Starting phenix.real_space_refine on Tue Sep 15 21:05:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6h5q_0141/09_2026/6h5q_0141.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h5q_0141/09_2026/6h5q_0141.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 { model { file = "/net/cci-nas-00/data/ceres_data/6h5q_0141/09_2026/6h5q_0141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h5q_0141/09_2026/6h5q_0141.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6h5q_0141/09_2026/6h5q_0141.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6h5q_0141/09_2026/6h5q_0141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6h5q_0141/09_2026/6h5q_0141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h5q_0141/09_2026/6h5q_0141.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 29370 2.51 5 N 8115 2.21 5 O 8910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 195 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 46650 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "R" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNAv2': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: A, D, F, H, J, L, N, P, S, U, W, Y, 0, 2, C, E, G, I, K, M, O, Q, T, V, X, Z, 1, 3 Time building chain proxies: 5.49, per 1000 atoms: 0.12 Number of scatterers: 46650 At special positions: 0 Unit cell: (203.184, 203.184, 135.456, 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 8910 8.00 N 8115 7.00 C 29370 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 2.0 seconds 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10530 Finding SS restraints... Secondary structure from input PDB file: 330 helices and 15 sheets defined 59.1% alpha, 4.7% beta 0 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'B' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA B 181 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 304 " --> pdb=" O MET B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 310 Processing helix chain 'B' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER B 328 " --> pdb=" O SER B 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 369 " --> pdb=" O GLY B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'A' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 Processing helix chain 'A' and resid 325 through 328 removed outlier: 3.724A 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 343 removed outlier: 4.463A pdb=" N GLU A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS D 15 " --> pdb=" O PHE D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA D 181 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'D' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 298 " --> pdb=" O SER D 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN D 304 " --> pdb=" O MET D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 Processing helix chain 'D' and resid 325 through 328 removed outlier: 3.725A 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 343 removed outlier: 4.462A pdb=" N GLU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 358 through 372 removed outlier: 3.602A pdb=" N PHE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS F 15 " --> pdb=" O PHE F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 removed outlier: 3.735A pdb=" N LEU F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE F 170 " --> pdb=" O ILE F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA F 181 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA F 189 " --> pdb=" O PRO F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG F 195 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL F 218 " --> pdb=" O LYS F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 269 through 276 Processing helix chain 'F' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 298 " --> pdb=" O SER F 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN F 304 " --> pdb=" O MET F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 310 Processing helix chain 'F' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER F 328 " --> pdb=" O SER F 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 328' Processing helix chain 'F' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 350 Processing helix chain 'F' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE F 362 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL F 369 " --> pdb=" O GLY F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 removed outlier: 3.616A pdb=" N LEU F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS H 15 " --> pdb=" O PHE H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG H 48 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG H 57 " --> pdb=" O ASP H 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN H 89 " --> pdb=" O GLY H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA H 181 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA H 189 " --> pdb=" O PRO H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL H 218 " --> pdb=" O LYS H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 261 No H-bonds generated for 'chain 'H' and resid 259 through 261' Processing helix chain 'H' and resid 269 through 276 Processing helix chain 'H' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU H 296 " --> pdb=" O GLU H 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN H 304 " --> pdb=" O MET H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 310 Processing helix chain 'H' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER H 328 " --> pdb=" O SER H 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 325 through 328' Processing helix chain 'H' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU H 342 " --> pdb=" O GLY H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 Processing helix chain 'H' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE H 362 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL H 369 " --> pdb=" O GLY H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU H 384 " --> pdb=" O LEU H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU H 393 " --> pdb=" O GLU H 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL H 394 " --> pdb=" O ASP H 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG J 6 " --> pdb=" O ALA J 2 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS J 15 " --> pdb=" O PHE J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG J 48 " --> pdb=" O SER J 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU J 87 " --> pdb=" O SER J 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN J 89 " --> pdb=" O GLY J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP J 128 " --> pdb=" O GLU J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE J 170 " --> pdb=" O ILE J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA J 181 " --> pdb=" O LEU J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA J 189 " --> pdb=" O PRO J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG J 195 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL J 218 " --> pdb=" O LYS J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE J 232 " --> pdb=" O SER J 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE J 237 " --> pdb=" O MET J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP J 256 " --> pdb=" O GLU J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 261 No H-bonds generated for 'chain 'J' and resid 259 through 261' Processing helix chain 'J' and resid 269 through 276 Processing helix chain 'J' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER J 298 " --> pdb=" O SER J 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN J 304 " --> pdb=" O MET J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 310 Processing helix chain 'J' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER J 328 " --> pdb=" O SER J 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 325 through 328' Processing helix chain 'J' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU J 342 " --> pdb=" O GLY J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 350 Processing helix chain 'J' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE J 362 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL J 369 " --> pdb=" O GLY J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU J 384 " --> pdb=" O LEU J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU J 393 " --> pdb=" O GLU J 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL J 394 " --> pdb=" O ASP J 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 17 removed outlier: 4.048A pdb=" N ARG L 6 " --> pdb=" O ALA L 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS L 15 " --> pdb=" O PHE L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN L 61 " --> pdb=" O ARG L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU L 69 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU L 87 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN L 89 " --> pdb=" O GLY L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE L 170 " --> pdb=" O ILE L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA L 181 " --> pdb=" O LEU L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA L 189 " --> pdb=" O PRO L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG L 195 " --> pdb=" O SER L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL L 218 " --> pdb=" O LYS L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE L 232 " --> pdb=" O SER L 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE L 237 " --> pdb=" O MET L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 261 No H-bonds generated for 'chain 'L' and resid 259 through 261' Processing helix chain 'L' and resid 269 through 276 Processing helix chain 'L' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU L 296 " --> pdb=" O GLU L 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER L 298 " --> pdb=" O SER L 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN L 304 " --> pdb=" O MET L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 310 Processing helix chain 'L' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER L 328 " --> pdb=" O SER L 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 325 through 328' Processing helix chain 'L' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU L 342 " --> pdb=" O GLY L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 350 Processing helix chain 'L' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE L 362 " --> pdb=" O ASP L 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL L 369 " --> pdb=" O GLY L 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU L 384 " --> pdb=" O LEU L 380 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU L 393 " --> pdb=" O GLU L 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL L 394 " --> pdb=" O ASP L 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG N 6 " --> pdb=" O ALA N 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS N 15 " --> pdb=" O PHE N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG N 48 " --> pdb=" O SER N 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG N 57 " --> pdb=" O ASP N 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN N 61 " --> pdb=" O ARG N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU N 69 " --> pdb=" O SER N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU N 87 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN N 89 " --> pdb=" O GLY N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP N 128 " --> pdb=" O GLU N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE N 170 " --> pdb=" O ILE N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA N 181 " --> pdb=" O LEU N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA N 189 " --> pdb=" O PRO N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG N 195 " --> pdb=" O SER N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL N 218 " --> pdb=" O LYS N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE N 232 " --> pdb=" O SER N 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE N 237 " --> pdb=" O MET N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP N 256 " --> pdb=" O GLU N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 261 No H-bonds generated for 'chain 'N' and resid 259 through 261' Processing helix chain 'N' and resid 269 through 276 Processing helix chain 'N' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU N 296 " --> pdb=" O GLU N 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER N 298 " --> pdb=" O SER N 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN N 304 " --> pdb=" O MET N 300 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 310 Processing helix chain 'N' and resid 325 through 328 removed outlier: 3.724A pdb=" N SER N 328 " --> pdb=" O SER N 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 325 through 328' Processing helix chain 'N' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU N 342 " --> pdb=" O GLY N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 350 Processing helix chain 'N' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE N 362 " --> pdb=" O ASP N 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL N 369 " --> pdb=" O GLY N 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU N 384 " --> pdb=" O LEU N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU N 393 " --> pdb=" O GLU N 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL N 394 " --> pdb=" O ASP N 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG P 6 " --> pdb=" O ALA P 2 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS P 15 " --> pdb=" O PHE P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG P 48 " --> pdb=" O SER P 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY P 60 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN P 61 " --> pdb=" O ARG P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU P 69 " --> pdb=" O SER P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU P 87 " --> pdb=" O SER P 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN P 89 " --> pdb=" O GLY P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP P 128 " --> pdb=" O GLU P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE P 170 " --> pdb=" O ILE P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA P 181 " --> pdb=" O LEU P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA P 189 " --> pdb=" O PRO P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG P 195 " --> pdb=" O SER P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL P 218 " --> pdb=" O LYS P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE P 232 " --> pdb=" O SER P 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE P 237 " --> pdb=" O MET P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP P 256 " --> pdb=" O GLU P 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 259 through 261 No H-bonds generated for 'chain 'P' and resid 259 through 261' Processing helix chain 'P' and resid 269 through 276 Processing helix chain 'P' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU P 296 " --> pdb=" O GLU P 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER P 298 " --> pdb=" O SER P 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN P 304 " --> pdb=" O MET P 300 " (cutoff:3.500A) Processing helix chain 'P' and resid 307 through 310 Processing helix chain 'P' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER P 328 " --> pdb=" O SER P 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 325 through 328' Processing helix chain 'P' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU P 342 " --> pdb=" O GLY P 338 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 350 Processing helix chain 'P' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE P 362 " --> pdb=" O ASP P 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL P 369 " --> pdb=" O GLY P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU P 384 " --> pdb=" O LEU P 380 " (cutoff:3.500A) Processing helix chain 'P' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU P 393 " --> pdb=" O GLU P 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG S 6 " --> pdb=" O ALA S 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN S 14 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS S 15 " --> pdb=" O PHE S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG S 48 " --> pdb=" O SER S 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG S 57 " --> pdb=" O ASP S 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY S 60 " --> pdb=" O VAL S 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN S 61 " --> pdb=" O ARG S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU S 69 " --> pdb=" O SER S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU S 87 " --> pdb=" O SER S 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN S 89 " --> pdb=" O GLY S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP S 128 " --> pdb=" O GLU S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE S 170 " --> pdb=" O ILE S 166 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA S 181 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA S 189 " --> pdb=" O PRO S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG S 195 " --> pdb=" O SER S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL S 218 " --> pdb=" O LYS S 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE S 232 " --> pdb=" O SER S 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE S 237 " --> pdb=" O MET S 233 " (cutoff:3.500A) Processing helix chain 'S' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP S 256 " --> pdb=" O GLU S 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'S' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU S 296 " --> pdb=" O GLU S 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER S 298 " --> pdb=" O SER S 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN S 304 " --> pdb=" O MET S 300 " (cutoff:3.500A) Processing helix chain 'S' and resid 307 through 310 Processing helix chain 'S' and resid 325 through 328 removed outlier: 3.725A 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 343 removed outlier: 4.462A pdb=" N GLU S 342 " --> pdb=" O GLY S 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 346 through 350 Processing helix chain 'S' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE S 362 " --> pdb=" O ASP S 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL S 369 " --> pdb=" O GLY S 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU S 384 " --> pdb=" O LEU S 380 " (cutoff:3.500A) Processing helix chain 'S' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU S 393 " --> pdb=" O GLU S 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL S 394 " --> pdb=" O ASP S 390 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG U 6 " --> pdb=" O ALA U 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN U 14 " --> pdb=" O LEU U 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS U 15 " --> pdb=" O PHE U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 61 removed outlier: 3.573A pdb=" N ARG U 48 " --> pdb=" O SER U 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY U 60 " --> pdb=" O VAL U 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN U 61 " --> pdb=" O ARG U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU U 69 " --> pdb=" O SER U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU U 87 " --> pdb=" O SER U 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN U 89 " --> pdb=" O GLY U 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP U 128 " --> pdb=" O GLU U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE U 170 " --> pdb=" O ILE U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA U 181 " --> pdb=" O LEU U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 189 removed outlier: 4.436A pdb=" N ALA U 189 " --> pdb=" O PRO U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG U 195 " --> pdb=" O SER U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL U 218 " --> pdb=" O LYS U 214 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE U 232 " --> pdb=" O SER U 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE U 237 " --> pdb=" O MET U 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP U 256 " --> pdb=" O GLU U 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'U' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU U 296 " --> pdb=" O GLU U 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER U 298 " --> pdb=" O SER U 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN U 304 " --> pdb=" O MET U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 307 through 310 Processing helix chain 'U' and resid 325 through 328 removed outlier: 3.725A 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 343 removed outlier: 4.463A pdb=" N GLU U 342 " --> pdb=" O GLY U 338 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE U 362 " --> pdb=" O ASP U 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL U 369 " --> pdb=" O GLY U 365 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 385 removed outlier: 3.616A pdb=" N LEU U 384 " --> pdb=" O LEU U 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU U 393 " --> pdb=" O GLU U 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL U 394 " --> pdb=" O ASP U 390 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG W 6 " --> pdb=" O ALA W 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN W 14 " --> pdb=" O LEU W 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS W 15 " --> pdb=" O PHE W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG W 48 " --> pdb=" O SER W 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG W 57 " --> pdb=" O ASP W 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY W 60 " --> pdb=" O VAL W 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU W 69 " --> pdb=" O SER W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 92 removed outlier: 3.735A pdb=" N LEU W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN W 89 " --> pdb=" O GLY W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP W 128 " --> pdb=" O GLU W 124 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE W 170 " --> pdb=" O ILE W 166 " (cutoff:3.500A) Processing helix chain 'W' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA W 181 " --> pdb=" O LEU W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA W 189 " --> pdb=" O PRO W 185 " (cutoff:3.500A) Processing helix chain 'W' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG W 195 " --> pdb=" O SER W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL W 218 " --> pdb=" O LYS W 214 " (cutoff:3.500A) Processing helix chain 'W' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE W 232 " --> pdb=" O SER W 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE W 237 " --> pdb=" O MET W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP W 256 " --> pdb=" O GLU W 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'W' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU W 296 " --> pdb=" O GLU W 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER W 298 " --> pdb=" O SER W 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN W 304 " --> pdb=" O MET W 300 " (cutoff:3.500A) Processing helix chain 'W' and resid 307 through 310 Processing helix chain 'W' and resid 325 through 328 removed outlier: 3.724A 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 343 removed outlier: 4.461A pdb=" N GLU W 342 " --> pdb=" O GLY W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 346 through 350 Processing helix chain 'W' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE W 362 " --> pdb=" O ASP W 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL W 369 " --> pdb=" O GLY W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU W 384 " --> pdb=" O LEU W 380 " (cutoff:3.500A) Processing helix chain 'W' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU W 393 " --> pdb=" O GLU W 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL W 394 " --> pdb=" O ASP W 390 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG Y 6 " --> pdb=" O ALA Y 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN Y 14 " --> pdb=" O LEU Y 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS Y 15 " --> pdb=" O PHE Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG Y 48 " --> pdb=" O SER Y 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG Y 57 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY Y 60 " --> pdb=" O VAL Y 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN Y 61 " --> pdb=" O ARG Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU Y 69 " --> pdb=" O SER Y 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU Y 87 " --> pdb=" O SER Y 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN Y 89 " --> pdb=" O GLY Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP Y 128 " --> pdb=" O GLU Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE Y 170 " --> pdb=" O ILE Y 166 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA Y 181 " --> pdb=" O LEU Y 178 " (cutoff:3.500A) Processing helix chain 'Y' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA Y 189 " --> pdb=" O PRO Y 185 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG Y 195 " --> pdb=" O SER Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL Y 218 " --> pdb=" O LYS Y 214 " (cutoff:3.500A) Processing helix chain 'Y' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE Y 232 " --> pdb=" O SER Y 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE Y 237 " --> pdb=" O MET Y 233 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP Y 256 " --> pdb=" O GLU Y 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'Y' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU Y 296 " --> pdb=" O GLU Y 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER Y 298 " --> pdb=" O SER Y 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN Y 304 " --> pdb=" O MET Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 307 through 310 Processing helix chain 'Y' and resid 325 through 328 removed outlier: 3.725A 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 343 removed outlier: 4.462A pdb=" N GLU Y 342 " --> pdb=" O GLY Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 346 through 350 Processing helix chain 'Y' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE Y 362 " --> pdb=" O ASP Y 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL Y 369 " --> pdb=" O GLY Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU Y 384 " --> pdb=" O LEU Y 380 " (cutoff:3.500A) Processing helix chain 'Y' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU Y 393 " --> pdb=" O GLU Y 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL Y 394 " --> pdb=" O ASP Y 390 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG 0 6 " --> pdb=" O ALA 0 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN 0 14 " --> pdb=" O LEU 0 10 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS 0 15 " --> pdb=" O PHE 0 11 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG 0 48 " --> pdb=" O SER 0 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG 0 57 " --> pdb=" O ASP 0 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY 0 60 " --> pdb=" O VAL 0 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN 0 61 " --> pdb=" O ARG 0 57 " (cutoff:3.500A) Processing helix chain '0' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU 0 69 " --> pdb=" O SER 0 65 " (cutoff:3.500A) Processing helix chain '0' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU 0 87 " --> pdb=" O SER 0 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN 0 89 " --> pdb=" O GLY 0 85 " (cutoff:3.500A) Processing helix chain '0' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP 0 128 " --> pdb=" O GLU 0 124 " (cutoff:3.500A) Processing helix chain '0' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE 0 170 " --> pdb=" O ILE 0 166 " (cutoff:3.500A) Processing helix chain '0' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA 0 181 " --> pdb=" O LEU 0 178 " (cutoff:3.500A) Processing helix chain '0' and resid 184 through 189 removed outlier: 4.436A pdb=" N ALA 0 189 " --> pdb=" O PRO 0 185 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG 0 195 " --> pdb=" O SER 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL 0 218 " --> pdb=" O LYS 0 214 " (cutoff:3.500A) Processing helix chain '0' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE 0 232 " --> pdb=" O SER 0 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE 0 237 " --> pdb=" O MET 0 233 " (cutoff:3.500A) Processing helix chain '0' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP 0 256 " --> pdb=" O GLU 0 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain '0' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU 0 296 " --> pdb=" O GLU 0 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER 0 298 " --> pdb=" O SER 0 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN 0 304 " --> pdb=" O MET 0 300 " (cutoff:3.500A) Processing helix chain '0' and resid 307 through 310 Processing helix chain '0' and resid 325 through 328 removed outlier: 3.724A 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 343 removed outlier: 4.461A pdb=" N GLU 0 342 " --> pdb=" O GLY 0 338 " (cutoff:3.500A) Processing helix chain '0' and resid 346 through 350 Processing helix chain '0' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE 0 362 " --> pdb=" O ASP 0 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL 0 369 " --> pdb=" O GLY 0 365 " (cutoff:3.500A) Processing helix chain '0' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU 0 384 " --> pdb=" O LEU 0 380 " (cutoff:3.500A) Processing helix chain '0' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU 0 393 " --> pdb=" O GLU 0 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL 0 394 " --> pdb=" O ASP 0 390 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG 2 6 " --> pdb=" O ALA 2 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN 2 14 " --> pdb=" O LEU 2 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS 2 15 " --> pdb=" O PHE 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG 2 48 " --> pdb=" O SER 2 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG 2 57 " --> pdb=" O ASP 2 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY 2 60 " --> pdb=" O VAL 2 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN 2 61 " --> pdb=" O ARG 2 57 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU 2 69 " --> pdb=" O SER 2 65 " (cutoff:3.500A) Processing helix chain '2' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU 2 87 " --> pdb=" O SER 2 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN 2 89 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) Processing helix chain '2' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP 2 128 " --> pdb=" O GLU 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE 2 170 " --> pdb=" O ILE 2 166 " (cutoff:3.500A) Processing helix chain '2' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA 2 181 " --> pdb=" O LEU 2 178 " (cutoff:3.500A) Processing helix chain '2' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA 2 189 " --> pdb=" O PRO 2 185 " (cutoff:3.500A) Processing helix chain '2' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG 2 195 " --> pdb=" O SER 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL 2 218 " --> pdb=" O LYS 2 214 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE 2 232 " --> pdb=" O SER 2 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE 2 237 " --> pdb=" O MET 2 233 " (cutoff:3.500A) Processing helix chain '2' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP 2 256 " --> pdb=" O GLU 2 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain '2' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU 2 296 " --> pdb=" O GLU 2 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER 2 298 " --> pdb=" O SER 2 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN 2 304 " --> pdb=" O MET 2 300 " (cutoff:3.500A) Processing helix chain '2' and resid 307 through 310 Processing helix chain '2' and resid 325 through 328 removed outlier: 3.725A 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 343 removed outlier: 4.461A pdb=" N GLU 2 342 " --> pdb=" O GLY 2 338 " (cutoff:3.500A) Processing helix chain '2' and resid 346 through 350 Processing helix chain '2' and resid 358 through 372 removed outlier: 3.604A pdb=" N PHE 2 362 " --> pdb=" O ASP 2 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL 2 369 " --> pdb=" O GLY 2 365 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU 2 384 " --> pdb=" O LEU 2 380 " (cutoff:3.500A) Processing helix chain '2' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU 2 393 " --> pdb=" O GLU 2 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL 2 394 " --> pdb=" O ASP 2 390 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'B' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS B 33 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG B 100 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE B 35 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 102 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 104 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 39 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN B 106 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS A 33 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG A 100 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 35 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 102 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 37 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 39 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN A 106 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'D' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS D 33 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG D 100 " --> pdb=" O HIS D 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE D 35 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU D 102 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL D 37 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL D 104 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 39 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN D 106 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'F' and resid 33 through 40 removed outlier: 5.818A pdb=" N HIS F 33 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG F 100 " --> pdb=" O HIS F 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE F 35 " --> pdb=" O ARG F 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU F 102 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL F 37 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL F 104 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE F 39 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N GLN F 106 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'H' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG H 100 " --> pdb=" O HIS H 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE H 35 " --> pdb=" O ARG H 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU H 102 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL H 37 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 104 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE H 39 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN H 106 " --> pdb=" O ILE H 39 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'J' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS J 33 " --> pdb=" O SER J 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG J 100 " --> pdb=" O HIS J 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE J 35 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU J 102 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL J 37 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 104 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE J 39 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN J 106 " --> pdb=" O ILE J 39 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'L' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS L 33 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG L 100 " --> pdb=" O HIS L 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE L 35 " --> pdb=" O ARG L 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU L 102 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL L 37 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL L 104 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE L 39 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN L 106 " --> pdb=" O ILE L 39 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'N' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS N 33 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG N 100 " --> pdb=" O HIS N 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE N 35 " --> pdb=" O ARG N 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU N 102 " --> pdb=" O ILE N 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL N 37 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL N 104 " --> pdb=" O VAL N 37 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE N 39 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN N 106 " --> pdb=" O ILE N 39 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'P' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS P 33 " --> pdb=" O SER P 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG P 100 " --> pdb=" O HIS P 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE P 35 " --> pdb=" O ARG P 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU P 102 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL P 37 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL P 104 " --> pdb=" O VAL P 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE P 39 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN P 106 " --> pdb=" O ILE P 39 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'S' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS S 33 " --> pdb=" O SER S 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG S 100 " --> pdb=" O HIS S 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE S 35 " --> pdb=" O ARG S 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU S 102 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL S 37 " --> pdb=" O LEU S 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL S 104 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE S 39 " --> pdb=" O VAL S 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN S 106 " --> pdb=" O ILE S 39 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'U' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS U 33 " --> pdb=" O SER U 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG U 100 " --> pdb=" O HIS U 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE U 35 " --> pdb=" O ARG U 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU U 102 " --> pdb=" O ILE U 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL U 37 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL U 104 " --> pdb=" O VAL U 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE U 39 " --> pdb=" O VAL U 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN U 106 " --> pdb=" O ILE U 39 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'W' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS W 33 " --> pdb=" O SER W 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG W 100 " --> pdb=" O HIS W 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE W 35 " --> pdb=" O ARG W 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU W 102 " --> pdb=" O ILE W 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL W 37 " --> pdb=" O LEU W 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL W 104 " --> pdb=" O VAL W 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE W 39 " --> pdb=" O VAL W 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN W 106 " --> pdb=" O ILE W 39 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'Y' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS Y 33 " --> pdb=" O SER Y 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG Y 100 " --> pdb=" O HIS Y 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE Y 35 " --> pdb=" O ARG Y 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU Y 102 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL Y 37 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL Y 104 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE Y 39 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN Y 106 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain '0' and resid 33 through 40 removed outlier: 5.818A pdb=" N HIS 0 33 " --> pdb=" O SER 0 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG 0 100 " --> pdb=" O HIS 0 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE 0 35 " --> pdb=" O ARG 0 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU 0 102 " --> pdb=" O ILE 0 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL 0 37 " --> pdb=" O LEU 0 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL 0 104 " --> pdb=" O VAL 0 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN 0 106 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain '2' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS 2 33 " --> pdb=" O SER 2 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG 2 100 " --> pdb=" O HIS 2 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE 2 35 " --> pdb=" O ARG 2 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU 2 102 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL 2 37 " --> pdb=" O LEU 2 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL 2 104 " --> pdb=" O VAL 2 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE 2 39 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN 2 106 " --> pdb=" O ILE 2 39 " (cutoff:3.500A) 1725 hydrogen bonds defined for protein. 4995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 9.40 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13738 1.33 - 1.45: 8354 1.45 - 1.57: 25083 1.57 - 1.69: 150 1.69 - 1.81: 345 Bond restraints: 47670 Sorted by residual: bond pdb=" CB PRO A 311 " pdb=" CG PRO A 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO L 311 " pdb=" CG PRO L 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO 0 311 " pdb=" CG PRO 0 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.73e+00 bond pdb=" CB PRO H 311 " pdb=" CG PRO H 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.73e+00 bond pdb=" CB PRO F 311 " pdb=" CG PRO F 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.73e+00 ... (remaining 47665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 62001 2.50 - 5.00: 2570 5.00 - 7.50: 199 7.50 - 9.99: 46 9.99 - 12.49: 44 Bond angle restraints: 64860 Sorted by residual: angle pdb=" C ASN 2 61 " pdb=" N PRO 2 62 " pdb=" CA PRO 2 62 " ideal model delta sigma weight residual 119.28 129.33 -10.05 1.10e+00 8.26e-01 8.35e+01 angle pdb=" C ASN H 61 " pdb=" N PRO H 62 " pdb=" CA PRO H 62 " ideal model delta sigma weight residual 119.28 129.33 -10.05 1.10e+00 8.26e-01 8.34e+01 angle pdb=" C ASN U 61 " pdb=" N PRO U 62 " pdb=" CA PRO U 62 " ideal model delta sigma weight residual 119.28 129.32 -10.04 1.10e+00 8.26e-01 8.32e+01 angle pdb=" C ASN N 61 " pdb=" N PRO N 62 " pdb=" CA PRO N 62 " ideal model delta sigma weight residual 119.28 129.31 -10.03 1.10e+00 8.26e-01 8.32e+01 angle pdb=" C ASN S 61 " pdb=" N PRO S 62 " pdb=" CA PRO S 62 " ideal model delta sigma weight residual 119.28 129.31 -10.03 1.10e+00 8.26e-01 8.32e+01 ... (remaining 64855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.29: 25815 14.29 - 28.58: 1950 28.58 - 42.87: 570 42.87 - 57.16: 195 57.16 - 71.45: 90 Dihedral angle restraints: 28620 sinusoidal: 12270 harmonic: 16350 Sorted by residual: dihedral pdb=" C4' A V 2 " pdb=" C3' A V 2 " pdb=" C2' A V 2 " pdb=" C1' A V 2 " ideal model delta sinusoidal sigma weight residual 36.34 -35.11 71.45 1 3.10e+00 1.04e-01 6.81e+02 dihedral pdb=" C4' A G 2 " pdb=" C3' A G 2 " pdb=" C2' A G 2 " pdb=" C1' A G 2 " ideal model delta sinusoidal sigma weight residual 36.35 -35.08 71.43 1 3.10e+00 1.04e-01 6.81e+02 dihedral pdb=" C4' A T 2 " pdb=" C3' A T 2 " pdb=" C2' A T 2 " pdb=" C1' A T 2 " ideal model delta sinusoidal sigma weight residual 36.35 -35.08 71.42 1 3.10e+00 1.04e-01 6.81e+02 ... (remaining 28617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4976 0.055 - 0.110: 1894 0.110 - 0.166: 417 0.166 - 0.221: 123 0.221 - 0.276: 60 Chirality restraints: 7470 Sorted by residual: chirality pdb=" CB VAL J 314 " pdb=" CA VAL J 314 " pdb=" CG1 VAL J 314 " pdb=" CG2 VAL J 314 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' A Q 2 " pdb=" C3' A Q 2 " pdb=" O2' A Q 2 " pdb=" C1' A Q 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL 2 314 " pdb=" CA VAL 2 314 " pdb=" CG1 VAL 2 314 " pdb=" CG2 VAL 2 314 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 7467 not shown) Planarity restraints: 7980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS N 375 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C LYS N 375 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS N 375 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL N 376 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 375 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C LYS L 375 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS L 375 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL L 376 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS U 375 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C LYS U 375 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS U 375 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL U 376 " 0.014 2.00e-02 2.50e+03 ... (remaining 7977 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 1202 2.66 - 3.22: 44778 3.22 - 3.78: 74048 3.78 - 4.34: 105750 4.34 - 4.90: 169818 Nonbonded interactions: 395596 Sorted by model distance: nonbonded pdb=" CA GLY D 26 " pdb=" ND2 ASN 2 345 " model vdw 2.105 2.816 nonbonded pdb=" CA GLY A 26 " pdb=" ND2 ASN 0 345 " model vdw 2.106 2.816 nonbonded pdb=" OD2 ASP L 358 " pdb=" CD2 TYR L 361 " model vdw 2.143 3.340 nonbonded pdb=" OD2 ASP S 358 " pdb=" CD2 TYR S 361 " model vdw 2.143 3.340 nonbonded pdb=" OD2 ASP A 358 " pdb=" CD2 TYR A 361 " model vdw 2.143 3.340 ... (remaining 395591 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: 0.15 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain '0' selection = chain '2' } ncs_group { reference = chain 'R' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain '1' selection = chain '3' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.910 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 39.250 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 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 0.451 47672 Z= 0.513 Angle : 1.160 12.492 64860 Z= 0.664 Chirality : 0.065 0.276 7470 Planarity : 0.007 0.049 7980 Dihedral : 12.451 71.454 18090 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.54 % Allowed : 3.40 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.09), residues: 5625 helix: -3.84 (0.05), residues: 3150 sheet: -0.57 (0.25), residues: 375 loop : -1.25 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 370 TYR 0.024 0.004 TYR 2 281 PHE 0.028 0.004 PHE N 352 TRP 0.028 0.004 TRP U 146 HIS 0.008 0.004 HIS P 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00987 / 0.42 (47670) covalent geometry : angle 1.16021 / 0.66 (64860) hydrogen bonds : bond 0.30023 / 19.45 ( 1725) hydrogen bonds : angle 9.62806 / 6.57 ( 4995) Misc. bond : bond 0.45077 / 22.63 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1580 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 1505 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9027 (pp) cc_final: 0.8811 (pp) REVERT: B 53 ASP cc_start: 0.8114 (t0) cc_final: 0.7714 (t0) REVERT: B 239 ASP cc_start: 0.7647 (t0) cc_final: 0.7391 (t0) REVERT: B 263 GLU cc_start: 0.7840 (mp0) cc_final: 0.7300 (mp0) REVERT: B 288 GLU cc_start: 0.7861 (mp0) cc_final: 0.7454 (mp0) REVERT: B 318 ASN cc_start: 0.8503 (t0) cc_final: 0.8231 (t0) REVERT: A 6 ARG cc_start: 0.7734 (ttp-110) cc_final: 0.7084 (mtm110) REVERT: A 217 ASP cc_start: 0.7725 (m-30) cc_final: 0.7317 (m-30) REVERT: A 288 GLU cc_start: 0.7662 (mp0) cc_final: 0.7361 (mp0) REVERT: A 318 ASN cc_start: 0.8462 (t0) cc_final: 0.8141 (t0) REVERT: A 323 LYS cc_start: 0.9024 (ttmp) cc_final: 0.8784 (ttmm) REVERT: A 358 ASP cc_start: 0.8324 (t70) cc_final: 0.8068 (t70) REVERT: D 61 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7449 (p0) REVERT: D 103 GLU cc_start: 0.8031 (mp0) cc_final: 0.7570 (mp0) REVERT: D 213 ARG cc_start: 0.6964 (mtm110) cc_final: 0.6758 (ttp-110) REVERT: D 217 ASP cc_start: 0.7596 (m-30) cc_final: 0.6978 (m-30) REVERT: D 221 ASN cc_start: 0.8385 (m110) cc_final: 0.8122 (m110) REVERT: D 239 ASP cc_start: 0.7823 (t0) cc_final: 0.7535 (t0) REVERT: D 288 GLU cc_start: 0.7685 (mp0) cc_final: 0.7309 (mp0) REVERT: D 318 ASN cc_start: 0.8582 (t0) cc_final: 0.8325 (t0) REVERT: F 86 GLN cc_start: 0.8578 (mt0) cc_final: 0.8338 (mt0) REVERT: F 213 ARG cc_start: 0.7121 (mtm110) cc_final: 0.6920 (ttp-110) REVERT: F 217 ASP cc_start: 0.7774 (m-30) cc_final: 0.7204 (m-30) REVERT: F 239 ASP cc_start: 0.7834 (t0) cc_final: 0.7584 (t0) REVERT: F 263 GLU cc_start: 0.8014 (mp0) cc_final: 0.7487 (mp0) REVERT: F 306 MET cc_start: 0.7966 (mtp) cc_final: 0.7766 (mtp) REVERT: F 318 ASN cc_start: 0.8653 (t0) cc_final: 0.8356 (t0) REVERT: F 358 ASP cc_start: 0.8203 (t70) cc_final: 0.7928 (t70) REVERT: H 7 SER cc_start: 0.9316 (t) cc_final: 0.9041 (t) REVERT: H 209 PHE cc_start: 0.8943 (m-80) cc_final: 0.8706 (m-80) REVERT: H 217 ASP cc_start: 0.7667 (m-30) cc_final: 0.7188 (m-30) REVERT: H 221 ASN cc_start: 0.8475 (m110) cc_final: 0.8263 (m110) REVERT: H 239 ASP cc_start: 0.7645 (t0) cc_final: 0.7281 (t0) REVERT: H 263 GLU cc_start: 0.7945 (mp0) cc_final: 0.7566 (mp0) REVERT: H 288 GLU cc_start: 0.7781 (mp0) cc_final: 0.7493 (mp0) REVERT: H 318 ASN cc_start: 0.8565 (t0) cc_final: 0.8275 (t0) REVERT: J 217 ASP cc_start: 0.7616 (m-30) cc_final: 0.7061 (m-30) REVERT: J 221 ASN cc_start: 0.8436 (m110) cc_final: 0.7976 (m110) REVERT: J 239 ASP cc_start: 0.7666 (t0) cc_final: 0.7360 (t0) REVERT: J 263 GLU cc_start: 0.7906 (mp0) cc_final: 0.7574 (mp0) REVERT: J 288 GLU cc_start: 0.7746 (mp0) cc_final: 0.7449 (mp0) REVERT: J 318 ASN cc_start: 0.8476 (t0) cc_final: 0.8100 (t0) REVERT: J 375 LYS cc_start: 0.8056 (ttmp) cc_final: 0.7728 (mptt) REVERT: L 100 ARG cc_start: 0.8246 (ppp80) cc_final: 0.8016 (ptt90) REVERT: L 109 GLN cc_start: 0.7976 (pt0) cc_final: 0.7606 (mm-40) REVERT: L 239 ASP cc_start: 0.7846 (t0) cc_final: 0.7545 (t0) REVERT: L 263 GLU cc_start: 0.7946 (mp0) cc_final: 0.7571 (mp0) REVERT: L 318 ASN cc_start: 0.8465 (t0) cc_final: 0.8205 (t0) REVERT: N 318 ASN cc_start: 0.8420 (t0) cc_final: 0.8211 (t0) REVERT: N 361 TYR cc_start: 0.8367 (m-80) cc_final: 0.8164 (m-80) REVERT: P 32 LYS cc_start: 0.8118 (mttm) cc_final: 0.7874 (mmtt) REVERT: P 86 GLN cc_start: 0.8665 (mt0) cc_final: 0.8438 (mt0) REVERT: P 150 LYS cc_start: 0.8251 (mppt) cc_final: 0.8044 (mppt) REVERT: P 217 ASP cc_start: 0.7660 (m-30) cc_final: 0.7150 (m-30) REVERT: P 239 ASP cc_start: 0.7741 (t0) cc_final: 0.7337 (t0) REVERT: P 263 GLU cc_start: 0.7916 (mp0) cc_final: 0.7539 (mp0) REVERT: P 288 GLU cc_start: 0.7782 (mp0) cc_final: 0.7410 (mp0) REVERT: P 318 ASN cc_start: 0.8392 (t0) cc_final: 0.8075 (t0) REVERT: S 126 GLU cc_start: 0.7550 (tt0) cc_final: 0.7331 (tt0) REVERT: S 150 LYS cc_start: 0.8432 (mppt) cc_final: 0.8215 (mppt) REVERT: S 221 ASN cc_start: 0.8353 (m110) cc_final: 0.8119 (m110) REVERT: S 239 ASP cc_start: 0.7743 (t0) cc_final: 0.7498 (t0) REVERT: S 280 MET cc_start: 0.7702 (mtm) cc_final: 0.7404 (mpp) REVERT: S 318 ASN cc_start: 0.8423 (t0) cc_final: 0.8110 (t0) REVERT: U 164 ASN cc_start: 0.8608 (t0) cc_final: 0.8031 (t0) REVERT: U 239 ASP cc_start: 0.7840 (t0) cc_final: 0.7552 (t0) REVERT: U 288 GLU cc_start: 0.7716 (mp0) cc_final: 0.7327 (mp0) REVERT: U 318 ASN cc_start: 0.8433 (t0) cc_final: 0.8140 (t0) REVERT: W 32 LYS cc_start: 0.8228 (mttm) cc_final: 0.8026 (mmtt) REVERT: W 144 PHE cc_start: 0.7924 (m-80) cc_final: 0.7683 (m-10) REVERT: W 150 LYS cc_start: 0.8726 (mppt) cc_final: 0.8389 (mppt) REVERT: W 217 ASP cc_start: 0.7726 (m-30) cc_final: 0.7144 (m-30) REVERT: W 221 ASN cc_start: 0.8308 (m110) cc_final: 0.7942 (m110) REVERT: W 239 ASP cc_start: 0.7741 (t0) cc_final: 0.7530 (t0) REVERT: W 288 GLU cc_start: 0.7767 (mp0) cc_final: 0.7544 (mp0) REVERT: Y 86 GLN cc_start: 0.8744 (mt0) cc_final: 0.8474 (mt0) REVERT: Y 129 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7886 (tm-30) REVERT: Y 164 ASN cc_start: 0.8650 (t0) cc_final: 0.8400 (t0) REVERT: Y 239 ASP cc_start: 0.7793 (t0) cc_final: 0.7521 (t0) REVERT: Y 260 TYR cc_start: 0.9069 (m-80) cc_final: 0.8811 (m-80) REVERT: Y 263 GLU cc_start: 0.7929 (mp0) cc_final: 0.7610 (mp0) REVERT: Y 288 GLU cc_start: 0.7778 (mp0) cc_final: 0.7439 (mp0) REVERT: Y 318 ASN cc_start: 0.8416 (t0) cc_final: 0.8188 (t0) REVERT: Y 361 TYR cc_start: 0.8266 (m-80) cc_final: 0.7750 (m-80) REVERT: 0 7 SER cc_start: 0.9394 (t) cc_final: 0.9088 (m) REVERT: 0 53 ASP cc_start: 0.8186 (t0) cc_final: 0.7915 (t0) REVERT: 0 239 ASP cc_start: 0.7655 (t0) cc_final: 0.7361 (t0) REVERT: 0 263 GLU cc_start: 0.7818 (mp0) cc_final: 0.7445 (mp0) REVERT: 0 288 GLU cc_start: 0.7645 (mp0) cc_final: 0.7236 (mp0) REVERT: 0 318 ASN cc_start: 0.8452 (t0) cc_final: 0.8098 (t0) REVERT: 2 86 GLN cc_start: 0.8731 (mt0) cc_final: 0.8479 (mt0) REVERT: 2 115 THR cc_start: 0.8555 (p) cc_final: 0.8266 (t) REVERT: 2 144 PHE cc_start: 0.8043 (m-80) cc_final: 0.7771 (m-80) REVERT: 2 217 ASP cc_start: 0.7516 (m-30) cc_final: 0.7235 (m-30) REVERT: 2 239 ASP cc_start: 0.7703 (t0) cc_final: 0.7356 (t0) REVERT: 2 288 GLU cc_start: 0.7705 (mp0) cc_final: 0.7211 (mp0) REVERT: 2 318 ASN cc_start: 0.8405 (t0) cc_final: 0.8011 (t0) REVERT: 2 361 TYR cc_start: 0.8284 (m-80) cc_final: 0.8010 (m-80) outliers start: 75 outliers final: 18 residues processed: 1553 average time/residue: 0.3075 time to fit residues: 771.2429 Evaluate side-chains 1189 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 1170 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain S residue 236 LEU Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 236 LEU Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain 0 residue 236 LEU Chi-restraints excluded: chain 2 residue 236 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 ASN B 322 ASN B 351 ASN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN A 322 ASN A 351 ASN D 61 ASN D 149 ASN D 221 ASN D 305 GLN D 322 ASN D 351 ASN F 305 GLN F 322 ASN F 351 ASN ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN H 351 ASN J 149 ASN ** J 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 ASN L 221 ASN L 322 ASN L 351 ASN N 221 ASN N 322 ASN N 351 ASN P 221 ASN P 322 ASN P 351 ASN S 322 ASN S 351 ASN U 149 ASN U 221 ASN U 322 ASN U 351 ASN W 221 ASN W 305 GLN W 322 ASN W 351 ASN Y 221 ASN Y 322 ASN Y 351 ASN 0 221 ASN 0 322 ASN 0 351 ASN 2 351 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.116991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.096182 restraints weight = 64682.603| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.98 r_work: 0.2836 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 47672 Z= 0.167 Angle : 0.741 9.936 64860 Z= 0.366 Chirality : 0.050 0.320 7470 Planarity : 0.005 0.033 7980 Dihedral : 11.840 129.523 7283 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.63 % Allowed : 9.22 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.10), residues: 5625 helix: -2.15 (0.08), residues: 3165 sheet: 0.23 (0.28), residues: 375 loop : -0.70 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 48 TYR 0.014 0.002 TYR U 361 PHE 0.014 0.002 PHE D 80 TRP 0.012 0.002 TRP L 146 HIS 0.007 0.002 HIS L 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (47670) covalent geometry : angle 0.74055 / 0.37 (64860) hydrogen bonds : bond 0.05617 / 3.69 ( 1725) hydrogen bonds : angle 4.85463 / 3.28 ( 4995) Misc. bond : bond 0.00267 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1244 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8171 (ttmm) REVERT: B 34 ILE cc_start: 0.8977 (pp) cc_final: 0.8693 (pp) REVERT: B 53 ASP cc_start: 0.8862 (t0) cc_final: 0.8539 (t0) REVERT: B 213 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7309 (ttp80) REVERT: B 217 ASP cc_start: 0.7964 (m-30) cc_final: 0.7516 (m-30) REVERT: B 239 ASP cc_start: 0.8794 (t0) cc_final: 0.8508 (t0) REVERT: B 280 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8436 (mmm) REVERT: B 288 GLU cc_start: 0.8303 (mp0) cc_final: 0.7847 (mp0) REVERT: B 318 ASN cc_start: 0.8713 (t0) cc_final: 0.8401 (t0) REVERT: B 344 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8097 (mm-30) REVERT: B 356 TYR cc_start: 0.9558 (p90) cc_final: 0.9193 (p90) REVERT: A 123 MET cc_start: 0.5936 (mmm) cc_final: 0.5529 (mmm) REVERT: A 213 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7292 (ttp-110) REVERT: A 217 ASP cc_start: 0.8091 (m-30) cc_final: 0.7667 (m-30) REVERT: A 225 GLU cc_start: 0.8280 (tp30) cc_final: 0.7907 (mm-30) REVERT: A 288 GLU cc_start: 0.8310 (mp0) cc_final: 0.7864 (mp0) REVERT: A 318 ASN cc_start: 0.8644 (t0) cc_final: 0.8371 (t0) REVERT: D 103 GLU cc_start: 0.8384 (mp0) cc_final: 0.8061 (mp0) REVERT: D 213 ARG cc_start: 0.7710 (mtm110) cc_final: 0.7464 (ttp-110) REVERT: D 217 ASP cc_start: 0.7807 (m-30) cc_final: 0.7440 (m-30) REVERT: D 226 ASP cc_start: 0.8176 (p0) cc_final: 0.7726 (p0) REVERT: D 280 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8511 (mpp) REVERT: D 288 GLU cc_start: 0.8288 (mp0) cc_final: 0.7862 (mp0) REVERT: F 12 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8259 (mttt) REVERT: F 53 ASP cc_start: 0.8786 (t0) cc_final: 0.8519 (t0) REVERT: F 213 ARG cc_start: 0.7840 (mtm110) cc_final: 0.7427 (ttp-110) REVERT: F 217 ASP cc_start: 0.8017 (m-30) cc_final: 0.7418 (m-30) REVERT: F 239 ASP cc_start: 0.8772 (t0) cc_final: 0.8398 (t0) REVERT: F 263 GLU cc_start: 0.8298 (mp0) cc_final: 0.7877 (mp0) REVERT: F 318 ASN cc_start: 0.8758 (t0) cc_final: 0.8458 (t0) REVERT: H 7 SER cc_start: 0.9199 (t) cc_final: 0.8910 (p) REVERT: H 53 ASP cc_start: 0.8823 (t0) cc_final: 0.8553 (t0) REVERT: H 213 ARG cc_start: 0.8293 (ttm110) cc_final: 0.7750 (ttp-110) REVERT: H 239 ASP cc_start: 0.8681 (t0) cc_final: 0.8212 (t0) REVERT: H 288 GLU cc_start: 0.8264 (mp0) cc_final: 0.7950 (mp0) REVERT: H 318 ASN cc_start: 0.8648 (t0) cc_final: 0.8392 (t0) REVERT: J 42 ASP cc_start: 0.7964 (p0) cc_final: 0.7470 (t0) REVERT: J 53 ASP cc_start: 0.8720 (t0) cc_final: 0.8484 (t0) REVERT: J 103 GLU cc_start: 0.8338 (mp0) cc_final: 0.8098 (mp0) REVERT: J 148 GLU cc_start: 0.7882 (pt0) cc_final: 0.7636 (mt-10) REVERT: J 213 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7648 (ttp-110) REVERT: J 217 ASP cc_start: 0.7901 (m-30) cc_final: 0.7299 (m-30) REVERT: J 221 ASN cc_start: 0.8770 (m110) cc_final: 0.8373 (m110) REVERT: J 239 ASP cc_start: 0.8633 (t0) cc_final: 0.8366 (t0) REVERT: J 255 CYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8386 (t) REVERT: J 263 GLU cc_start: 0.8211 (mp0) cc_final: 0.7768 (mp0) REVERT: J 280 MET cc_start: 0.8856 (mtm) cc_final: 0.8632 (mpp) REVERT: J 288 GLU cc_start: 0.8332 (mp0) cc_final: 0.7977 (mp0) REVERT: J 313 MET cc_start: 0.8986 (ptp) cc_final: 0.8657 (ptp) REVERT: J 318 ASN cc_start: 0.8678 (t0) cc_final: 0.8305 (t0) REVERT: J 375 LYS cc_start: 0.8279 (ttmp) cc_final: 0.7867 (mptt) REVERT: L 29 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.7764 (mtm-85) REVERT: L 213 ARG cc_start: 0.8319 (ttp-110) cc_final: 0.7535 (ttp-110) REVERT: L 217 ASP cc_start: 0.7994 (m-30) cc_final: 0.7517 (m-30) REVERT: L 239 ASP cc_start: 0.8882 (t0) cc_final: 0.8617 (t0) REVERT: L 318 ASN cc_start: 0.8704 (t0) cc_final: 0.8479 (t0) REVERT: N 53 ASP cc_start: 0.8798 (t70) cc_final: 0.8591 (t0) REVERT: N 82 GLU cc_start: 0.8134 (tp30) cc_final: 0.7905 (tt0) REVERT: N 217 ASP cc_start: 0.8143 (m-30) cc_final: 0.7773 (m-30) REVERT: N 239 ASP cc_start: 0.8770 (t0) cc_final: 0.8320 (t0) REVERT: N 263 GLU cc_start: 0.8243 (mp0) cc_final: 0.7880 (mp0) REVERT: N 280 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8402 (mmm) REVERT: P 32 LYS cc_start: 0.8228 (mttm) cc_final: 0.7974 (mmtt) REVERT: P 53 ASP cc_start: 0.8796 (t0) cc_final: 0.8590 (t0) REVERT: P 217 ASP cc_start: 0.7915 (m-30) cc_final: 0.7656 (m-30) REVERT: P 239 ASP cc_start: 0.8692 (t0) cc_final: 0.8262 (t0) REVERT: P 263 GLU cc_start: 0.8335 (mp0) cc_final: 0.7809 (mp0) REVERT: P 318 ASN cc_start: 0.8565 (t0) cc_final: 0.8219 (t0) REVERT: S 7 SER cc_start: 0.9221 (t) cc_final: 0.8865 (m) REVERT: S 54 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8718 (mpt180) REVERT: S 103 GLU cc_start: 0.8257 (mp0) cc_final: 0.7998 (mp0) REVERT: S 209 PHE cc_start: 0.8927 (m-80) cc_final: 0.8714 (m-10) REVERT: S 213 ARG cc_start: 0.8443 (ttm110) cc_final: 0.7564 (ttp-110) REVERT: S 217 ASP cc_start: 0.8082 (m-30) cc_final: 0.7594 (m-30) REVERT: S 239 ASP cc_start: 0.8760 (t0) cc_final: 0.8464 (t0) REVERT: S 280 MET cc_start: 0.8634 (mtm) cc_final: 0.8301 (mmm) REVERT: S 318 ASN cc_start: 0.8637 (t0) cc_final: 0.8219 (t0) REVERT: U 144 PHE cc_start: 0.8294 (m-10) cc_final: 0.7994 (m-10) REVERT: U 213 ARG cc_start: 0.8291 (ttp-110) cc_final: 0.7379 (ttp80) REVERT: U 217 ASP cc_start: 0.7953 (m-30) cc_final: 0.7539 (m-30) REVERT: U 239 ASP cc_start: 0.8757 (t0) cc_final: 0.8510 (t0) REVERT: U 280 MET cc_start: 0.8914 (tpp) cc_final: 0.8598 (tpp) REVERT: U 288 GLU cc_start: 0.8294 (mp0) cc_final: 0.7874 (mp0) REVERT: U 318 ASN cc_start: 0.8555 (t0) cc_final: 0.8326 (t0) REVERT: W 150 LYS cc_start: 0.8729 (mppt) cc_final: 0.8454 (mppt) REVERT: W 217 ASP cc_start: 0.8102 (m-30) cc_final: 0.7467 (m-30) REVERT: W 221 ASN cc_start: 0.8769 (m-40) cc_final: 0.8475 (m110) REVERT: W 239 ASP cc_start: 0.8778 (t0) cc_final: 0.8464 (t0) REVERT: W 280 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8238 (mpp) REVERT: W 288 GLU cc_start: 0.8335 (mp0) cc_final: 0.8000 (mp0) REVERT: Y 7 SER cc_start: 0.9227 (t) cc_final: 0.8906 (m) REVERT: Y 20 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8725 (pp) REVERT: Y 53 ASP cc_start: 0.8789 (t0) cc_final: 0.8552 (t0) REVERT: Y 86 GLN cc_start: 0.8904 (mt0) cc_final: 0.8598 (mt0) REVERT: Y 89 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8677 (mm-40) REVERT: Y 213 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7401 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8126 (m-30) cc_final: 0.7697 (m-30) REVERT: Y 239 ASP cc_start: 0.8833 (t0) cc_final: 0.8526 (t0) REVERT: Y 263 GLU cc_start: 0.8254 (mp0) cc_final: 0.7703 (mp0) REVERT: Y 280 MET cc_start: 0.8527 (mpp) cc_final: 0.8255 (mmm) REVERT: Y 288 GLU cc_start: 0.8336 (mp0) cc_final: 0.7825 (mp0) REVERT: Y 292 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8160 (mt-10) REVERT: Y 318 ASN cc_start: 0.8532 (t0) cc_final: 0.8316 (t0) REVERT: 0 7 SER cc_start: 0.9183 (t) cc_final: 0.8959 (m) REVERT: 0 15 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8456 (ttmm) REVERT: 0 89 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8852 (mm-40) REVERT: 0 217 ASP cc_start: 0.8030 (m-30) cc_final: 0.7588 (m-30) REVERT: 0 226 ASP cc_start: 0.8343 (p0) cc_final: 0.8104 (p0) REVERT: 0 239 ASP cc_start: 0.8696 (t0) cc_final: 0.8380 (t0) REVERT: 0 288 GLU cc_start: 0.8175 (mp0) cc_final: 0.7811 (mp0) REVERT: 0 318 ASN cc_start: 0.8595 (t0) cc_final: 0.8143 (t0) REVERT: 2 29 ARG cc_start: 0.8125 (mtm110) cc_final: 0.7854 (mtm110) REVERT: 2 115 THR cc_start: 0.8841 (p) cc_final: 0.8543 (t) REVERT: 2 213 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7669 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7915 (m-30) cc_final: 0.7667 (m-30) REVERT: 2 239 ASP cc_start: 0.8738 (t0) cc_final: 0.8421 (t0) REVERT: 2 280 MET cc_start: 0.8853 (tpp) cc_final: 0.8550 (mmm) REVERT: 2 288 GLU cc_start: 0.8376 (mp0) cc_final: 0.7908 (mp0) REVERT: 2 318 ASN cc_start: 0.8648 (t0) cc_final: 0.8245 (t0) outliers start: 128 outliers final: 79 residues processed: 1329 average time/residue: 0.2776 time to fit residues: 612.7819 Evaluate side-chains 1155 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 1069 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 255 CYS Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 280 MET Chi-restraints excluded: chain N residue 288 GLU Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain S residue 44 SER Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 236 LEU Chi-restraints excluded: chain S residue 255 CYS Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 193 LEU Chi-restraints excluded: chain U residue 236 LEU Chi-restraints excluded: chain U residue 255 CYS Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 280 MET Chi-restraints excluded: chain Y residue 20 ILE Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 45 ILE Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 236 LEU Chi-restraints excluded: chain 0 residue 255 CYS Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 149 ASN Chi-restraints excluded: chain 2 residue 190 ASP Chi-restraints excluded: chain 2 residue 213 ARG Chi-restraints excluded: chain 2 residue 236 LEU Chi-restraints excluded: chain 2 residue 255 CYS Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 395 optimal weight: 0.0870 chunk 530 optimal weight: 6.9990 chunk 548 optimal weight: 0.9990 chunk 297 optimal weight: 2.9990 chunk 544 optimal weight: 0.6980 chunk 429 optimal weight: 6.9990 chunk 375 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 33 HIS H 164 ASN J 164 ASN Y 305 GLN 2 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.097643 restraints weight = 64292.509| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.96 r_work: 0.2858 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 47672 Z= 0.123 Angle : 0.624 9.133 64860 Z= 0.310 Chirality : 0.046 0.244 7470 Planarity : 0.004 0.050 7980 Dihedral : 10.731 137.075 7279 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.20 % Allowed : 12.14 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.11), residues: 5625 helix: -1.03 (0.09), residues: 3165 sheet: 0.33 (0.27), residues: 375 loop : -0.44 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 203 TYR 0.013 0.001 TYR W 260 PHE 0.017 0.002 PHE F 275 TRP 0.007 0.001 TRP L 215 HIS 0.003 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (47670) covalent geometry : angle 0.62407 / 0.31 (64860) hydrogen bonds : bond 0.03907 / 2.58 ( 1725) hydrogen bonds : angle 4.15769 / 2.80 ( 4995) Misc. bond : bond 0.00181 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1192 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8639 (pp) REVERT: B 53 ASP cc_start: 0.8944 (t0) cc_final: 0.8659 (t0) REVERT: B 129 GLN cc_start: 0.8443 (mt0) cc_final: 0.8133 (tm-30) REVERT: B 209 PHE cc_start: 0.8891 (m-80) cc_final: 0.8590 (m-10) REVERT: B 213 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7404 (ttp80) REVERT: B 217 ASP cc_start: 0.7939 (m-30) cc_final: 0.7474 (m-30) REVERT: B 239 ASP cc_start: 0.8765 (t0) cc_final: 0.8473 (t0) REVERT: B 280 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8336 (mmm) REVERT: B 288 GLU cc_start: 0.8323 (mp0) cc_final: 0.7921 (mp0) REVERT: B 318 ASN cc_start: 0.8693 (t0) cc_final: 0.8366 (t0) REVERT: A 103 GLU cc_start: 0.8390 (mp0) cc_final: 0.7928 (mp0) REVERT: A 115 THR cc_start: 0.8910 (p) cc_final: 0.8612 (t) REVERT: A 123 MET cc_start: 0.6128 (mmm) cc_final: 0.5826 (mmm) REVERT: A 164 ASN cc_start: 0.8706 (t0) cc_final: 0.8289 (t0) REVERT: A 213 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7604 (ttp-110) REVERT: A 217 ASP cc_start: 0.7933 (m-30) cc_final: 0.7413 (m-30) REVERT: A 225 GLU cc_start: 0.8241 (tp30) cc_final: 0.7918 (mm-30) REVERT: A 236 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8727 (tp) REVERT: A 280 MET cc_start: 0.8905 (mtm) cc_final: 0.8666 (mpp) REVERT: A 288 GLU cc_start: 0.8301 (mp0) cc_final: 0.7960 (mp0) REVERT: A 318 ASN cc_start: 0.8550 (t0) cc_final: 0.8301 (t0) REVERT: A 342 GLU cc_start: 0.7394 (mp0) cc_final: 0.7074 (mp0) REVERT: D 12 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8350 (mmtt) REVERT: D 103 GLU cc_start: 0.8424 (mp0) cc_final: 0.8074 (mp0) REVERT: D 123 MET cc_start: 0.5274 (mmt) cc_final: 0.4724 (mmm) REVERT: D 213 ARG cc_start: 0.7750 (mtm110) cc_final: 0.7523 (ttp-110) REVERT: D 217 ASP cc_start: 0.7836 (m-30) cc_final: 0.7441 (m-30) REVERT: D 225 GLU cc_start: 0.8086 (tp30) cc_final: 0.7703 (mm-30) REVERT: D 239 ASP cc_start: 0.8808 (t0) cc_final: 0.8414 (t0) REVERT: D 280 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8334 (mmt) REVERT: D 288 GLU cc_start: 0.8263 (mp0) cc_final: 0.7964 (mp0) REVERT: D 342 GLU cc_start: 0.7264 (mp0) cc_final: 0.6929 (mp0) REVERT: F 12 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8325 (mttt) REVERT: F 213 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7477 (ttp-110) REVERT: F 217 ASP cc_start: 0.7941 (m-30) cc_final: 0.7334 (m-30) REVERT: F 239 ASP cc_start: 0.8649 (t0) cc_final: 0.8255 (t0) REVERT: H 53 ASP cc_start: 0.8803 (t0) cc_final: 0.8445 (t0) REVERT: H 213 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7750 (ttp-110) REVERT: H 239 ASP cc_start: 0.8663 (t0) cc_final: 0.8265 (t0) REVERT: H 280 MET cc_start: 0.8585 (mpp) cc_final: 0.8361 (mmm) REVERT: H 288 GLU cc_start: 0.8236 (mp0) cc_final: 0.7959 (mp0) REVERT: J 42 ASP cc_start: 0.7999 (p0) cc_final: 0.7505 (t70) REVERT: J 53 ASP cc_start: 0.8725 (t0) cc_final: 0.8504 (t0) REVERT: J 213 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7528 (ttp-110) REVERT: J 217 ASP cc_start: 0.7812 (m-30) cc_final: 0.7373 (m-30) REVERT: J 239 ASP cc_start: 0.8604 (t0) cc_final: 0.8315 (t0) REVERT: J 255 CYS cc_start: 0.8856 (t) cc_final: 0.8490 (t) REVERT: J 263 GLU cc_start: 0.8051 (mp0) cc_final: 0.7582 (mp0) REVERT: J 288 GLU cc_start: 0.8383 (mp0) cc_final: 0.8023 (mp0) REVERT: J 318 ASN cc_start: 0.8607 (t0) cc_final: 0.8297 (t0) REVERT: J 344 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7956 (mm-30) REVERT: J 375 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7800 (mptt) REVERT: L 102 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8403 (pp) REVERT: L 103 GLU cc_start: 0.8474 (mp0) cc_final: 0.8103 (mp0) REVERT: L 208 GLU cc_start: 0.7446 (pm20) cc_final: 0.7145 (mp0) REVERT: L 213 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.7648 (ttp-110) REVERT: L 217 ASP cc_start: 0.7960 (m-30) cc_final: 0.7489 (m-30) REVERT: L 225 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7539 (mm-30) REVERT: L 236 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8697 (tp) REVERT: L 239 ASP cc_start: 0.8877 (t0) cc_final: 0.8609 (t0) REVERT: L 318 ASN cc_start: 0.8666 (t0) cc_final: 0.8464 (t0) REVERT: N 29 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.8111 (mtm110) REVERT: N 164 ASN cc_start: 0.8793 (t0) cc_final: 0.8483 (t0) REVERT: N 217 ASP cc_start: 0.8178 (m-30) cc_final: 0.7756 (m-30) REVERT: N 236 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8574 (tp) REVERT: N 239 ASP cc_start: 0.8786 (t0) cc_final: 0.8492 (t0) REVERT: N 263 GLU cc_start: 0.8168 (mp0) cc_final: 0.7874 (mp0) REVERT: N 308 GLU cc_start: 0.8509 (pt0) cc_final: 0.8298 (pt0) REVERT: P 32 LYS cc_start: 0.8253 (mttm) cc_final: 0.7997 (mmtt) REVERT: P 217 ASP cc_start: 0.7968 (m-30) cc_final: 0.7703 (m-30) REVERT: P 239 ASP cc_start: 0.8674 (t0) cc_final: 0.8238 (t0) REVERT: P 288 GLU cc_start: 0.8354 (mp0) cc_final: 0.7902 (mp0) REVERT: P 318 ASN cc_start: 0.8474 (t0) cc_final: 0.8145 (t0) REVERT: P 371 ARG cc_start: 0.8690 (mmt90) cc_final: 0.8475 (mmt90) REVERT: S 103 GLU cc_start: 0.8284 (mp0) cc_final: 0.8076 (mp0) REVERT: S 209 PHE cc_start: 0.8908 (m-80) cc_final: 0.8704 (m-10) REVERT: S 213 ARG cc_start: 0.8468 (ttm110) cc_final: 0.7495 (ttp-110) REVERT: S 217 ASP cc_start: 0.8012 (m-30) cc_final: 0.7584 (m-30) REVERT: S 239 ASP cc_start: 0.8692 (t0) cc_final: 0.8402 (t0) REVERT: S 280 MET cc_start: 0.8550 (mtm) cc_final: 0.8269 (mmm) REVERT: S 318 ASN cc_start: 0.8631 (t0) cc_final: 0.8202 (t0) REVERT: S 371 ARG cc_start: 0.8620 (mmt90) cc_final: 0.8397 (mmt90) REVERT: U 213 ARG cc_start: 0.8253 (ttp-110) cc_final: 0.7385 (ttp80) REVERT: U 217 ASP cc_start: 0.7986 (m-30) cc_final: 0.7527 (m-30) REVERT: U 225 GLU cc_start: 0.8198 (tp30) cc_final: 0.7966 (tp30) REVERT: U 236 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8626 (tp) REVERT: U 239 ASP cc_start: 0.8724 (t0) cc_final: 0.8500 (t0) REVERT: U 280 MET cc_start: 0.8862 (tpp) cc_final: 0.8619 (tpp) REVERT: U 288 GLU cc_start: 0.8305 (mp0) cc_final: 0.7869 (mp0) REVERT: U 318 ASN cc_start: 0.8490 (t0) cc_final: 0.8270 (t0) REVERT: W 86 GLN cc_start: 0.8792 (mt0) cc_final: 0.8569 (mt0) REVERT: W 126 GLU cc_start: 0.7698 (tt0) cc_final: 0.7366 (tt0) REVERT: W 217 ASP cc_start: 0.8049 (m-30) cc_final: 0.7557 (m-30) REVERT: W 236 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8505 (tp) REVERT: W 239 ASP cc_start: 0.8748 (t0) cc_final: 0.8412 (t0) REVERT: W 280 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8102 (mmm) REVERT: W 288 GLU cc_start: 0.8340 (mp0) cc_final: 0.7984 (mp0) REVERT: W 371 ARG cc_start: 0.8744 (mmt90) cc_final: 0.8511 (mmt90) REVERT: Y 86 GLN cc_start: 0.8846 (mt0) cc_final: 0.8555 (mt0) REVERT: Y 89 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8719 (mm-40) REVERT: Y 213 ARG cc_start: 0.8192 (ttp-110) cc_final: 0.7448 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8065 (m-30) cc_final: 0.7664 (m-30) REVERT: Y 239 ASP cc_start: 0.8825 (t0) cc_final: 0.8495 (t0) REVERT: Y 280 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8246 (mmm) REVERT: Y 288 GLU cc_start: 0.8317 (mp0) cc_final: 0.7838 (mp0) REVERT: Y 292 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8110 (mt-10) REVERT: Y 318 ASN cc_start: 0.8538 (t0) cc_final: 0.8292 (t0) REVERT: 0 89 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8859 (mm-40) REVERT: 0 148 GLU cc_start: 0.7939 (pt0) cc_final: 0.7573 (mt-10) REVERT: 0 217 ASP cc_start: 0.8014 (m-30) cc_final: 0.7598 (m-30) REVERT: 0 225 GLU cc_start: 0.8026 (tp30) cc_final: 0.7699 (mm-30) REVERT: 0 239 ASP cc_start: 0.8645 (t0) cc_final: 0.8303 (t0) REVERT: 0 288 GLU cc_start: 0.8198 (mp0) cc_final: 0.7815 (mp0) REVERT: 0 318 ASN cc_start: 0.8513 (t0) cc_final: 0.8077 (t0) REVERT: 2 29 ARG cc_start: 0.8097 (mtm110) cc_final: 0.7846 (mtm110) REVERT: 2 213 ARG cc_start: 0.8255 (mtp-110) cc_final: 0.7726 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7870 (m-30) cc_final: 0.7650 (m-30) REVERT: 2 239 ASP cc_start: 0.8647 (t0) cc_final: 0.8285 (t0) REVERT: 2 263 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7901 (mt-10) REVERT: 2 280 MET cc_start: 0.8842 (tpp) cc_final: 0.8532 (mmm) REVERT: 2 288 GLU cc_start: 0.8332 (mp0) cc_final: 0.7988 (mp0) REVERT: 2 318 ASN cc_start: 0.8530 (t0) cc_final: 0.8169 (t0) outliers start: 107 outliers final: 45 residues processed: 1256 average time/residue: 0.2868 time to fit residues: 594.3214 Evaluate side-chains 1114 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1057 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain S residue 44 SER Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 236 LEU Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 280 MET Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 280 MET Chi-restraints excluded: chain Y residue 304 GLN Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 355 SER Chi-restraints excluded: chain 0 residue 380 LEU Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain 2 residue 149 ASN Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 427 optimal weight: 7.9990 chunk 510 optimal weight: 5.9990 chunk 395 optimal weight: 6.9990 chunk 344 optimal weight: 20.0000 chunk 558 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 227 optimal weight: 20.0000 chunk 122 optimal weight: 0.0170 chunk 39 optimal weight: 0.0970 chunk 553 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN H 164 ASN P 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.096049 restraints weight = 64842.016| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.95 r_work: 0.2833 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 47672 Z= 0.146 Angle : 0.615 9.013 64860 Z= 0.307 Chirality : 0.046 0.278 7470 Planarity : 0.004 0.057 7980 Dihedral : 9.946 134.126 7259 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.47 % Allowed : 13.13 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.11), residues: 5625 helix: -0.35 (0.09), residues: 3195 sheet: 0.37 (0.27), residues: 375 loop : -0.28 (0.15), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 213 TYR 0.014 0.001 TYR W 260 PHE 0.018 0.002 PHE U 209 TRP 0.009 0.001 TRP J 215 HIS 0.003 0.001 HIS 0 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (47670) covalent geometry : angle 0.61453 / 0.31 (64860) hydrogen bonds : bond 0.03645 / 2.41 ( 1725) hydrogen bonds : angle 3.95727 / 2.67 ( 4995) Misc. bond : bond 0.00125 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1108 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8695 (pp) REVERT: B 129 GLN cc_start: 0.8331 (mt0) cc_final: 0.8128 (tm-30) REVERT: B 148 GLU cc_start: 0.7718 (pt0) cc_final: 0.7505 (mt-10) REVERT: B 213 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7430 (ttp80) REVERT: B 217 ASP cc_start: 0.7959 (m-30) cc_final: 0.7511 (m-30) REVERT: B 239 ASP cc_start: 0.8809 (t0) cc_final: 0.8527 (t0) REVERT: B 280 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8370 (mmm) REVERT: B 288 GLU cc_start: 0.8411 (mp0) cc_final: 0.7887 (mp0) REVERT: B 306 MET cc_start: 0.8451 (mtp) cc_final: 0.8145 (mtp) REVERT: B 318 ASN cc_start: 0.8703 (t0) cc_final: 0.8348 (t0) REVERT: A 103 GLU cc_start: 0.8382 (mp0) cc_final: 0.7994 (mp0) REVERT: A 115 THR cc_start: 0.8898 (p) cc_final: 0.8640 (t) REVERT: A 123 MET cc_start: 0.6225 (mmm) cc_final: 0.5624 (mmm) REVERT: A 164 ASN cc_start: 0.8728 (t0) cc_final: 0.8305 (t0) REVERT: A 213 ARG cc_start: 0.8298 (ttp-110) cc_final: 0.7656 (ttp-110) REVERT: A 217 ASP cc_start: 0.7975 (m-30) cc_final: 0.7378 (m-30) REVERT: A 225 GLU cc_start: 0.8286 (tp30) cc_final: 0.7966 (mm-30) REVERT: A 280 MET cc_start: 0.8846 (mtm) cc_final: 0.8592 (mpp) REVERT: A 288 GLU cc_start: 0.8448 (mp0) cc_final: 0.8007 (mp0) REVERT: A 318 ASN cc_start: 0.8569 (t0) cc_final: 0.8310 (t0) REVERT: A 344 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8207 (mm-30) REVERT: D 103 GLU cc_start: 0.8449 (mp0) cc_final: 0.8107 (mp0) REVERT: D 123 MET cc_start: 0.5309 (mmt) cc_final: 0.4795 (mmm) REVERT: D 213 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7459 (ttp-110) REVERT: D 217 ASP cc_start: 0.7899 (m-30) cc_final: 0.7492 (m-30) REVERT: D 225 GLU cc_start: 0.8173 (tp30) cc_final: 0.7868 (mm-30) REVERT: D 239 ASP cc_start: 0.8833 (t0) cc_final: 0.8466 (t0) REVERT: D 280 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8346 (mmt) REVERT: D 288 GLU cc_start: 0.8309 (mp0) cc_final: 0.8032 (mp0) REVERT: F 12 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8304 (mttt) REVERT: F 57 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8112 (mtp180) REVERT: F 213 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7535 (ttp-110) REVERT: F 217 ASP cc_start: 0.7912 (m-30) cc_final: 0.7311 (m-30) REVERT: F 225 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7752 (mm-30) REVERT: F 239 ASP cc_start: 0.8618 (t0) cc_final: 0.8237 (t0) REVERT: H 53 ASP cc_start: 0.8827 (t0) cc_final: 0.8504 (t0) REVERT: H 213 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7767 (ttp-110) REVERT: H 239 ASP cc_start: 0.8600 (t0) cc_final: 0.8224 (t0) REVERT: H 280 MET cc_start: 0.8548 (mpp) cc_final: 0.8335 (mmm) REVERT: H 288 GLU cc_start: 0.8301 (mp0) cc_final: 0.8039 (mp0) REVERT: H 318 ASN cc_start: 0.8591 (t0) cc_final: 0.8301 (t0) REVERT: J 42 ASP cc_start: 0.8039 (p0) cc_final: 0.7446 (t0) REVERT: J 164 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8442 (t0) REVERT: J 213 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7682 (ttp-110) REVERT: J 217 ASP cc_start: 0.7841 (m-30) cc_final: 0.7449 (m-30) REVERT: J 225 GLU cc_start: 0.8213 (tp30) cc_final: 0.7789 (mm-30) REVERT: J 239 ASP cc_start: 0.8548 (t0) cc_final: 0.8278 (t0) REVERT: J 249 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8560 (ptm160) REVERT: J 263 GLU cc_start: 0.8081 (mp0) cc_final: 0.7711 (mp0) REVERT: J 288 GLU cc_start: 0.8415 (mp0) cc_final: 0.8040 (mp0) REVERT: J 300 MET cc_start: 0.8991 (mtm) cc_final: 0.8758 (mtt) REVERT: J 318 ASN cc_start: 0.8580 (t0) cc_final: 0.8322 (t0) REVERT: J 344 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7793 (mm-30) REVERT: J 375 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7802 (mptt) REVERT: L 102 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8362 (pp) REVERT: L 103 GLU cc_start: 0.8495 (mp0) cc_final: 0.8127 (mp0) REVERT: L 208 GLU cc_start: 0.7532 (pm20) cc_final: 0.7152 (mp0) REVERT: L 213 ARG cc_start: 0.8366 (ttp-110) cc_final: 0.7713 (ttp-110) REVERT: L 217 ASP cc_start: 0.8061 (m-30) cc_final: 0.7585 (m-30) REVERT: L 225 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7936 (mm-30) REVERT: L 239 ASP cc_start: 0.8860 (t0) cc_final: 0.8592 (t0) REVERT: L 393 LEU cc_start: 0.8274 (tt) cc_final: 0.7381 (mp) REVERT: N 31 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7150 (pp) REVERT: N 164 ASN cc_start: 0.8823 (t0) cc_final: 0.8548 (t0) REVERT: N 213 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7671 (ttp-110) REVERT: N 217 ASP cc_start: 0.8198 (m-30) cc_final: 0.7740 (m-30) REVERT: N 225 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7892 (mm-30) REVERT: N 239 ASP cc_start: 0.8771 (t0) cc_final: 0.8510 (t0) REVERT: N 249 ARG cc_start: 0.8819 (ppp-140) cc_final: 0.8613 (ptm160) REVERT: N 263 GLU cc_start: 0.8146 (mp0) cc_final: 0.7942 (mp0) REVERT: N 280 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8372 (mmm) REVERT: N 314 VAL cc_start: 0.9195 (p) cc_final: 0.8950 (t) REVERT: N 317 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7980 (mm-30) REVERT: P 32 LYS cc_start: 0.8283 (mttm) cc_final: 0.8048 (mmtt) REVERT: P 217 ASP cc_start: 0.7932 (m-30) cc_final: 0.7633 (m-30) REVERT: P 239 ASP cc_start: 0.8625 (t0) cc_final: 0.8196 (t0) REVERT: P 308 GLU cc_start: 0.8263 (pm20) cc_final: 0.7980 (pm20) REVERT: P 318 ASN cc_start: 0.8501 (t0) cc_final: 0.8214 (t0) REVERT: S 103 GLU cc_start: 0.8328 (mp0) cc_final: 0.8122 (mp0) REVERT: S 129 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: S 209 PHE cc_start: 0.8933 (m-80) cc_final: 0.8698 (m-10) REVERT: S 213 ARG cc_start: 0.8470 (ttm110) cc_final: 0.7517 (ttp-110) REVERT: S 217 ASP cc_start: 0.7983 (m-30) cc_final: 0.7583 (m-30) REVERT: S 239 ASP cc_start: 0.8706 (t0) cc_final: 0.8424 (t0) REVERT: S 280 MET cc_start: 0.8601 (mtm) cc_final: 0.8299 (mmm) REVERT: S 318 ASN cc_start: 0.8639 (t0) cc_final: 0.8217 (t0) REVERT: S 371 ARG cc_start: 0.8567 (mmt90) cc_final: 0.8345 (mmt90) REVERT: U 103 GLU cc_start: 0.8448 (mp0) cc_final: 0.8024 (mp0) REVERT: U 213 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7338 (ttp80) REVERT: U 217 ASP cc_start: 0.8004 (m-30) cc_final: 0.7517 (m-30) REVERT: U 225 GLU cc_start: 0.8253 (tp30) cc_final: 0.7835 (mm-30) REVERT: U 239 ASP cc_start: 0.8726 (t0) cc_final: 0.8513 (t0) REVERT: U 271 LEU cc_start: 0.8569 (mt) cc_final: 0.8328 (mt) REVERT: U 280 MET cc_start: 0.8846 (tpp) cc_final: 0.8611 (tpp) REVERT: U 318 ASN cc_start: 0.8484 (t0) cc_final: 0.8271 (t0) REVERT: W 7 SER cc_start: 0.9287 (t) cc_final: 0.9034 (m) REVERT: W 32 LYS cc_start: 0.8380 (mttm) cc_final: 0.8164 (mmtt) REVERT: W 86 GLN cc_start: 0.8861 (mt0) cc_final: 0.8624 (mt0) REVERT: W 217 ASP cc_start: 0.8060 (m-30) cc_final: 0.7563 (m-30) REVERT: W 225 GLU cc_start: 0.8345 (tp30) cc_final: 0.8065 (mm-30) REVERT: W 239 ASP cc_start: 0.8769 (t0) cc_final: 0.8415 (t0) REVERT: W 280 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8140 (mmm) REVERT: W 288 GLU cc_start: 0.8340 (mp0) cc_final: 0.8004 (mp0) REVERT: W 371 ARG cc_start: 0.8732 (mmt90) cc_final: 0.8508 (mmt90) REVERT: Y 86 GLN cc_start: 0.8867 (mt0) cc_final: 0.8606 (mt0) REVERT: Y 99 ILE cc_start: 0.9183 (mm) cc_final: 0.8934 (tp) REVERT: Y 129 GLN cc_start: 0.8311 (mp10) cc_final: 0.8079 (mp10) REVERT: Y 208 GLU cc_start: 0.7560 (pm20) cc_final: 0.7188 (mp0) REVERT: Y 213 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7587 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8040 (m-30) cc_final: 0.7732 (m-30) REVERT: Y 239 ASP cc_start: 0.8751 (t0) cc_final: 0.8424 (t0) REVERT: Y 280 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8216 (mmm) REVERT: Y 288 GLU cc_start: 0.8302 (mp0) cc_final: 0.7970 (mp0) REVERT: Y 292 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8114 (mt-10) REVERT: Y 318 ASN cc_start: 0.8500 (t0) cc_final: 0.8092 (t0) REVERT: 0 86 GLN cc_start: 0.8803 (mt0) cc_final: 0.8596 (mt0) REVERT: 0 148 GLU cc_start: 0.7959 (pt0) cc_final: 0.7650 (mt-10) REVERT: 0 217 ASP cc_start: 0.8024 (m-30) cc_final: 0.7547 (m-30) REVERT: 0 239 ASP cc_start: 0.8670 (t0) cc_final: 0.8299 (t0) REVERT: 0 288 GLU cc_start: 0.8287 (mp0) cc_final: 0.7903 (mp0) REVERT: 0 318 ASN cc_start: 0.8500 (t0) cc_final: 0.8097 (t0) REVERT: 0 337 MET cc_start: 0.9227 (mmp) cc_final: 0.8994 (mmp) REVERT: 2 213 ARG cc_start: 0.8273 (mtp-110) cc_final: 0.7796 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7928 (m-30) cc_final: 0.7669 (m-30) REVERT: 2 239 ASP cc_start: 0.8657 (t0) cc_final: 0.8253 (t0) REVERT: 2 280 MET cc_start: 0.8896 (tpp) cc_final: 0.8551 (mmm) REVERT: 2 288 GLU cc_start: 0.8365 (mp0) cc_final: 0.8030 (mp0) REVERT: 2 318 ASN cc_start: 0.8504 (t0) cc_final: 0.8157 (t0) outliers start: 120 outliers final: 70 residues processed: 1172 average time/residue: 0.2932 time to fit residues: 564.0206 Evaluate side-chains 1098 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1015 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 164 ASN Chi-restraints excluded: chain J residue 249 ARG Chi-restraints excluded: chain J residue 255 CYS Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 258 ASP Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 258 ASP Chi-restraints excluded: chain N residue 280 MET Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 304 GLN Chi-restraints excluded: chain P residue 355 SER Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 44 SER Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 129 GLN Chi-restraints excluded: chain S residue 255 CYS Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 193 LEU Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 280 MET Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 166 ILE Chi-restraints excluded: chain Y residue 258 ASP Chi-restraints excluded: chain Y residue 280 MET Chi-restraints excluded: chain Y residue 304 GLN Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain Y residue 380 LEU Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 255 CYS Chi-restraints excluded: chain 0 residue 258 ASP Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 355 SER Chi-restraints excluded: chain 0 residue 369 VAL Chi-restraints excluded: chain 0 residue 380 LEU Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 149 ASN Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 262 optimal weight: 6.9990 chunk 501 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 350 optimal weight: 0.5980 chunk 351 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 415 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 164 ASN W 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.093530 restraints weight = 64950.626| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.94 r_work: 0.2789 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 47672 Z= 0.195 Angle : 0.635 9.172 64860 Z= 0.317 Chirality : 0.047 0.275 7470 Planarity : 0.005 0.063 7980 Dihedral : 9.515 136.655 7249 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.54 % Allowed : 12.86 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.12), residues: 5625 helix: -0.06 (0.09), residues: 3210 sheet: 0.42 (0.28), residues: 375 loop : -0.24 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 29 TYR 0.017 0.001 TYR 0 361 PHE 0.020 0.002 PHE P 209 TRP 0.009 0.001 TRP H 215 HIS 0.003 0.001 HIS J 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (47670) covalent geometry : angle 0.63510 / 0.32 (64860) hydrogen bonds : bond 0.03685 / 2.43 ( 1725) hydrogen bonds : angle 3.91069 / 2.63 ( 4995) Misc. bond : bond 0.00243 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1113 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 SER cc_start: 0.9271 (t) cc_final: 0.8973 (m) REVERT: B 34 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8784 (pp) REVERT: B 129 GLN cc_start: 0.8388 (mt0) cc_final: 0.8150 (tm-30) REVERT: B 148 GLU cc_start: 0.7761 (pt0) cc_final: 0.7543 (mt-10) REVERT: B 213 ARG cc_start: 0.8265 (ttp-110) cc_final: 0.7452 (ttp80) REVERT: B 217 ASP cc_start: 0.8000 (m-30) cc_final: 0.7540 (m-30) REVERT: B 239 ASP cc_start: 0.8827 (t0) cc_final: 0.8508 (t0) REVERT: B 280 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8396 (mmm) REVERT: B 288 GLU cc_start: 0.8400 (mp0) cc_final: 0.7853 (mp0) REVERT: B 306 MET cc_start: 0.8539 (mtp) cc_final: 0.8235 (mtp) REVERT: B 318 ASN cc_start: 0.8731 (t0) cc_final: 0.8395 (t0) REVERT: A 103 GLU cc_start: 0.8421 (mp0) cc_final: 0.7932 (mp0) REVERT: A 115 THR cc_start: 0.8875 (p) cc_final: 0.8605 (t) REVERT: A 123 MET cc_start: 0.6308 (mmm) cc_final: 0.5416 (mmm) REVERT: A 164 ASN cc_start: 0.8741 (t0) cc_final: 0.8301 (t0) REVERT: A 213 ARG cc_start: 0.8312 (ttp-110) cc_final: 0.7636 (ttp-110) REVERT: A 217 ASP cc_start: 0.7983 (m-30) cc_final: 0.7401 (m-30) REVERT: A 225 GLU cc_start: 0.8345 (tp30) cc_final: 0.8024 (mm-30) REVERT: A 280 MET cc_start: 0.8832 (mtm) cc_final: 0.8536 (mpp) REVERT: A 288 GLU cc_start: 0.8522 (mp0) cc_final: 0.8071 (mp0) REVERT: A 318 ASN cc_start: 0.8591 (t0) cc_final: 0.8345 (t0) REVERT: A 344 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8221 (mm-30) REVERT: D 103 GLU cc_start: 0.8466 (mp0) cc_final: 0.8114 (mp0) REVERT: D 123 MET cc_start: 0.5297 (mmt) cc_final: 0.4718 (mmm) REVERT: D 213 ARG cc_start: 0.7710 (mtm110) cc_final: 0.7423 (ttp-110) REVERT: D 217 ASP cc_start: 0.7967 (m-30) cc_final: 0.7581 (m-30) REVERT: D 225 GLU cc_start: 0.8187 (tp30) cc_final: 0.7894 (mm-30) REVERT: D 239 ASP cc_start: 0.8868 (t0) cc_final: 0.8416 (t0) REVERT: D 280 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8385 (tpp) REVERT: D 288 GLU cc_start: 0.8352 (mp0) cc_final: 0.8067 (mp0) REVERT: F 57 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8074 (mtp180) REVERT: F 110 SER cc_start: 0.8215 (t) cc_final: 0.7998 (t) REVERT: F 213 ARG cc_start: 0.7857 (mtm110) cc_final: 0.7548 (ttp-110) REVERT: F 217 ASP cc_start: 0.7904 (m-30) cc_final: 0.7350 (m-30) REVERT: F 225 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8090 (mm-30) REVERT: F 239 ASP cc_start: 0.8596 (t0) cc_final: 0.8249 (t0) REVERT: F 323 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8868 (ttmm) REVERT: F 332 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9169 (tm) REVERT: H 239 ASP cc_start: 0.8628 (t0) cc_final: 0.8227 (t0) REVERT: H 318 ASN cc_start: 0.8618 (t0) cc_final: 0.8340 (t0) REVERT: J 42 ASP cc_start: 0.8138 (p0) cc_final: 0.7456 (t70) REVERT: J 164 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8436 (t0) REVERT: J 208 GLU cc_start: 0.7661 (pt0) cc_final: 0.7364 (mp0) REVERT: J 213 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.7638 (ttp-110) REVERT: J 217 ASP cc_start: 0.7860 (m-30) cc_final: 0.7404 (m-30) REVERT: J 225 GLU cc_start: 0.8287 (tp30) cc_final: 0.7781 (mm-30) REVERT: J 239 ASP cc_start: 0.8587 (t0) cc_final: 0.8305 (t0) REVERT: J 249 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8551 (ptm160) REVERT: J 263 GLU cc_start: 0.8113 (mp0) cc_final: 0.7649 (mp0) REVERT: J 280 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8275 (mpp) REVERT: J 318 ASN cc_start: 0.8608 (t0) cc_final: 0.8359 (t0) REVERT: J 344 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7852 (mm-30) REVERT: J 375 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7767 (mptt) REVERT: L 213 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.7759 (ttp-110) REVERT: L 217 ASP cc_start: 0.8082 (m-30) cc_final: 0.7606 (m-30) REVERT: L 225 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8091 (mm-30) REVERT: L 239 ASP cc_start: 0.8823 (t0) cc_final: 0.8544 (t0) REVERT: L 393 LEU cc_start: 0.8342 (tt) cc_final: 0.7333 (mp) REVERT: N 31 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7341 (pp) REVERT: N 148 GLU cc_start: 0.7980 (pt0) cc_final: 0.7559 (mt-10) REVERT: N 225 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8062 (mm-30) REVERT: N 239 ASP cc_start: 0.8793 (t0) cc_final: 0.8552 (t0) REVERT: N 317 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8019 (mm-30) REVERT: N 342 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: P 32 LYS cc_start: 0.8347 (mttm) cc_final: 0.8102 (mmtt) REVERT: P 217 ASP cc_start: 0.7950 (m-30) cc_final: 0.7727 (m-30) REVERT: P 239 ASP cc_start: 0.8672 (t0) cc_final: 0.8248 (t0) REVERT: P 288 GLU cc_start: 0.8475 (mp0) cc_final: 0.8106 (mp0) REVERT: P 308 GLU cc_start: 0.8257 (pm20) cc_final: 0.7955 (pm20) REVERT: P 318 ASN cc_start: 0.8541 (t0) cc_final: 0.8295 (t0) REVERT: S 12 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8401 (mttp) REVERT: S 103 GLU cc_start: 0.8360 (mp0) cc_final: 0.8140 (mp0) REVERT: S 209 PHE cc_start: 0.9037 (m-80) cc_final: 0.8788 (m-10) REVERT: S 213 ARG cc_start: 0.8512 (ttm110) cc_final: 0.7639 (ttp-110) REVERT: S 217 ASP cc_start: 0.8012 (m-30) cc_final: 0.7655 (m-30) REVERT: S 280 MET cc_start: 0.8667 (mtm) cc_final: 0.8319 (mmm) REVERT: S 318 ASN cc_start: 0.8626 (t0) cc_final: 0.8236 (t0) REVERT: S 380 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7322 (tt) REVERT: U 213 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7345 (ttp80) REVERT: U 217 ASP cc_start: 0.8105 (m-30) cc_final: 0.7608 (m-30) REVERT: U 225 GLU cc_start: 0.8279 (tp30) cc_final: 0.8058 (tp30) REVERT: U 239 ASP cc_start: 0.8785 (t0) cc_final: 0.8556 (t0) REVERT: U 252 GLU cc_start: 0.8692 (tt0) cc_final: 0.8442 (mt-10) REVERT: U 280 MET cc_start: 0.8891 (tpp) cc_final: 0.8640 (tpp) REVERT: U 318 ASN cc_start: 0.8529 (t0) cc_final: 0.8329 (t0) REVERT: W 15 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7776 (tptp) REVERT: W 129 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: W 192 GLU cc_start: 0.8018 (mp0) cc_final: 0.7814 (mt-10) REVERT: W 217 ASP cc_start: 0.8162 (m-30) cc_final: 0.7598 (m-30) REVERT: W 225 GLU cc_start: 0.8410 (tp30) cc_final: 0.8119 (mm-30) REVERT: W 239 ASP cc_start: 0.8745 (t0) cc_final: 0.8542 (t0) REVERT: W 280 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8344 (tpp) REVERT: Y 86 GLN cc_start: 0.8944 (mt0) cc_final: 0.8637 (mt0) REVERT: Y 115 THR cc_start: 0.8851 (p) cc_final: 0.8543 (t) REVERT: Y 164 ASN cc_start: 0.8821 (t0) cc_final: 0.8475 (t0) REVERT: Y 213 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.7645 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8056 (m-30) cc_final: 0.7748 (m-30) REVERT: Y 225 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7996 (mm-30) REVERT: Y 239 ASP cc_start: 0.8768 (t0) cc_final: 0.8424 (t0) REVERT: Y 280 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8139 (tpp) REVERT: Y 288 GLU cc_start: 0.8340 (mp0) cc_final: 0.7929 (mp0) REVERT: Y 292 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8136 (mt-10) REVERT: Y 318 ASN cc_start: 0.8527 (t0) cc_final: 0.8202 (t0) REVERT: Y 323 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8741 (ttmm) REVERT: Y 357 PHE cc_start: 0.8875 (t80) cc_final: 0.8624 (t80) REVERT: 0 86 GLN cc_start: 0.8882 (mt0) cc_final: 0.8672 (mt0) REVERT: 0 89 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8863 (mm-40) REVERT: 0 115 THR cc_start: 0.8842 (p) cc_final: 0.8528 (t) REVERT: 0 148 GLU cc_start: 0.7983 (pt0) cc_final: 0.7697 (mt-10) REVERT: 0 225 GLU cc_start: 0.8162 (tp30) cc_final: 0.7853 (mm-30) REVERT: 0 239 ASP cc_start: 0.8706 (t0) cc_final: 0.8483 (t0) REVERT: 0 288 GLU cc_start: 0.8353 (mp0) cc_final: 0.7954 (mp0) REVERT: 0 318 ASN cc_start: 0.8540 (t0) cc_final: 0.8130 (t0) REVERT: 0 337 MET cc_start: 0.9268 (mmp) cc_final: 0.9050 (mmp) REVERT: 2 164 ASN cc_start: 0.8846 (t0) cc_final: 0.8139 (t0) REVERT: 2 213 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7868 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7907 (m-30) cc_final: 0.7635 (m-30) REVERT: 2 239 ASP cc_start: 0.8688 (t0) cc_final: 0.8325 (t0) REVERT: 2 280 MET cc_start: 0.8942 (tpp) cc_final: 0.8641 (mmm) REVERT: 2 288 GLU cc_start: 0.8482 (mp0) cc_final: 0.8139 (mp0) REVERT: 2 318 ASN cc_start: 0.8517 (t0) cc_final: 0.8210 (t0) outliers start: 172 outliers final: 91 residues processed: 1212 average time/residue: 0.2908 time to fit residues: 580.2391 Evaluate side-chains 1118 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1010 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 164 ASN Chi-restraints excluded: chain J residue 249 ARG Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 280 MET Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 355 SER Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 258 ASP Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 258 ASP Chi-restraints excluded: chain N residue 304 GLN Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 367 GLU Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 304 GLN Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 355 SER Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 129 GLN Chi-restraints excluded: chain S residue 255 CYS Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 380 LEU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 193 LEU Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 280 MET Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 258 ASP Chi-restraints excluded: chain Y residue 280 MET Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 323 LYS Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 45 ILE Chi-restraints excluded: chain 0 residue 258 ASP Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 355 SER Chi-restraints excluded: chain 0 residue 380 LEU Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain 2 residue 149 ASN Chi-restraints excluded: chain 2 residue 297 GLU Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 171 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 489 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 334 optimal weight: 0.8980 chunk 435 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 chunk 283 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 541 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 305 GLN H 164 ASN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 GLN 2 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.095414 restraints weight = 64587.644| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.94 r_work: 0.2842 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47672 Z= 0.134 Angle : 0.606 8.772 64860 Z= 0.301 Chirality : 0.045 0.269 7470 Planarity : 0.004 0.057 7980 Dihedral : 9.375 134.622 7247 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.63 % Allowed : 14.71 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 5625 helix: 0.29 (0.09), residues: 3165 sheet: 0.43 (0.28), residues: 375 loop : -0.14 (0.15), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 392 TYR 0.013 0.001 TYR 0 361 PHE 0.012 0.001 PHE H 163 TRP 0.010 0.001 TRP F 215 HIS 0.003 0.001 HIS J 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (47670) covalent geometry : angle 0.60584 / 0.30 (64860) hydrogen bonds : bond 0.03410 / 2.24 ( 1725) hydrogen bonds : angle 3.82593 / 2.57 ( 4995) Misc. bond : bond 0.00264 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1072 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 SER cc_start: 0.9281 (t) cc_final: 0.8974 (m) REVERT: B 34 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8743 (pp) REVERT: B 129 GLN cc_start: 0.8398 (mt0) cc_final: 0.8183 (tm-30) REVERT: B 213 ARG cc_start: 0.8255 (ttp-110) cc_final: 0.7471 (ttp80) REVERT: B 217 ASP cc_start: 0.7929 (m-30) cc_final: 0.7502 (m-30) REVERT: B 239 ASP cc_start: 0.8755 (t0) cc_final: 0.8485 (t0) REVERT: B 306 MET cc_start: 0.8495 (mtp) cc_final: 0.8204 (mtp) REVERT: A 103 GLU cc_start: 0.8412 (mp0) cc_final: 0.8066 (mp0) REVERT: A 123 MET cc_start: 0.6461 (mmm) cc_final: 0.5629 (mmm) REVERT: A 164 ASN cc_start: 0.8723 (t0) cc_final: 0.8306 (t0) REVERT: A 208 GLU cc_start: 0.7700 (pt0) cc_final: 0.7439 (pm20) REVERT: A 213 ARG cc_start: 0.8341 (ttp-110) cc_final: 0.7627 (ttp-110) REVERT: A 217 ASP cc_start: 0.7962 (m-30) cc_final: 0.7358 (m-30) REVERT: A 225 GLU cc_start: 0.8294 (tp30) cc_final: 0.8019 (mm-30) REVERT: A 280 MET cc_start: 0.8788 (mtm) cc_final: 0.8520 (mpp) REVERT: A 288 GLU cc_start: 0.8470 (mp0) cc_final: 0.8112 (mp0) REVERT: A 312 TYR cc_start: 0.9338 (m-80) cc_final: 0.9137 (m-80) REVERT: A 318 ASN cc_start: 0.8487 (t0) cc_final: 0.8274 (t0) REVERT: D 103 GLU cc_start: 0.8438 (mp0) cc_final: 0.8067 (mp0) REVERT: D 123 MET cc_start: 0.5346 (mmt) cc_final: 0.4837 (mmm) REVERT: D 213 ARG cc_start: 0.7738 (mtm110) cc_final: 0.7418 (ttp-110) REVERT: D 217 ASP cc_start: 0.7847 (m-30) cc_final: 0.7429 (m-30) REVERT: D 225 GLU cc_start: 0.8175 (tp30) cc_final: 0.7932 (mm-30) REVERT: D 239 ASP cc_start: 0.8818 (t0) cc_final: 0.8342 (t0) REVERT: D 280 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8308 (mmt) REVERT: D 342 GLU cc_start: 0.7237 (mp0) cc_final: 0.6997 (mp0) REVERT: F 12 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8359 (mttt) REVERT: F 57 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8061 (mtp180) REVERT: F 110 SER cc_start: 0.8200 (t) cc_final: 0.7993 (t) REVERT: F 213 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7512 (ttp-110) REVERT: F 217 ASP cc_start: 0.7841 (m-30) cc_final: 0.7294 (m-30) REVERT: F 225 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7986 (mm-30) REVERT: F 239 ASP cc_start: 0.8536 (t0) cc_final: 0.8231 (t0) REVERT: F 323 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8826 (ttmm) REVERT: F 332 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9182 (tp) REVERT: H 213 ARG cc_start: 0.8342 (ttm110) cc_final: 0.7865 (ttp-110) REVERT: H 239 ASP cc_start: 0.8583 (t0) cc_final: 0.8189 (t0) REVERT: H 318 ASN cc_start: 0.8586 (t0) cc_final: 0.8335 (t0) REVERT: J 164 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8417 (t0) REVERT: J 208 GLU cc_start: 0.7570 (pt0) cc_final: 0.7219 (mp0) REVERT: J 213 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7546 (ttp-110) REVERT: J 217 ASP cc_start: 0.7799 (m-30) cc_final: 0.7254 (m-30) REVERT: J 225 GLU cc_start: 0.8287 (tp30) cc_final: 0.8002 (mm-30) REVERT: J 239 ASP cc_start: 0.8548 (t0) cc_final: 0.8334 (t0) REVERT: J 263 GLU cc_start: 0.8010 (mp0) cc_final: 0.7576 (mp0) REVERT: J 280 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8264 (mmt) REVERT: J 375 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7755 (mptt) REVERT: L 103 GLU cc_start: 0.8534 (mp0) cc_final: 0.8177 (mp0) REVERT: L 213 ARG cc_start: 0.8441 (ttp-110) cc_final: 0.7809 (ttp-110) REVERT: L 217 ASP cc_start: 0.8029 (m-30) cc_final: 0.7572 (m-30) REVERT: L 239 ASP cc_start: 0.8754 (t0) cc_final: 0.8510 (t0) REVERT: L 393 LEU cc_start: 0.8301 (tt) cc_final: 0.7333 (mp) REVERT: N 148 GLU cc_start: 0.7904 (pt0) cc_final: 0.7579 (mt-10) REVERT: N 164 ASN cc_start: 0.8826 (t0) cc_final: 0.8501 (t0) REVERT: N 225 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8089 (mm-30) REVERT: N 239 ASP cc_start: 0.8737 (t0) cc_final: 0.8524 (t0) REVERT: N 317 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8077 (mm-30) REVERT: N 342 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: P 217 ASP cc_start: 0.7904 (m-30) cc_final: 0.7666 (m-30) REVERT: P 239 ASP cc_start: 0.8642 (t0) cc_final: 0.8248 (t0) REVERT: P 308 GLU cc_start: 0.8211 (pm20) cc_final: 0.7918 (pm20) REVERT: P 318 ASN cc_start: 0.8446 (t0) cc_final: 0.8216 (t0) REVERT: S 213 ARG cc_start: 0.8517 (ttm110) cc_final: 0.7635 (ttp-110) REVERT: S 217 ASP cc_start: 0.7948 (m-30) cc_final: 0.7599 (m-30) REVERT: S 225 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8221 (mm-30) REVERT: S 239 ASP cc_start: 0.8823 (t0) cc_final: 0.8617 (t0) REVERT: S 241 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8574 (mmtt) REVERT: S 249 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8482 (ptm160) REVERT: S 252 GLU cc_start: 0.8655 (tt0) cc_final: 0.8444 (mt-10) REVERT: S 280 MET cc_start: 0.8627 (mtm) cc_final: 0.8321 (mmm) REVERT: S 318 ASN cc_start: 0.8558 (t0) cc_final: 0.8182 (t0) REVERT: S 380 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7306 (tt) REVERT: U 103 GLU cc_start: 0.8462 (mp0) cc_final: 0.8029 (mp0) REVERT: U 213 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.7358 (ttp80) REVERT: U 217 ASP cc_start: 0.8061 (m-30) cc_final: 0.7577 (m-30) REVERT: U 225 GLU cc_start: 0.8248 (tp30) cc_final: 0.7919 (mm-30) REVERT: U 239 ASP cc_start: 0.8753 (t0) cc_final: 0.8522 (t0) REVERT: U 252 GLU cc_start: 0.8671 (tt0) cc_final: 0.8443 (mt-10) REVERT: U 280 MET cc_start: 0.8851 (tpp) cc_final: 0.8612 (tpp) REVERT: U 361 TYR cc_start: 0.9292 (m-80) cc_final: 0.9080 (m-80) REVERT: W 15 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7853 (tptp) REVERT: W 129 GLN cc_start: 0.8231 (mp10) cc_final: 0.7971 (mp10) REVERT: W 192 GLU cc_start: 0.7972 (mp0) cc_final: 0.7762 (mt-10) REVERT: W 217 ASP cc_start: 0.8106 (m-30) cc_final: 0.7599 (m-30) REVERT: W 280 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8282 (mmm) REVERT: W 380 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7577 (tt) REVERT: Y 86 GLN cc_start: 0.8915 (mt0) cc_final: 0.8607 (mt0) REVERT: Y 115 THR cc_start: 0.8888 (p) cc_final: 0.8582 (t) REVERT: Y 164 ASN cc_start: 0.8816 (t0) cc_final: 0.8581 (t0) REVERT: Y 213 ARG cc_start: 0.8245 (ttp-110) cc_final: 0.7665 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8068 (m-30) cc_final: 0.7759 (m-30) REVERT: Y 239 ASP cc_start: 0.8718 (t0) cc_final: 0.8341 (t0) REVERT: Y 280 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8091 (tpp) REVERT: Y 288 GLU cc_start: 0.8265 (mp0) cc_final: 0.8003 (mp0) REVERT: Y 318 ASN cc_start: 0.8464 (t0) cc_final: 0.8182 (t0) REVERT: 0 115 THR cc_start: 0.8852 (p) cc_final: 0.8573 (t) REVERT: 0 148 GLU cc_start: 0.7972 (pt0) cc_final: 0.7716 (mt-10) REVERT: 0 225 GLU cc_start: 0.8101 (tp30) cc_final: 0.7901 (tp30) REVERT: 0 288 GLU cc_start: 0.8334 (mp0) cc_final: 0.7909 (mp0) REVERT: 0 318 ASN cc_start: 0.8487 (t0) cc_final: 0.8159 (t0) REVERT: 2 213 ARG cc_start: 0.8333 (mtp-110) cc_final: 0.7869 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7823 (m-30) cc_final: 0.7560 (m-30) REVERT: 2 239 ASP cc_start: 0.8748 (t0) cc_final: 0.8514 (t0) REVERT: 2 280 MET cc_start: 0.8881 (tpp) cc_final: 0.8595 (mmm) REVERT: 2 288 GLU cc_start: 0.8433 (mp0) cc_final: 0.8129 (mp0) REVERT: 2 318 ASN cc_start: 0.8505 (t0) cc_final: 0.8255 (t0) outliers start: 128 outliers final: 73 residues processed: 1148 average time/residue: 0.2780 time to fit residues: 523.9394 Evaluate side-chains 1103 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1016 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 164 ASN Chi-restraints excluded: chain J residue 280 MET Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 258 ASP Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 166 ILE Chi-restraints excluded: chain N residue 304 GLN Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 129 GLN Chi-restraints excluded: chain S residue 249 ARG Chi-restraints excluded: chain S residue 255 CYS Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain S residue 380 LEU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 255 CYS Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 280 MET Chi-restraints excluded: chain W residue 367 GLU Chi-restraints excluded: chain W residue 380 LEU Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 258 ASP Chi-restraints excluded: chain Y residue 280 MET Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 45 ILE Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 258 ASP Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 355 SER Chi-restraints excluded: chain 0 residue 367 GLU Chi-restraints excluded: chain 0 residue 380 LEU Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 255 CYS Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 319 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 515 optimal weight: 5.9990 chunk 431 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 229 optimal weight: 0.0770 chunk 297 optimal weight: 5.9990 chunk 505 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 380 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 426 optimal weight: 7.9990 chunk 567 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 ASN D 305 GLN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 321 GLN W 86 GLN W 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.114288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.093884 restraints weight = 65039.357| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.94 r_work: 0.2817 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 47672 Z= 0.177 Angle : 0.629 8.859 64860 Z= 0.312 Chirality : 0.046 0.265 7470 Planarity : 0.004 0.058 7980 Dihedral : 9.274 135.516 7247 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.86 % Allowed : 14.88 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.12), residues: 5625 helix: 0.55 (0.10), residues: 3075 sheet: 0.41 (0.28), residues: 375 loop : -0.19 (0.14), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 392 TYR 0.014 0.001 TYR Y 361 PHE 0.028 0.002 PHE U 209 TRP 0.010 0.001 TRP J 215 HIS 0.003 0.001 HIS W 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (47670) covalent geometry : angle 0.62917 / 0.31 (64860) hydrogen bonds : bond 0.03454 / 2.27 ( 1725) hydrogen bonds : angle 3.80977 / 2.56 ( 4995) Misc. bond : bond 0.00194 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1065 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8776 (pp) REVERT: B 129 GLN cc_start: 0.8412 (mt0) cc_final: 0.8185 (tm-30) REVERT: B 164 ASN cc_start: 0.8843 (t0) cc_final: 0.8237 (t0) REVERT: B 213 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7414 (ttp80) REVERT: B 217 ASP cc_start: 0.7984 (m-30) cc_final: 0.7505 (m-30) REVERT: B 225 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7961 (mm-30) REVERT: B 239 ASP cc_start: 0.8797 (t0) cc_final: 0.8590 (t0) REVERT: B 306 MET cc_start: 0.8489 (mtp) cc_final: 0.8224 (mtp) REVERT: A 103 GLU cc_start: 0.8427 (mp0) cc_final: 0.8010 (mp0) REVERT: A 123 MET cc_start: 0.6476 (mmm) cc_final: 0.5552 (mmm) REVERT: A 164 ASN cc_start: 0.8724 (t0) cc_final: 0.8289 (t0) REVERT: A 208 GLU cc_start: 0.7646 (pt0) cc_final: 0.7401 (pm20) REVERT: A 217 ASP cc_start: 0.7988 (m-30) cc_final: 0.7396 (m-30) REVERT: A 225 GLU cc_start: 0.8306 (tp30) cc_final: 0.8027 (mm-30) REVERT: A 280 MET cc_start: 0.8837 (mtm) cc_final: 0.8524 (mpp) REVERT: A 288 GLU cc_start: 0.8498 (mp0) cc_final: 0.8130 (mp0) REVERT: A 318 ASN cc_start: 0.8544 (t0) cc_final: 0.8310 (t0) REVERT: D 103 GLU cc_start: 0.8509 (mp0) cc_final: 0.8172 (mp0) REVERT: D 123 MET cc_start: 0.5470 (mmt) cc_final: 0.4927 (mmm) REVERT: D 164 ASN cc_start: 0.8849 (t0) cc_final: 0.8493 (t0) REVERT: D 213 ARG cc_start: 0.7778 (mtm110) cc_final: 0.7432 (ttp-110) REVERT: D 217 ASP cc_start: 0.7894 (m-30) cc_final: 0.7469 (m-30) REVERT: D 239 ASP cc_start: 0.8807 (t0) cc_final: 0.8334 (t0) REVERT: D 280 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8453 (mmt) REVERT: D 342 GLU cc_start: 0.7315 (mp0) cc_final: 0.7044 (mp0) REVERT: F 12 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8380 (mtpt) REVERT: F 57 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8064 (mtp180) REVERT: F 110 SER cc_start: 0.8184 (t) cc_final: 0.7959 (t) REVERT: F 213 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7623 (ttp-110) REVERT: F 217 ASP cc_start: 0.7878 (m-30) cc_final: 0.7398 (m-30) REVERT: F 239 ASP cc_start: 0.8549 (t0) cc_final: 0.8224 (t0) REVERT: F 323 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8862 (ttmm) REVERT: F 332 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9195 (tp) REVERT: H 213 ARG cc_start: 0.8367 (ttm110) cc_final: 0.7944 (ttp-110) REVERT: H 239 ASP cc_start: 0.8566 (t0) cc_final: 0.8189 (t0) REVERT: H 318 ASN cc_start: 0.8591 (t0) cc_final: 0.8338 (t0) REVERT: J 15 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7971 (tptp) REVERT: J 192 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: J 213 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.7648 (ttp-110) REVERT: J 217 ASP cc_start: 0.7837 (m-30) cc_final: 0.7267 (m-30) REVERT: J 225 GLU cc_start: 0.8322 (tp30) cc_final: 0.8027 (mm-30) REVERT: J 239 ASP cc_start: 0.8590 (t0) cc_final: 0.8366 (t0) REVERT: J 263 GLU cc_start: 0.8031 (mp0) cc_final: 0.7664 (mp0) REVERT: J 280 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8206 (mpp) REVERT: J 375 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7677 (mptt) REVERT: L 103 GLU cc_start: 0.8497 (mp0) cc_final: 0.8193 (mp0) REVERT: L 213 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.7866 (ttp-110) REVERT: L 217 ASP cc_start: 0.8032 (m-30) cc_final: 0.7576 (m-30) REVERT: L 225 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7837 (mm-30) REVERT: L 239 ASP cc_start: 0.8785 (t0) cc_final: 0.8567 (t0) REVERT: L 342 GLU cc_start: 0.7192 (mp0) cc_final: 0.6974 (mp0) REVERT: L 393 LEU cc_start: 0.8353 (tt) cc_final: 0.7397 (mp) REVERT: N 148 GLU cc_start: 0.7878 (pt0) cc_final: 0.7588 (mt-10) REVERT: N 164 ASN cc_start: 0.8889 (t0) cc_final: 0.8556 (t0) REVERT: N 225 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8146 (mm-30) REVERT: N 239 ASP cc_start: 0.8755 (t0) cc_final: 0.8546 (t0) REVERT: N 317 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8089 (mm-30) REVERT: N 342 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: P 32 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8125 (mmmm) REVERT: P 209 PHE cc_start: 0.8283 (m-10) cc_final: 0.7984 (m-10) REVERT: P 213 ARG cc_start: 0.8344 (ttp-110) cc_final: 0.7887 (ttp-110) REVERT: P 217 ASP cc_start: 0.7957 (m-30) cc_final: 0.7703 (m-30) REVERT: P 239 ASP cc_start: 0.8640 (t0) cc_final: 0.8403 (t0) REVERT: P 288 GLU cc_start: 0.8571 (mp0) cc_final: 0.8217 (mp0) REVERT: P 308 GLU cc_start: 0.8256 (pm20) cc_final: 0.7920 (pm20) REVERT: P 318 ASN cc_start: 0.8480 (t0) cc_final: 0.8260 (t0) REVERT: S 213 ARG cc_start: 0.8569 (ttm110) cc_final: 0.7775 (ttp-110) REVERT: S 217 ASP cc_start: 0.8001 (m-30) cc_final: 0.7654 (m-30) REVERT: S 225 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8211 (mm-30) REVERT: S 239 ASP cc_start: 0.8855 (t0) cc_final: 0.8617 (t0) REVERT: S 241 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8597 (mmtt) REVERT: S 249 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8484 (ptm160) REVERT: S 280 MET cc_start: 0.8653 (mtm) cc_final: 0.8324 (mmm) REVERT: S 318 ASN cc_start: 0.8541 (t0) cc_final: 0.8199 (t0) REVERT: S 380 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7244 (tt) REVERT: U 103 GLU cc_start: 0.8443 (mp0) cc_final: 0.7992 (mp0) REVERT: U 164 ASN cc_start: 0.8929 (t0) cc_final: 0.8567 (t0) REVERT: U 213 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.7926 (ttp80) REVERT: U 225 GLU cc_start: 0.8278 (tp30) cc_final: 0.7923 (mm-30) REVERT: U 239 ASP cc_start: 0.8762 (t0) cc_final: 0.8533 (t0) REVERT: U 280 MET cc_start: 0.8865 (tpp) cc_final: 0.8620 (tpp) REVERT: W 15 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7815 (tptp) REVERT: W 129 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: W 164 ASN cc_start: 0.8854 (t0) cc_final: 0.8596 (t0) REVERT: W 192 GLU cc_start: 0.7988 (mp0) cc_final: 0.7753 (mt-10) REVERT: W 239 ASP cc_start: 0.8851 (t0) cc_final: 0.8599 (t0) REVERT: W 280 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8314 (mmm) REVERT: W 342 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: W 380 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7630 (tt) REVERT: Y 86 GLN cc_start: 0.8952 (mt0) cc_final: 0.8675 (mt0) REVERT: Y 115 THR cc_start: 0.8890 (p) cc_final: 0.8576 (t) REVERT: Y 164 ASN cc_start: 0.8786 (t0) cc_final: 0.8473 (t0) REVERT: Y 213 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7729 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8047 (m-30) cc_final: 0.7800 (m-30) REVERT: Y 225 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7895 (mm-30) REVERT: Y 239 ASP cc_start: 0.8724 (t0) cc_final: 0.8354 (t0) REVERT: Y 280 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8141 (tpp) REVERT: Y 288 GLU cc_start: 0.8307 (mp0) cc_final: 0.8008 (mp0) REVERT: Y 318 ASN cc_start: 0.8479 (t0) cc_final: 0.8185 (t0) REVERT: 0 115 THR cc_start: 0.8845 (p) cc_final: 0.8537 (t) REVERT: 0 148 GLU cc_start: 0.7998 (pt0) cc_final: 0.7791 (mt-10) REVERT: 0 239 ASP cc_start: 0.8826 (t0) cc_final: 0.8574 (t0) REVERT: 0 288 GLU cc_start: 0.8383 (mp0) cc_final: 0.7976 (mp0) REVERT: 0 318 ASN cc_start: 0.8474 (t0) cc_final: 0.8153 (t0) REVERT: 2 123 MET cc_start: 0.7078 (mmt) cc_final: 0.6621 (mmt) REVERT: 2 164 ASN cc_start: 0.8818 (t0) cc_final: 0.8349 (t0) REVERT: 2 213 ARG cc_start: 0.8349 (mtp-110) cc_final: 0.7912 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7881 (m-30) cc_final: 0.7615 (m-30) REVERT: 2 239 ASP cc_start: 0.8761 (t0) cc_final: 0.8521 (t0) REVERT: 2 280 MET cc_start: 0.8905 (tpp) cc_final: 0.8594 (mmm) REVERT: 2 288 GLU cc_start: 0.8397 (mp0) cc_final: 0.8102 (mp0) REVERT: 2 318 ASN cc_start: 0.8507 (t0) cc_final: 0.8268 (t0) outliers start: 139 outliers final: 90 residues processed: 1144 average time/residue: 0.2579 time to fit residues: 484.3634 Evaluate side-chains 1109 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1003 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 367 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 280 MET Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 258 ASP Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 304 GLN Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 367 GLU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 129 GLN Chi-restraints excluded: chain S residue 249 ARG Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain S residue 380 LEU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 255 CYS Chi-restraints excluded: chain U residue 321 GLN Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 280 MET Chi-restraints excluded: chain W residue 342 GLU Chi-restraints excluded: chain W residue 367 GLU Chi-restraints excluded: chain W residue 380 LEU Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 258 ASP Chi-restraints excluded: chain Y residue 280 MET Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 45 ILE Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 105 VAL Chi-restraints excluded: chain 0 residue 258 ASP Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 355 SER Chi-restraints excluded: chain 0 residue 367 GLU Chi-restraints excluded: chain 0 residue 380 LEU Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 255 CYS Chi-restraints excluded: chain 2 residue 297 GLU Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 51 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 562 optimal weight: 10.0000 chunk 424 optimal weight: 0.9990 chunk 318 optimal weight: 0.0050 chunk 563 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 449 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 321 GLN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 ASN W 86 GLN 2 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.117388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.097100 restraints weight = 64728.974| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.94 r_work: 0.2872 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 47672 Z= 0.119 Angle : 0.597 10.292 64860 Z= 0.296 Chirality : 0.044 0.257 7470 Planarity : 0.004 0.058 7980 Dihedral : 9.168 133.741 7247 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.22 % Allowed : 16.13 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.12), residues: 5625 helix: 0.74 (0.10), residues: 3075 sheet: 0.36 (0.28), residues: 375 loop : -0.04 (0.15), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 392 TYR 0.011 0.001 TYR U 260 PHE 0.012 0.001 PHE J 209 TRP 0.011 0.001 TRP J 215 HIS 0.003 0.001 HIS J 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (47670) covalent geometry : angle 0.59658 / 0.30 (64860) hydrogen bonds : bond 0.03187 / 2.10 ( 1725) hydrogen bonds : angle 3.71469 / 2.49 ( 4995) Misc. bond : bond 0.00180 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1097 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8718 (pp) REVERT: B 129 GLN cc_start: 0.8425 (mt0) cc_final: 0.8163 (tm-30) REVERT: B 213 ARG cc_start: 0.8169 (ttp-110) cc_final: 0.7369 (ttp80) REVERT: B 217 ASP cc_start: 0.7914 (m-30) cc_final: 0.7424 (m-30) REVERT: B 306 MET cc_start: 0.8465 (mtp) cc_final: 0.8220 (mtp) REVERT: A 103 GLU cc_start: 0.8418 (mp0) cc_final: 0.8004 (mp0) REVERT: A 123 MET cc_start: 0.6483 (mmm) cc_final: 0.5670 (mmm) REVERT: A 164 ASN cc_start: 0.8700 (t0) cc_final: 0.8311 (t0) REVERT: A 213 ARG cc_start: 0.8335 (ttp-110) cc_final: 0.7553 (ttp-110) REVERT: A 217 ASP cc_start: 0.7951 (m-30) cc_final: 0.7313 (m-30) REVERT: A 225 GLU cc_start: 0.8262 (tp30) cc_final: 0.7989 (mm-30) REVERT: A 280 MET cc_start: 0.8724 (mtm) cc_final: 0.8457 (mpp) REVERT: A 288 GLU cc_start: 0.8448 (mp0) cc_final: 0.8136 (mp0) REVERT: A 318 ASN cc_start: 0.8471 (t0) cc_final: 0.8241 (t0) REVERT: D 12 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8378 (mmtt) REVERT: D 103 GLU cc_start: 0.8503 (mp0) cc_final: 0.8121 (mp0) REVERT: D 123 MET cc_start: 0.5471 (mmt) cc_final: 0.4938 (mmm) REVERT: D 164 ASN cc_start: 0.8835 (t0) cc_final: 0.8568 (t0) REVERT: D 213 ARG cc_start: 0.7738 (mtm110) cc_final: 0.7415 (ttp-110) REVERT: D 217 ASP cc_start: 0.7833 (m-30) cc_final: 0.7392 (m-30) REVERT: D 225 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7888 (mm-30) REVERT: D 239 ASP cc_start: 0.8750 (t0) cc_final: 0.8292 (t0) REVERT: D 280 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8404 (mmt) REVERT: D 342 GLU cc_start: 0.7317 (mp0) cc_final: 0.7024 (mp0) REVERT: D 371 ARG cc_start: 0.8472 (mmt90) cc_final: 0.8224 (mmt90) REVERT: F 12 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8508 (mmmt) REVERT: F 110 SER cc_start: 0.8152 (t) cc_final: 0.7935 (t) REVERT: F 213 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7612 (ttp-110) REVERT: F 217 ASP cc_start: 0.7806 (m-30) cc_final: 0.7322 (m-30) REVERT: F 225 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7927 (mm-30) REVERT: F 239 ASP cc_start: 0.8494 (t0) cc_final: 0.8202 (t0) REVERT: F 323 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8819 (ttmm) REVERT: H 12 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8048 (mmtt) REVERT: H 213 ARG cc_start: 0.8304 (ttm110) cc_final: 0.7833 (ttp-110) REVERT: H 239 ASP cc_start: 0.8515 (t0) cc_final: 0.8207 (t0) REVERT: H 280 MET cc_start: 0.8571 (mpp) cc_final: 0.8360 (mmm) REVERT: J 192 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: J 208 GLU cc_start: 0.7474 (pt0) cc_final: 0.7206 (mp0) REVERT: J 213 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.7505 (ttp-110) REVERT: J 217 ASP cc_start: 0.7774 (m-30) cc_final: 0.7165 (m-30) REVERT: J 239 ASP cc_start: 0.8542 (t0) cc_final: 0.8320 (t0) REVERT: J 263 GLU cc_start: 0.7952 (mp0) cc_final: 0.7580 (mp0) REVERT: J 375 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7636 (mptt) REVERT: L 103 GLU cc_start: 0.8529 (mp0) cc_final: 0.8176 (mp0) REVERT: L 213 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.7770 (ttp-110) REVERT: L 217 ASP cc_start: 0.7939 (m-30) cc_final: 0.7483 (m-30) REVERT: L 225 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7790 (mm-30) REVERT: L 226 ASP cc_start: 0.8161 (p0) cc_final: 0.7952 (p0) REVERT: L 239 ASP cc_start: 0.8743 (t0) cc_final: 0.8523 (t0) REVERT: L 393 LEU cc_start: 0.8308 (tt) cc_final: 0.7377 (mp) REVERT: N 148 GLU cc_start: 0.7802 (pt0) cc_final: 0.7596 (mt-10) REVERT: N 164 ASN cc_start: 0.8838 (t0) cc_final: 0.8528 (t0) REVERT: N 192 GLU cc_start: 0.8126 (mp0) cc_final: 0.7863 (mt-10) REVERT: N 225 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8098 (mm-30) REVERT: N 263 GLU cc_start: 0.8118 (mp0) cc_final: 0.7853 (mp0) REVERT: N 317 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8091 (mm-30) REVERT: N 342 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: P 12 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8187 (mttt) REVERT: P 32 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8106 (mmmm) REVERT: P 164 ASN cc_start: 0.8772 (t0) cc_final: 0.8522 (t0) REVERT: P 213 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7859 (ttp-110) REVERT: P 217 ASP cc_start: 0.7963 (m-30) cc_final: 0.7719 (m-30) REVERT: P 239 ASP cc_start: 0.8559 (t0) cc_final: 0.8335 (t0) REVERT: P 288 GLU cc_start: 0.8583 (mp0) cc_final: 0.8258 (mp0) REVERT: P 308 GLU cc_start: 0.8257 (pm20) cc_final: 0.7893 (pm20) REVERT: P 318 ASN cc_start: 0.8402 (t0) cc_final: 0.8163 (t0) REVERT: S 213 ARG cc_start: 0.8514 (ttm110) cc_final: 0.7702 (ttp-110) REVERT: S 217 ASP cc_start: 0.7933 (m-30) cc_final: 0.7595 (m-30) REVERT: S 225 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8221 (mm-30) REVERT: S 241 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8592 (mmtt) REVERT: S 280 MET cc_start: 0.8599 (mtm) cc_final: 0.8314 (mmm) REVERT: S 318 ASN cc_start: 0.8469 (t0) cc_final: 0.8143 (t0) REVERT: S 380 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7187 (tt) REVERT: U 32 LYS cc_start: 0.8361 (mttp) cc_final: 0.8093 (mmtp) REVERT: U 103 GLU cc_start: 0.8466 (mp0) cc_final: 0.8058 (mp0) REVERT: U 164 ASN cc_start: 0.8923 (t0) cc_final: 0.8534 (t0) REVERT: U 213 ARG cc_start: 0.8174 (ttp-110) cc_final: 0.7486 (ttp80) REVERT: U 217 ASP cc_start: 0.8114 (m-30) cc_final: 0.7767 (m-30) REVERT: U 225 GLU cc_start: 0.8265 (tp30) cc_final: 0.7927 (mm-30) REVERT: U 239 ASP cc_start: 0.8697 (t0) cc_final: 0.8488 (t0) REVERT: U 280 MET cc_start: 0.8763 (tpp) cc_final: 0.8519 (tpp) REVERT: U 337 MET cc_start: 0.9201 (mmp) cc_final: 0.8999 (mmp) REVERT: U 342 GLU cc_start: 0.7246 (mp0) cc_final: 0.6862 (mp0) REVERT: U 361 TYR cc_start: 0.9315 (m-80) cc_final: 0.9034 (m-80) REVERT: W 86 GLN cc_start: 0.8809 (mt0) cc_final: 0.8604 (mt0) REVERT: W 103 GLU cc_start: 0.8543 (mp0) cc_final: 0.8138 (mp0) REVERT: W 129 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: W 164 ASN cc_start: 0.8842 (t0) cc_final: 0.8598 (t0) REVERT: W 192 GLU cc_start: 0.7985 (mp0) cc_final: 0.7728 (mt-10) REVERT: W 225 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8022 (mm-30) REVERT: W 239 ASP cc_start: 0.8749 (t0) cc_final: 0.8482 (t0) REVERT: W 380 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7573 (tt) REVERT: Y 86 GLN cc_start: 0.8932 (mt0) cc_final: 0.8652 (mt0) REVERT: Y 115 THR cc_start: 0.8891 (p) cc_final: 0.8580 (t) REVERT: Y 164 ASN cc_start: 0.8758 (t0) cc_final: 0.8532 (t0) REVERT: Y 213 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7658 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8010 (m-30) cc_final: 0.7744 (m-30) REVERT: Y 225 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7900 (mm-30) REVERT: Y 239 ASP cc_start: 0.8681 (t0) cc_final: 0.8387 (t0) REVERT: Y 277 ILE cc_start: 0.9287 (mm) cc_final: 0.9048 (mm) REVERT: Y 280 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8118 (mmm) REVERT: Y 288 GLU cc_start: 0.8133 (mp0) cc_final: 0.7844 (mp0) REVERT: Y 306 MET cc_start: 0.8404 (mtp) cc_final: 0.8110 (mtp) REVERT: Y 318 ASN cc_start: 0.8408 (t0) cc_final: 0.8133 (t0) REVERT: Y 367 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: 0 115 THR cc_start: 0.8837 (p) cc_final: 0.8553 (t) REVERT: 0 217 ASP cc_start: 0.8001 (m-30) cc_final: 0.7485 (m-30) REVERT: 0 225 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7873 (mm-30) REVERT: 0 239 ASP cc_start: 0.8802 (t0) cc_final: 0.8574 (t0) REVERT: 0 288 GLU cc_start: 0.8390 (mp0) cc_final: 0.8012 (mp0) REVERT: 0 306 MET cc_start: 0.8293 (mtp) cc_final: 0.8042 (mtp) REVERT: 0 318 ASN cc_start: 0.8397 (t0) cc_final: 0.8099 (t0) REVERT: 2 53 ASP cc_start: 0.8753 (t0) cc_final: 0.8486 (t0) REVERT: 2 123 MET cc_start: 0.7100 (mmt) cc_final: 0.6663 (mmt) REVERT: 2 164 ASN cc_start: 0.8787 (t0) cc_final: 0.8306 (t0) REVERT: 2 213 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7855 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7821 (m-30) cc_final: 0.7551 (m-30) REVERT: 2 239 ASP cc_start: 0.8700 (t0) cc_final: 0.8470 (t0) REVERT: 2 252 GLU cc_start: 0.8615 (tt0) cc_final: 0.8412 (mt-10) REVERT: 2 280 MET cc_start: 0.8847 (tpp) cc_final: 0.8554 (mmm) REVERT: 2 288 GLU cc_start: 0.8319 (mp0) cc_final: 0.8099 (mp0) REVERT: 2 318 ASN cc_start: 0.8440 (t0) cc_final: 0.8206 (t0) outliers start: 108 outliers final: 66 residues processed: 1161 average time/residue: 0.2281 time to fit residues: 435.0565 Evaluate side-chains 1090 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1013 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 367 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 255 CYS Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 347 MET Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 343 LEU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain S residue 380 LEU Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 255 CYS Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 380 LEU Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 258 ASP Chi-restraints excluded: chain Y residue 280 MET Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 367 GLU Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 258 ASP Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 380 LEU Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 322 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 478 optimal weight: 0.4980 chunk 555 optimal weight: 7.9990 chunk 418 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN Y 305 GLN 2 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.116368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096018 restraints weight = 64662.982| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.93 r_work: 0.2826 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 47672 Z= 0.151 Angle : 0.625 11.349 64860 Z= 0.308 Chirality : 0.046 0.249 7470 Planarity : 0.004 0.058 7980 Dihedral : 9.120 134.836 7247 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.98 % Allowed : 16.79 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.12), residues: 5625 helix: 0.84 (0.10), residues: 3075 sheet: 0.26 (0.28), residues: 375 loop : -0.04 (0.15), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 392 TYR 0.014 0.001 TYR U 260 PHE 0.019 0.001 PHE U 209 TRP 0.009 0.001 TRP H 215 HIS 0.003 0.001 HIS S 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (47670) covalent geometry : angle 0.62456 / 0.31 (64860) hydrogen bonds : bond 0.03253 / 2.15 ( 1725) hydrogen bonds : angle 3.70946 / 2.49 ( 4995) Misc. bond : bond 0.00157 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1041 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8749 (pp) REVERT: B 92 THR cc_start: 0.8415 (m) cc_final: 0.8207 (m) REVERT: B 129 GLN cc_start: 0.8368 (mt0) cc_final: 0.8109 (tm-30) REVERT: B 164 ASN cc_start: 0.8824 (t0) cc_final: 0.8591 (t0) REVERT: B 213 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7439 (ttp80) REVERT: B 217 ASP cc_start: 0.7985 (m-30) cc_final: 0.7481 (m-30) REVERT: A 103 GLU cc_start: 0.8354 (mp0) cc_final: 0.8076 (mp0) REVERT: A 123 MET cc_start: 0.6328 (mmm) cc_final: 0.5412 (mmm) REVERT: A 164 ASN cc_start: 0.8717 (t0) cc_final: 0.8263 (t0) REVERT: A 217 ASP cc_start: 0.7986 (m-30) cc_final: 0.7326 (m-30) REVERT: A 225 GLU cc_start: 0.8302 (tp30) cc_final: 0.7989 (mm-30) REVERT: A 280 MET cc_start: 0.8740 (mtm) cc_final: 0.8432 (mpp) REVERT: A 288 GLU cc_start: 0.8482 (mp0) cc_final: 0.8138 (mp0) REVERT: A 318 ASN cc_start: 0.8506 (t0) cc_final: 0.8246 (t0) REVERT: D 103 GLU cc_start: 0.8540 (mp0) cc_final: 0.8145 (mp0) REVERT: D 123 MET cc_start: 0.5488 (mmt) cc_final: 0.4941 (mmm) REVERT: D 164 ASN cc_start: 0.8848 (t0) cc_final: 0.8560 (t0) REVERT: D 213 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7345 (ttp-110) REVERT: D 217 ASP cc_start: 0.7867 (m-30) cc_final: 0.7405 (m-30) REVERT: D 225 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7785 (mm-30) REVERT: D 239 ASP cc_start: 0.8714 (t0) cc_final: 0.8274 (t0) REVERT: D 280 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8319 (mmt) REVERT: D 371 ARG cc_start: 0.8457 (mmt90) cc_final: 0.8188 (mmt90) REVERT: F 12 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8437 (mmmt) REVERT: F 110 SER cc_start: 0.8118 (t) cc_final: 0.7889 (t) REVERT: F 213 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7587 (ttp-110) REVERT: F 217 ASP cc_start: 0.7841 (m-30) cc_final: 0.7353 (m-30) REVERT: F 225 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7822 (mm-30) REVERT: F 239 ASP cc_start: 0.8541 (t0) cc_final: 0.8224 (t0) REVERT: F 280 MET cc_start: 0.8766 (mmm) cc_final: 0.8430 (tpp) REVERT: F 323 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8856 (ttmm) REVERT: H 12 LYS cc_start: 0.8277 (mmtt) cc_final: 0.8028 (mmtt) REVERT: H 239 ASP cc_start: 0.8628 (t0) cc_final: 0.8284 (t0) REVERT: H 280 MET cc_start: 0.8638 (mpp) cc_final: 0.8361 (mmm) REVERT: H 342 GLU cc_start: 0.7389 (mp0) cc_final: 0.7184 (mp0) REVERT: J 164 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8341 (t0) REVERT: J 192 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: J 213 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.7578 (ttp-110) REVERT: J 217 ASP cc_start: 0.7814 (m-30) cc_final: 0.7189 (m-30) REVERT: J 239 ASP cc_start: 0.8553 (t0) cc_final: 0.8320 (t0) REVERT: J 263 GLU cc_start: 0.8066 (mp0) cc_final: 0.7684 (mp0) REVERT: J 375 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7629 (mptt) REVERT: L 103 GLU cc_start: 0.8515 (mp0) cc_final: 0.8273 (mp0) REVERT: L 213 ARG cc_start: 0.8445 (ttp-110) cc_final: 0.7806 (ttp-110) REVERT: L 217 ASP cc_start: 0.7973 (m-30) cc_final: 0.7496 (m-30) REVERT: L 239 ASP cc_start: 0.8758 (t0) cc_final: 0.8492 (t0) REVERT: L 393 LEU cc_start: 0.8345 (tt) cc_final: 0.7402 (mp) REVERT: N 164 ASN cc_start: 0.8870 (t0) cc_final: 0.8542 (t0) REVERT: N 192 GLU cc_start: 0.8180 (mp0) cc_final: 0.7886 (mt-10) REVERT: N 212 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7836 (mt-10) REVERT: N 225 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8088 (mm-30) REVERT: N 317 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8079 (mm-30) REVERT: N 342 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: P 12 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8141 (mttt) REVERT: P 32 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8175 (mmmm) REVERT: P 164 ASN cc_start: 0.8848 (t0) cc_final: 0.8564 (t0) REVERT: P 213 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7803 (ttp-110) REVERT: P 217 ASP cc_start: 0.8061 (m-30) cc_final: 0.7788 (m-30) REVERT: P 239 ASP cc_start: 0.8573 (t0) cc_final: 0.8335 (t0) REVERT: P 288 GLU cc_start: 0.8577 (mp0) cc_final: 0.8228 (mp0) REVERT: P 308 GLU cc_start: 0.8250 (pm20) cc_final: 0.7834 (pm20) REVERT: P 318 ASN cc_start: 0.8471 (t0) cc_final: 0.8215 (t0) REVERT: S 129 GLN cc_start: 0.8424 (mt0) cc_final: 0.8125 (tm-30) REVERT: S 209 PHE cc_start: 0.8336 (m-10) cc_final: 0.8088 (m-10) REVERT: S 213 ARG cc_start: 0.8530 (ttm110) cc_final: 0.7705 (ttp-110) REVERT: S 217 ASP cc_start: 0.8058 (m-30) cc_final: 0.7722 (m-30) REVERT: S 225 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8186 (mm-30) REVERT: S 241 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8557 (mmtt) REVERT: S 280 MET cc_start: 0.8608 (mtm) cc_final: 0.8242 (mmm) REVERT: S 380 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7177 (tt) REVERT: U 32 LYS cc_start: 0.8412 (mttp) cc_final: 0.7824 (mmtp) REVERT: U 103 GLU cc_start: 0.8493 (mp0) cc_final: 0.8067 (mp0) REVERT: U 164 ASN cc_start: 0.8883 (t0) cc_final: 0.8478 (t0) REVERT: U 213 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7426 (ttp80) REVERT: U 217 ASP cc_start: 0.8144 (m-30) cc_final: 0.7805 (m-30) REVERT: U 225 GLU cc_start: 0.8314 (tp30) cc_final: 0.7930 (mm-30) REVERT: U 239 ASP cc_start: 0.8730 (t0) cc_final: 0.8517 (t0) REVERT: U 280 MET cc_start: 0.8795 (tpp) cc_final: 0.8540 (tpp) REVERT: W 129 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: W 164 ASN cc_start: 0.8893 (t0) cc_final: 0.8623 (t0) REVERT: W 192 GLU cc_start: 0.7996 (mp0) cc_final: 0.7766 (mt-10) REVERT: W 209 PHE cc_start: 0.8334 (m-10) cc_final: 0.8082 (m-80) REVERT: W 239 ASP cc_start: 0.8868 (t0) cc_final: 0.8572 (t0) REVERT: W 380 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7619 (tt) REVERT: Y 32 LYS cc_start: 0.8386 (mttp) cc_final: 0.8138 (mmtp) REVERT: Y 86 GLN cc_start: 0.8962 (mt0) cc_final: 0.8682 (mt0) REVERT: Y 115 THR cc_start: 0.8856 (p) cc_final: 0.8543 (t) REVERT: Y 164 ASN cc_start: 0.8728 (t0) cc_final: 0.8387 (t0) REVERT: Y 213 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7711 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8041 (m-30) cc_final: 0.7769 (m-30) REVERT: Y 225 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7855 (mm-30) REVERT: Y 239 ASP cc_start: 0.8772 (t0) cc_final: 0.8534 (t0) REVERT: Y 280 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8101 (tpp) REVERT: Y 288 GLU cc_start: 0.8214 (mp0) cc_final: 0.7811 (mp0) REVERT: Y 306 MET cc_start: 0.8499 (mtp) cc_final: 0.8159 (mtp) REVERT: Y 318 ASN cc_start: 0.8440 (t0) cc_final: 0.8139 (t0) REVERT: Y 357 PHE cc_start: 0.8736 (t80) cc_final: 0.8493 (t80) REVERT: Y 371 ARG cc_start: 0.8573 (mmt90) cc_final: 0.8371 (mmt90) REVERT: 0 32 LYS cc_start: 0.8379 (mttm) cc_final: 0.8155 (mmtt) REVERT: 0 115 THR cc_start: 0.8807 (p) cc_final: 0.8510 (t) REVERT: 0 225 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7792 (mm-30) REVERT: 0 288 GLU cc_start: 0.8396 (mp0) cc_final: 0.7962 (mp0) REVERT: 0 306 MET cc_start: 0.8344 (mtp) cc_final: 0.8115 (mtp) REVERT: 0 318 ASN cc_start: 0.8422 (t0) cc_final: 0.8117 (t0) REVERT: 2 53 ASP cc_start: 0.8745 (t0) cc_final: 0.8494 (t0) REVERT: 2 123 MET cc_start: 0.7095 (mmt) cc_final: 0.6665 (mmt) REVERT: 2 164 ASN cc_start: 0.8816 (t0) cc_final: 0.8307 (t0) REVERT: 2 213 ARG cc_start: 0.8249 (mtp-110) cc_final: 0.7792 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7813 (m-30) cc_final: 0.7530 (m-30) REVERT: 2 239 ASP cc_start: 0.8725 (t0) cc_final: 0.8466 (t0) REVERT: 2 280 MET cc_start: 0.8876 (tpp) cc_final: 0.8562 (mmm) REVERT: 2 288 GLU cc_start: 0.8390 (mp0) cc_final: 0.8109 (mp0) REVERT: 2 308 GLU cc_start: 0.8065 (pm20) cc_final: 0.7755 (pm20) REVERT: 2 318 ASN cc_start: 0.8487 (t0) cc_final: 0.8206 (t0) outliers start: 96 outliers final: 65 residues processed: 1103 average time/residue: 0.2050 time to fit residues: 373.1856 Evaluate side-chains 1079 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1003 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 367 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 164 ASN Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 343 LEU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain S residue 380 LEU Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 255 CYS Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 380 LEU Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 258 ASP Chi-restraints excluded: chain Y residue 280 MET Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 105 VAL Chi-restraints excluded: chain 0 residue 258 ASP Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 367 GLU Chi-restraints excluded: chain 0 residue 380 LEU Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 297 GLU Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 87 optimal weight: 5.9990 chunk 361 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 291 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 528 optimal weight: 0.9980 chunk 476 optimal weight: 0.8980 chunk 345 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 chunk 323 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 321 GLN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 321 GLN U 86 GLN W 86 GLN 2 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099025 restraints weight = 64787.222| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.93 r_work: 0.2874 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 47672 Z= 0.114 Angle : 0.602 11.928 64860 Z= 0.297 Chirality : 0.044 0.244 7470 Planarity : 0.004 0.059 7980 Dihedral : 9.042 133.474 7247 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.75 % Allowed : 17.24 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.12), residues: 5625 helix: 0.76 (0.10), residues: 3165 sheet: 0.15 (0.28), residues: 375 loop : -0.06 (0.15), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 392 TYR 0.010 0.001 TYR N 281 PHE 0.011 0.001 PHE A 11 TRP 0.010 0.001 TRP F 215 HIS 0.004 0.001 HIS S 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (47670) covalent geometry : angle 0.60239 / 0.30 (64860) hydrogen bonds : bond 0.03041 / 2.01 ( 1725) hydrogen bonds : angle 3.66349 / 2.46 ( 4995) Misc. bond : bond 0.00146 / 0.07 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1082 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8696 (pp) REVERT: B 92 THR cc_start: 0.8423 (m) cc_final: 0.8179 (m) REVERT: B 129 GLN cc_start: 0.8302 (mt0) cc_final: 0.8088 (tm-30) REVERT: B 164 ASN cc_start: 0.8810 (t0) cc_final: 0.8376 (t0) REVERT: B 213 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7414 (ttp80) REVERT: B 217 ASP cc_start: 0.7958 (m-30) cc_final: 0.7479 (m-30) REVERT: B 288 GLU cc_start: 0.8436 (mp0) cc_final: 0.7837 (mp0) REVERT: A 103 GLU cc_start: 0.8339 (mp0) cc_final: 0.8117 (mp0) REVERT: A 123 MET cc_start: 0.6397 (mmm) cc_final: 0.5520 (mmm) REVERT: A 129 GLN cc_start: 0.8322 (mt0) cc_final: 0.8052 (tm-30) REVERT: A 164 ASN cc_start: 0.8699 (t0) cc_final: 0.8221 (t0) REVERT: A 201 GLN cc_start: 0.8858 (mm110) cc_final: 0.8655 (mm110) REVERT: A 217 ASP cc_start: 0.7943 (m-30) cc_final: 0.7283 (m-30) REVERT: A 225 GLU cc_start: 0.8251 (tp30) cc_final: 0.7984 (mm-30) REVERT: A 280 MET cc_start: 0.8652 (mtm) cc_final: 0.8422 (mpp) REVERT: A 288 GLU cc_start: 0.8485 (mp0) cc_final: 0.8033 (mp0) REVERT: A 318 ASN cc_start: 0.8424 (t0) cc_final: 0.8187 (t0) REVERT: D 103 GLU cc_start: 0.8514 (mp0) cc_final: 0.8108 (mp0) REVERT: D 123 MET cc_start: 0.5495 (mmt) cc_final: 0.4935 (mmm) REVERT: D 164 ASN cc_start: 0.8821 (t0) cc_final: 0.8541 (t0) REVERT: D 213 ARG cc_start: 0.7725 (mtm110) cc_final: 0.7353 (ttp-110) REVERT: D 217 ASP cc_start: 0.7824 (m-30) cc_final: 0.7340 (m-30) REVERT: D 225 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7815 (mm-30) REVERT: D 239 ASP cc_start: 0.8690 (t0) cc_final: 0.8475 (t70) REVERT: D 280 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8267 (mmt) REVERT: F 12 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8458 (mmmt) REVERT: F 110 SER cc_start: 0.8091 (t) cc_final: 0.7872 (t) REVERT: F 213 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7557 (ttp-110) REVERT: F 217 ASP cc_start: 0.7793 (m-30) cc_final: 0.7285 (m-30) REVERT: F 225 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7847 (mm-30) REVERT: F 239 ASP cc_start: 0.8486 (t0) cc_final: 0.8157 (t0) REVERT: F 280 MET cc_start: 0.8730 (mmm) cc_final: 0.8393 (tpp) REVERT: F 323 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8810 (ttmm) REVERT: H 12 LYS cc_start: 0.8237 (mmtt) cc_final: 0.8005 (mmtt) REVERT: H 213 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7936 (ttp-110) REVERT: H 342 GLU cc_start: 0.7373 (mp0) cc_final: 0.7167 (mp0) REVERT: H 364 LEU cc_start: 0.8753 (tt) cc_final: 0.8550 (tp) REVERT: J 164 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8331 (t0) REVERT: J 192 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: J 208 GLU cc_start: 0.7289 (pt0) cc_final: 0.7072 (pm20) REVERT: J 213 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.7586 (ttp-110) REVERT: J 217 ASP cc_start: 0.7719 (m-30) cc_final: 0.7093 (m-30) REVERT: J 239 ASP cc_start: 0.8513 (t0) cc_final: 0.8273 (t0) REVERT: J 263 GLU cc_start: 0.8012 (mp0) cc_final: 0.7625 (mp0) REVERT: J 371 ARG cc_start: 0.8553 (mmt90) cc_final: 0.8304 (mmt90) REVERT: J 375 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7502 (mptt) REVERT: L 213 ARG cc_start: 0.8438 (ttp-110) cc_final: 0.7783 (ttp-110) REVERT: L 217 ASP cc_start: 0.7913 (m-30) cc_final: 0.7419 (m-30) REVERT: L 393 LEU cc_start: 0.8288 (tt) cc_final: 0.7355 (mp) REVERT: N 53 ASP cc_start: 0.8718 (t70) cc_final: 0.8371 (t0) REVERT: N 164 ASN cc_start: 0.8834 (t0) cc_final: 0.8509 (t0) REVERT: N 192 GLU cc_start: 0.8195 (mp0) cc_final: 0.7881 (mt-10) REVERT: N 225 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8060 (mm-30) REVERT: N 263 GLU cc_start: 0.8243 (mp0) cc_final: 0.7632 (mp0) REVERT: N 300 MET cc_start: 0.8313 (mtt) cc_final: 0.8077 (mtt) REVERT: N 317 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8075 (mm-30) REVERT: N 342 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: P 12 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8326 (mttt) REVERT: P 32 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8150 (mmmm) REVERT: P 89 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8582 (mm-40) REVERT: P 164 ASN cc_start: 0.8828 (t0) cc_final: 0.8500 (t0) REVERT: P 213 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7759 (ttp-110) REVERT: P 217 ASP cc_start: 0.7979 (m-30) cc_final: 0.7715 (m-30) REVERT: P 239 ASP cc_start: 0.8534 (t0) cc_final: 0.8303 (t0) REVERT: P 288 GLU cc_start: 0.8561 (mp0) cc_final: 0.8226 (mp0) REVERT: P 306 MET cc_start: 0.8474 (mtp) cc_final: 0.8251 (mtt) REVERT: P 308 GLU cc_start: 0.8244 (pm20) cc_final: 0.7835 (pm20) REVERT: P 318 ASN cc_start: 0.8417 (t0) cc_final: 0.8153 (t0) REVERT: S 28 ILE cc_start: 0.8929 (mt) cc_final: 0.8726 (mt) REVERT: S 67 PRO cc_start: 0.8551 (Cg_exo) cc_final: 0.8283 (Cg_endo) REVERT: S 164 ASN cc_start: 0.8804 (t0) cc_final: 0.8361 (t0) REVERT: S 213 ARG cc_start: 0.8510 (ttm110) cc_final: 0.7664 (ttp-110) REVERT: S 217 ASP cc_start: 0.8020 (m-30) cc_final: 0.7682 (m-30) REVERT: S 225 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8194 (mm-30) REVERT: S 241 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8594 (mmtt) REVERT: S 280 MET cc_start: 0.8552 (mtm) cc_final: 0.8240 (mmm) REVERT: S 380 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7156 (tt) REVERT: U 103 GLU cc_start: 0.8455 (mp0) cc_final: 0.8065 (mp0) REVERT: U 164 ASN cc_start: 0.8877 (t0) cc_final: 0.8439 (t0) REVERT: U 213 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7444 (ttp80) REVERT: U 217 ASP cc_start: 0.8076 (m-30) cc_final: 0.7724 (m-30) REVERT: U 225 GLU cc_start: 0.8290 (tp30) cc_final: 0.7920 (mm-30) REVERT: U 239 ASP cc_start: 0.8684 (t0) cc_final: 0.8436 (t0) REVERT: U 280 MET cc_start: 0.8757 (tpp) cc_final: 0.8518 (tpp) REVERT: U 342 GLU cc_start: 0.7681 (mp0) cc_final: 0.7365 (mp0) REVERT: U 361 TYR cc_start: 0.9333 (m-80) cc_final: 0.9091 (m-80) REVERT: U 367 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6582 (mt-10) REVERT: W 53 ASP cc_start: 0.8704 (t0) cc_final: 0.8498 (t0) REVERT: W 86 GLN cc_start: 0.8800 (mt0) cc_final: 0.8583 (mt0) REVERT: W 129 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: W 164 ASN cc_start: 0.8888 (t0) cc_final: 0.8604 (t0) REVERT: W 192 GLU cc_start: 0.7968 (mp0) cc_final: 0.7688 (mt-10) REVERT: W 209 PHE cc_start: 0.8142 (m-10) cc_final: 0.7723 (m-10) REVERT: W 217 ASP cc_start: 0.8039 (m-30) cc_final: 0.7687 (m-30) REVERT: W 225 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7918 (mm-30) REVERT: W 239 ASP cc_start: 0.8783 (t0) cc_final: 0.8509 (t0) REVERT: W 241 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8590 (mmtt) REVERT: W 296 LEU cc_start: 0.9121 (tp) cc_final: 0.8874 (tp) REVERT: W 361 TYR cc_start: 0.9339 (m-80) cc_final: 0.9026 (m-80) REVERT: W 380 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7538 (tt) REVERT: Y 86 GLN cc_start: 0.8943 (mt0) cc_final: 0.8665 (mt0) REVERT: Y 115 THR cc_start: 0.8854 (p) cc_final: 0.8545 (t) REVERT: Y 164 ASN cc_start: 0.8719 (t0) cc_final: 0.8298 (t0) REVERT: Y 213 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7620 (ttp-110) REVERT: Y 217 ASP cc_start: 0.7998 (m-30) cc_final: 0.7699 (m-30) REVERT: Y 225 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7890 (mm-30) REVERT: Y 239 ASP cc_start: 0.8754 (t0) cc_final: 0.8523 (t0) REVERT: Y 280 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8048 (mmm) REVERT: Y 288 GLU cc_start: 0.8114 (mp0) cc_final: 0.7745 (mp0) REVERT: Y 306 MET cc_start: 0.8412 (mtp) cc_final: 0.8167 (mtp) REVERT: Y 318 ASN cc_start: 0.8393 (t0) cc_final: 0.8130 (t0) REVERT: 0 32 LYS cc_start: 0.8343 (mttm) cc_final: 0.7822 (mmtt) REVERT: 0 115 THR cc_start: 0.8806 (p) cc_final: 0.8514 (t) REVERT: 0 217 ASP cc_start: 0.7978 (m-30) cc_final: 0.7525 (m-30) REVERT: 0 288 GLU cc_start: 0.8356 (mp0) cc_final: 0.7975 (mp0) REVERT: 0 318 ASN cc_start: 0.8350 (t0) cc_final: 0.8041 (t0) REVERT: 2 53 ASP cc_start: 0.8739 (t0) cc_final: 0.8470 (t0) REVERT: 2 123 MET cc_start: 0.7102 (mmt) cc_final: 0.6684 (mmt) REVERT: 2 164 ASN cc_start: 0.8809 (t0) cc_final: 0.8186 (t0) REVERT: 2 213 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7757 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7785 (m-30) cc_final: 0.7487 (m-30) REVERT: 2 239 ASP cc_start: 0.8680 (t0) cc_final: 0.8427 (t0) REVERT: 2 252 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8370 (mt-10) REVERT: 2 280 MET cc_start: 0.8814 (tpp) cc_final: 0.8516 (mmm) REVERT: 2 288 GLU cc_start: 0.8324 (mp0) cc_final: 0.8115 (mp0) REVERT: 2 308 GLU cc_start: 0.8102 (pm20) cc_final: 0.7778 (pm20) REVERT: 2 318 ASN cc_start: 0.8396 (t0) cc_final: 0.8153 (t0) outliers start: 85 outliers final: 54 residues processed: 1138 average time/residue: 0.1878 time to fit residues: 354.0460 Evaluate side-chains 1094 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 1027 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 164 ASN Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 343 LEU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain S residue 380 LEU Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 380 LEU Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 258 ASP Chi-restraints excluded: chain Y residue 280 MET Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 258 ASP Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 367 GLU Chi-restraints excluded: chain 0 residue 380 LEU Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 252 GLU Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 233 optimal weight: 4.9990 chunk 302 optimal weight: 7.9990 chunk 563 optimal weight: 6.9990 chunk 546 optimal weight: 9.9990 chunk 377 optimal weight: 3.9990 chunk 458 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 548 optimal weight: 7.9990 chunk 249 optimal weight: 0.9980 chunk 463 optimal weight: 3.9990 chunk 413 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 321 GLN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.114304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.093819 restraints weight = 65268.994| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.94 r_work: 0.2794 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 47672 Z= 0.206 Angle : 0.659 11.579 64860 Z= 0.326 Chirality : 0.047 0.251 7470 Planarity : 0.005 0.061 7980 Dihedral : 9.117 135.544 7247 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.81 % Allowed : 17.61 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.12), residues: 5625 helix: 0.75 (0.10), residues: 3165 sheet: 0.09 (0.28), residues: 375 loop : -0.14 (0.15), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 392 TYR 0.015 0.001 TYR 0 361 PHE 0.023 0.002 PHE U 209 TRP 0.011 0.001 TRP D 146 HIS 0.003 0.001 HIS W 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (47670) covalent geometry : angle 0.65877 / 0.33 (64860) hydrogen bonds : bond 0.03420 / 2.26 ( 1725) hydrogen bonds : angle 3.71307 / 2.50 ( 4995) Misc. bond : bond 0.00154 / 0.07 ( 2) =============================================================================== Job complete usr+sys time: 13315.78 seconds wall clock time: 227 minutes 20.32 seconds (13640.32 seconds total)