: 0 201 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: 0 225 GLU cc_start: 0.8016 (tt0) cc_final: 0.7654 (tt0) REVERT: 0 325 SER cc_start: 0.9110 (t) cc_final: 0.8774 (p) REVERT: 0 371 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6869 (mtp180) REVERT: 2 53 ASP cc_start: 0.8812 (t0) cc_final: 0.8528 (t0) REVERT: 2 54 ARG cc_start: 0.8010 (mmp80) cc_final: 0.7702 (mmt-90) REVERT: 2 150 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8086 (mtpp) REVERT: 2 161 GLU cc_start: 0.7843 (pt0) cc_final: 0.7499 (pt0) REVERT: 2 201 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: 2 256 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8020 (t0) REVERT: 2 317 GLU cc_start: 0.5556 (tm-30) cc_final: 0.4014 (tm-30) REVERT: 2 371 ARG cc_start: 0.7261 (mtp180) cc_final: 0.6753 (mtp180) outliers start: 118 outliers final: 80 residues processed: 969 average time/residue: 0.6721 time to fit residues: 1024.8843 Evaluate side-chains 936 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 828 time to evaluate : 4.972 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 GLU 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 201 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain G residue 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 227 LEU Chi-restraints excluded: chain I residue 256 ASP 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 35 ILE Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 228 SER Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 82 GLU 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 34 ILE Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 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 Q residue 367 GLU Chi-restraints excluded: chain S residue 29 ARG 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 201 GLN Chi-restraints excluded: chain S residue 237 ILE Chi-restraints excluded: chain S residue 256 ASP Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 164 ASN 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 341 VAL 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 201 GLN Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 5 LEU 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 201 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 323 LYS Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain Y residue 367 GLU 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 227 LEU 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 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 256 ASP Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 3.9990 chunk 456 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 395 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 429 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 440 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 HIS G 33 HIS I 33 HIS K 164 ASN K 246 ASN ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 ASN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 33 HIS ** Y 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.092249 restraints weight = 67938.052| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.94 r_work: 0.2861 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45690 Z= 0.195 Angle : 0.538 9.348 62145 Z= 0.275 Chirality : 0.042 0.129 7110 Planarity : 0.004 0.042 7650 Dihedral : 10.292 73.423 7170 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 2.43 % Allowed : 14.67 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 5355 helix: 0.50 (0.10), residues: 3150 sheet: -1.79 (0.25), residues: 390 loop : -0.87 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 333 HIS 0.008 0.002 HIS U 33 PHE 0.024 0.001 PHE 0 209 TYR 0.021 0.001 TYR D 303 ARG 0.010 0.000 ARG 0 213 =============================================================================== Job complete usr+sys time: 15265.69 seconds wall clock time: 277 minutes 42.47 seconds (16662.47 seconds total)