Starting phenix.real_space_refine on Sun Jun 7 23:08:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h5q_0141/06_2026/6h5q_0141.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h5q_0141/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6h5q_0141/06_2026/6h5q_0141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h5q_0141/06_2026/6h5q_0141.map" model { file = "/net/cci-nas-00/data/ceres_data/6h5q_0141/06_2026/6h5q_0141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h5q_0141/06_2026/6h5q_0141.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/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: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} 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: 5.04, per 1000 atoms: 0.11 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: 3.48 Conformation dependent library (CDL) restraints added in 1.9 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: 6.09 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: 9.41 Time building geometry restraints manager: 4.40 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: 62151 2.50 - 5.00: 2420 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 - 13.07: 25486 13.07 - 26.14: 2194 26.14 - 39.21: 655 39.21 - 52.28: 195 52.28 - 65.35: 90 Dihedral angle restraints: 28620 sinusoidal: 12270 harmonic: 16350 Sorted by residual: dihedral pdb=" CA THR J 187 " pdb=" C THR J 187 " pdb=" N ALA J 188 " pdb=" CA ALA J 188 " ideal model delta harmonic sigma weight residual 180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR Y 187 " pdb=" C THR Y 187 " pdb=" N ALA Y 188 " pdb=" CA ALA Y 188 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR 0 187 " pdb=" C THR 0 187 " pdb=" N ALA 0 188 " pdb=" CA ALA 0 188 " ideal model delta harmonic sigma weight residual -180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 28617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5066 0.055 - 0.110: 1909 0.110 - 0.166: 410 0.166 - 0.221: 70 0.221 - 0.276: 15 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=" 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 chirality pdb=" CB VAL 0 314 " pdb=" CA VAL 0 314 " pdb=" CG1 VAL 0 314 " pdb=" CG2 VAL 0 314 " 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: 3.000 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: 0.030 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 38.820 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.200 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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= 0.514 Angle : 1.145 12.492 64860 Z= 0.660 Chirality : 0.059 0.276 7470 Planarity : 0.007 0.049 7980 Dihedral : 11.787 65.352 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 0.00985 / 0.42 (47670) covalent geometry : angle 1.14491 / 0.66 (64860) hydrogen bonds : bond 0.30023 / 19.45 ( 1725) hydrogen bonds : angle 9.62806 / 6.63 ( 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 : 1.746 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: 0.2821 time to fit residues: 702.9195 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 : 1.608 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 0 305 GLN 0 322 ASN 0 351 ASN 2 351 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.116992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.096172 restraints weight = 64474.474| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.98 r_work: 0.2837 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 47672 Z= 0.155 Angle : 0.682 9.428 64860 Z= 0.349 Chirality : 0.043 0.182 7470 Planarity : 0.005 0.033 7980 Dihedral : 9.348 68.776 7283 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.47 % Allowed : 9.34 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.34 (0.10), residues: 5625 helix: -2.06 (0.08), residues: 3165 sheet: 0.26 (0.28), residues: 375 loop : -0.70 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 222 TYR 0.013 0.002 TYR N 260 PHE 0.013 0.002 PHE L 209 TRP 0.009 0.002 TRP L 146 HIS 0.005 0.001 HIS L 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (47670) covalent geometry : angle 0.68163 / 0.35 (64860) hydrogen bonds : bond 0.05189 / 3.41 ( 1725) hydrogen bonds : angle 4.77167 / 3.26 ( 4995) Misc. bond : bond 0.00024 / 0.01 ( 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 1375 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1255 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 SER cc_start: 0.9261 (t) cc_final: 0.8922 (m) REVERT: B 15 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8164 (ttmm) REVERT: B 34 ILE cc_start: 0.8980 (pp) cc_final: 0.8692 (pp) REVERT: B 53 ASP cc_start: 0.8851 (t0) cc_final: 0.8529 (t0) REVERT: B 213 ARG cc_start: 0.8135 (ttp-110) cc_final: 0.7279 (ttp80) REVERT: B 217 ASP cc_start: 0.7961 (m-30) cc_final: 0.7520 (m-30) REVERT: B 239 ASP cc_start: 0.8790 (t0) cc_final: 0.8506 (t0) REVERT: B 280 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8429 (mmm) REVERT: B 288 GLU cc_start: 0.8291 (mp0) cc_final: 0.7841 (mp0) REVERT: B 318 ASN cc_start: 0.8713 (t0) cc_final: 0.8404 (t0) REVERT: B 344 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8135 (mm-30) REVERT: B 356 TYR cc_start: 0.9553 (p90) cc_final: 0.9186 (p90) REVERT: A 123 MET cc_start: 0.5921 (mmm) cc_final: 0.5518 (mmm) REVERT: A 213 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7284 (ttp-110) REVERT: A 217 ASP cc_start: 0.8083 (m-30) cc_final: 0.7664 (m-30) REVERT: A 225 GLU cc_start: 0.8284 (tp30) cc_final: 0.7921 (mm-30) REVERT: A 288 GLU cc_start: 0.8311 (mp0) cc_final: 0.7864 (mp0) REVERT: A 318 ASN cc_start: 0.8643 (t0) cc_final: 0.8367 (t0) REVERT: D 103 GLU cc_start: 0.8358 (mp0) cc_final: 0.8032 (mp0) REVERT: D 213 ARG cc_start: 0.7698 (mtm110) cc_final: 0.7457 (ttp-110) REVERT: D 217 ASP cc_start: 0.7824 (m-30) cc_final: 0.7451 (m-30) REVERT: D 226 ASP cc_start: 0.8178 (p0) cc_final: 0.7727 (p0) REVERT: D 280 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8488 (mpp) REVERT: D 288 GLU cc_start: 0.8283 (mp0) cc_final: 0.7853 (mp0) REVERT: F 12 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8235 (mttt) REVERT: F 53 ASP cc_start: 0.8787 (t0) cc_final: 0.8510 (t0) REVERT: F 213 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7367 (ttp-110) REVERT: F 217 ASP cc_start: 0.8008 (m-30) cc_final: 0.7412 (m-30) REVERT: F 239 ASP cc_start: 0.8773 (t0) cc_final: 0.8406 (t0) REVERT: F 263 GLU cc_start: 0.8303 (mp0) cc_final: 0.7839 (mp0) REVERT: F 318 ASN cc_start: 0.8768 (t0) cc_final: 0.8458 (t0) REVERT: H 53 ASP cc_start: 0.8809 (t0) cc_final: 0.8535 (t0) REVERT: H 213 ARG cc_start: 0.8289 (ttm110) cc_final: 0.7763 (ttp-110) REVERT: H 239 ASP cc_start: 0.8690 (t0) cc_final: 0.8231 (t0) REVERT: H 288 GLU cc_start: 0.8269 (mp0) cc_final: 0.7940 (mp0) REVERT: H 318 ASN cc_start: 0.8648 (t0) cc_final: 0.8385 (t0) REVERT: H 357 PHE cc_start: 0.9020 (t80) cc_final: 0.8737 (t80) REVERT: J 15 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8331 (ttmm) REVERT: J 42 ASP cc_start: 0.7971 (p0) cc_final: 0.7468 (t0) REVERT: J 53 ASP cc_start: 0.8721 (t0) cc_final: 0.8479 (t0) REVERT: J 103 GLU cc_start: 0.8337 (mp0) cc_final: 0.8096 (mp0) REVERT: J 148 GLU cc_start: 0.7867 (pt0) cc_final: 0.7634 (mt-10) REVERT: J 213 ARG cc_start: 0.8106 (ttp-110) cc_final: 0.7639 (ttp-110) REVERT: J 217 ASP cc_start: 0.7874 (m-30) cc_final: 0.7277 (m-30) REVERT: J 221 ASN cc_start: 0.8789 (m110) cc_final: 0.8392 (m110) REVERT: J 239 ASP cc_start: 0.8628 (t0) cc_final: 0.8361 (t0) REVERT: J 263 GLU cc_start: 0.8204 (mp0) cc_final: 0.7757 (mp0) REVERT: J 280 MET cc_start: 0.8853 (mtm) cc_final: 0.8630 (mpp) REVERT: J 288 GLU cc_start: 0.8327 (mp0) cc_final: 0.7970 (mp0) REVERT: J 318 ASN cc_start: 0.8675 (t0) cc_final: 0.8305 (t0) REVERT: J 375 LYS cc_start: 0.8270 (ttmp) cc_final: 0.7851 (mptt) REVERT: L 29 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.7738 (mtm-85) REVERT: L 213 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.7489 (ttp-110) REVERT: L 217 ASP cc_start: 0.7974 (m-30) cc_final: 0.7494 (m-30) REVERT: L 239 ASP cc_start: 0.8886 (t0) cc_final: 0.8620 (t0) REVERT: L 318 ASN cc_start: 0.8702 (t0) cc_final: 0.8483 (t0) REVERT: N 82 GLU cc_start: 0.8125 (tp30) cc_final: 0.7904 (tt0) REVERT: N 217 ASP cc_start: 0.8137 (m-30) cc_final: 0.7764 (m-30) REVERT: N 239 ASP cc_start: 0.8772 (t0) cc_final: 0.8322 (t0) REVERT: N 280 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8390 (mmm) REVERT: P 53 ASP cc_start: 0.8788 (t0) cc_final: 0.8577 (t0) REVERT: P 86 GLN cc_start: 0.8835 (mt0) cc_final: 0.8632 (mt0) REVERT: P 217 ASP cc_start: 0.7884 (m-30) cc_final: 0.7631 (m-30) REVERT: P 239 ASP cc_start: 0.8700 (t0) cc_final: 0.8272 (t0) REVERT: P 263 GLU cc_start: 0.8345 (mp0) cc_final: 0.7829 (mp0) REVERT: P 318 ASN cc_start: 0.8566 (t0) cc_final: 0.8217 (t0) REVERT: S 7 SER cc_start: 0.9209 (t) cc_final: 0.8835 (m) REVERT: S 54 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8715 (mpt180) REVERT: S 103 GLU cc_start: 0.8271 (mp0) cc_final: 0.8010 (mp0) REVERT: S 209 PHE cc_start: 0.8927 (m-80) cc_final: 0.8715 (m-10) REVERT: S 213 ARG cc_start: 0.8430 (ttm110) cc_final: 0.7565 (ttp-110) REVERT: S 217 ASP cc_start: 0.8061 (m-30) cc_final: 0.7550 (m-30) REVERT: S 239 ASP cc_start: 0.8763 (t0) cc_final: 0.8468 (t0) REVERT: S 280 MET cc_start: 0.8618 (mtm) cc_final: 0.8286 (mmm) REVERT: S 318 ASN cc_start: 0.8644 (t0) cc_final: 0.8218 (t0) REVERT: U 213 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7378 (ttp80) REVERT: U 217 ASP cc_start: 0.7951 (m-30) cc_final: 0.7543 (m-30) REVERT: U 239 ASP cc_start: 0.8736 (t0) cc_final: 0.8496 (t0) REVERT: U 280 MET cc_start: 0.8911 (tpp) cc_final: 0.8599 (tpp) REVERT: U 288 GLU cc_start: 0.8273 (mp0) cc_final: 0.7860 (mp0) REVERT: U 318 ASN cc_start: 0.8565 (t0) cc_final: 0.8335 (t0) REVERT: U 361 TYR cc_start: 0.9158 (m-80) cc_final: 0.8929 (m-80) REVERT: W 150 LYS cc_start: 0.8744 (mppt) cc_final: 0.8303 (mppt) REVERT: W 217 ASP cc_start: 0.8076 (m-30) cc_final: 0.7439 (m-30) REVERT: W 221 ASN cc_start: 0.8772 (m-40) cc_final: 0.8456 (m110) REVERT: W 239 ASP cc_start: 0.8763 (t0) cc_final: 0.8451 (t0) REVERT: W 280 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8283 (mpp) REVERT: W 288 GLU cc_start: 0.8334 (mp0) cc_final: 0.8010 (mp0) REVERT: Y 7 SER cc_start: 0.9222 (t) cc_final: 0.8903 (m) REVERT: Y 20 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8720 (pp) REVERT: Y 53 ASP cc_start: 0.8797 (t0) cc_final: 0.8559 (t0) REVERT: Y 86 GLN cc_start: 0.8913 (mt0) cc_final: 0.8612 (mt0) REVERT: Y 89 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8668 (mm-40) REVERT: Y 213 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7343 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8095 (m-30) cc_final: 0.7633 (m-30) REVERT: Y 239 ASP cc_start: 0.8828 (t0) cc_final: 0.8523 (t0) REVERT: Y 280 MET cc_start: 0.8561 (mpp) cc_final: 0.8272 (mmm) REVERT: Y 288 GLU cc_start: 0.8327 (mp0) cc_final: 0.7813 (mp0) REVERT: Y 292 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8133 (mt-10) REVERT: Y 318 ASN cc_start: 0.8526 (t0) cc_final: 0.8313 (t0) REVERT: 0 7 SER cc_start: 0.9180 (t) cc_final: 0.8953 (m) REVERT: 0 15 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8440 (ttmm) REVERT: 0 89 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8853 (mm-40) REVERT: 0 217 ASP cc_start: 0.8025 (m-30) cc_final: 0.7582 (m-30) REVERT: 0 239 ASP cc_start: 0.8693 (t0) cc_final: 0.8379 (t0) REVERT: 0 288 GLU cc_start: 0.8180 (mp0) cc_final: 0.7819 (mp0) REVERT: 0 318 ASN cc_start: 0.8598 (t0) cc_final: 0.8148 (t0) REVERT: 2 29 ARG cc_start: 0.8103 (mtm110) cc_final: 0.7833 (mtm110) REVERT: 2 115 THR cc_start: 0.8836 (p) cc_final: 0.8539 (t) REVERT: 2 128 ASP cc_start: 0.7932 (t0) cc_final: 0.7710 (t0) REVERT: 2 213 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7663 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7925 (m-30) cc_final: 0.7668 (m-30) REVERT: 2 239 ASP cc_start: 0.8745 (t0) cc_final: 0.8410 (t0) REVERT: 2 280 MET cc_start: 0.8872 (tpp) cc_final: 0.8566 (mmm) REVERT: 2 288 GLU cc_start: 0.8388 (mp0) cc_final: 0.7914 (mp0) REVERT: 2 318 ASN cc_start: 0.8644 (t0) cc_final: 0.8241 (t0) outliers start: 120 outliers final: 72 residues processed: 1337 average time/residue: 0.2613 time to fit residues: 576.3171 Evaluate side-chains 1130 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1051 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 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 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 15 LYS 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 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 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 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 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 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: 0.6980 chunk 530 optimal weight: 5.9990 chunk 548 optimal weight: 0.7980 chunk 297 optimal weight: 0.9990 chunk 544 optimal weight: 10.0000 chunk 429 optimal weight: 4.9990 chunk 375 optimal weight: 9.9990 chunk 388 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 33 HIS H 164 ASN Y 305 GLN 2 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.118421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.098249 restraints weight = 64157.016| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.93 r_work: 0.2867 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 47672 Z= 0.120 Angle : 0.581 9.516 64860 Z= 0.297 Chirality : 0.041 0.185 7470 Planarity : 0.004 0.052 7980 Dihedral : 8.763 69.960 7273 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.16 % Allowed : 12.28 % Favored : 85.56 % 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: -1.22 (0.11), residues: 5625 helix: -0.97 (0.09), residues: 3150 sheet: 0.33 (0.27), residues: 375 loop : -0.46 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 213 TYR 0.013 0.001 TYR W 260 PHE 0.017 0.002 PHE F 275 TRP 0.008 0.001 TRP H 215 HIS 0.003 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (47670) covalent geometry : angle 0.58073 / 0.30 (64860) hydrogen bonds : bond 0.03873 / 2.57 ( 1725) hydrogen bonds : angle 4.13826 / 2.82 ( 4995) Misc. bond : bond 0.00126 / 0.06 ( 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 1302 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1197 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 SER cc_start: 0.9152 (t) cc_final: 0.8934 (m) REVERT: B 34 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8631 (pp) REVERT: B 53 ASP cc_start: 0.8920 (t0) cc_final: 0.8645 (t0) REVERT: B 129 GLN cc_start: 0.8380 (mt0) cc_final: 0.8131 (tm-30) REVERT: B 209 PHE cc_start: 0.8917 (m-80) cc_final: 0.8576 (m-10) REVERT: B 213 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7376 (ttp80) REVERT: B 217 ASP cc_start: 0.7921 (m-30) cc_final: 0.7466 (m-30) REVERT: B 239 ASP cc_start: 0.8732 (t0) cc_final: 0.8451 (t0) REVERT: B 280 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8339 (mmm) REVERT: B 288 GLU cc_start: 0.8332 (mp0) cc_final: 0.7946 (mp0) REVERT: B 318 ASN cc_start: 0.8658 (t0) cc_final: 0.8290 (t0) REVERT: A 103 GLU cc_start: 0.8337 (mp0) cc_final: 0.7865 (mp0) REVERT: A 115 THR cc_start: 0.8908 (p) cc_final: 0.8605 (t) REVERT: A 123 MET cc_start: 0.6146 (mmm) cc_final: 0.5815 (mmm) REVERT: A 164 ASN cc_start: 0.8710 (t0) cc_final: 0.8300 (t0) REVERT: A 213 ARG cc_start: 0.8195 (ttp-110) cc_final: 0.7577 (ttp-110) REVERT: A 217 ASP cc_start: 0.7906 (m-30) cc_final: 0.7385 (m-30) REVERT: A 225 GLU cc_start: 0.8270 (tp30) cc_final: 0.7944 (mm-30) REVERT: A 280 MET cc_start: 0.8877 (mtm) cc_final: 0.8658 (mpp) REVERT: A 288 GLU cc_start: 0.8253 (mp0) cc_final: 0.7932 (mp0) REVERT: A 312 TYR cc_start: 0.9308 (m-80) cc_final: 0.9013 (m-80) REVERT: A 318 ASN cc_start: 0.8552 (t0) cc_final: 0.8293 (t0) REVERT: A 342 GLU cc_start: 0.7365 (mp0) cc_final: 0.7029 (mp0) REVERT: D 103 GLU cc_start: 0.8422 (mp0) cc_final: 0.8074 (mp0) REVERT: D 123 MET cc_start: 0.5329 (mmt) cc_final: 0.4778 (mmm) REVERT: D 217 ASP cc_start: 0.7820 (m-30) cc_final: 0.7427 (m-30) REVERT: D 225 GLU cc_start: 0.8069 (tp30) cc_final: 0.7672 (mm-30) REVERT: D 239 ASP cc_start: 0.8795 (t0) cc_final: 0.8413 (t0) REVERT: D 280 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8324 (mmt) REVERT: D 288 GLU cc_start: 0.8289 (mp0) cc_final: 0.7885 (mp0) REVERT: F 12 LYS cc_start: 0.8565 (mtpp) cc_final: 0.8306 (mttt) REVERT: F 213 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7453 (ttp-110) REVERT: F 217 ASP cc_start: 0.7865 (m-30) cc_final: 0.7250 (m-30) REVERT: F 239 ASP cc_start: 0.8575 (t0) cc_final: 0.8159 (t0) REVERT: H 53 ASP cc_start: 0.8814 (t0) cc_final: 0.8453 (t0) REVERT: H 213 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7748 (ttp-110) REVERT: H 239 ASP cc_start: 0.8632 (t0) cc_final: 0.8210 (t0) REVERT: H 280 MET cc_start: 0.8625 (mpp) cc_final: 0.8398 (mmm) REVERT: H 288 GLU cc_start: 0.8239 (mp0) cc_final: 0.7986 (mp0) REVERT: J 42 ASP cc_start: 0.7971 (p0) cc_final: 0.7501 (t70) REVERT: J 213 ARG cc_start: 0.8122 (ttp-110) cc_final: 0.7518 (ttp-110) REVERT: J 217 ASP cc_start: 0.7794 (m-30) cc_final: 0.7362 (m-30) REVERT: J 239 ASP cc_start: 0.8590 (t0) cc_final: 0.8307 (t0) REVERT: J 252 GLU cc_start: 0.8492 (tt0) cc_final: 0.8289 (mt-10) REVERT: J 255 CYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8475 (t) REVERT: J 263 GLU cc_start: 0.7996 (mp0) cc_final: 0.7524 (mp0) REVERT: J 288 GLU cc_start: 0.8395 (mp0) cc_final: 0.8049 (mp0) REVERT: J 318 ASN cc_start: 0.8567 (t0) cc_final: 0.8279 (t0) REVERT: J 375 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7802 (mptt) REVERT: L 102 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8378 (pp) REVERT: L 103 GLU cc_start: 0.8473 (mp0) cc_final: 0.8110 (mp0) REVERT: L 208 GLU cc_start: 0.7391 (pm20) cc_final: 0.7108 (mp0) REVERT: L 213 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.7646 (ttp-110) REVERT: L 217 ASP cc_start: 0.7919 (m-30) cc_final: 0.7453 (m-30) REVERT: L 225 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7430 (mm-30) REVERT: L 239 ASP cc_start: 0.8834 (t0) cc_final: 0.8567 (t0) REVERT: N 31 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7428 (pp) REVERT: N 217 ASP cc_start: 0.8126 (m-30) cc_final: 0.7704 (m-30) REVERT: N 236 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8563 (tp) REVERT: N 239 ASP cc_start: 0.8763 (t0) cc_final: 0.8474 (t0) REVERT: N 263 GLU cc_start: 0.8168 (mp0) cc_final: 0.7870 (mp0) REVERT: N 308 GLU cc_start: 0.8526 (pt0) cc_final: 0.8312 (pt0) REVERT: P 32 LYS cc_start: 0.8226 (mttm) cc_final: 0.8007 (mmtt) REVERT: P 86 GLN cc_start: 0.8833 (mt0) cc_final: 0.8627 (mt0) REVERT: P 217 ASP cc_start: 0.7923 (m-30) cc_final: 0.7659 (m-30) REVERT: P 239 ASP cc_start: 0.8665 (t0) cc_final: 0.8228 (t0) REVERT: P 288 GLU cc_start: 0.8333 (mp0) cc_final: 0.7892 (mp0) REVERT: P 318 ASN cc_start: 0.8460 (t0) cc_final: 0.8134 (t0) REVERT: P 371 ARG cc_start: 0.8704 (mmt90) cc_final: 0.8435 (mmt90) REVERT: S 103 GLU cc_start: 0.8299 (mp0) cc_final: 0.8087 (mp0) REVERT: S 209 PHE cc_start: 0.8927 (m-80) cc_final: 0.8716 (m-10) REVERT: S 213 ARG cc_start: 0.8514 (ttm110) cc_final: 0.7521 (ttp-110) REVERT: S 217 ASP cc_start: 0.7955 (m-30) cc_final: 0.7516 (m-30) REVERT: S 239 ASP cc_start: 0.8657 (t0) cc_final: 0.8367 (t0) REVERT: S 280 MET cc_start: 0.8543 (mtm) cc_final: 0.8265 (mmm) REVERT: S 318 ASN cc_start: 0.8618 (t0) cc_final: 0.8180 (t0) REVERT: S 371 ARG cc_start: 0.8607 (mmt90) cc_final: 0.8389 (mmt90) REVERT: U 213 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.7394 (ttp80) REVERT: U 217 ASP cc_start: 0.7989 (m-30) cc_final: 0.7542 (m-30) REVERT: U 225 GLU cc_start: 0.8172 (tp30) cc_final: 0.7957 (tp30) REVERT: U 236 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8658 (tp) REVERT: U 239 ASP cc_start: 0.8691 (t0) cc_final: 0.8473 (t0) REVERT: U 280 MET cc_start: 0.8848 (tpp) cc_final: 0.8605 (tpp) REVERT: U 318 ASN cc_start: 0.8472 (t0) cc_final: 0.8258 (t0) REVERT: U 361 TYR cc_start: 0.9315 (m-80) cc_final: 0.9058 (m-80) REVERT: W 86 GLN cc_start: 0.8790 (mt0) cc_final: 0.8565 (mt0) REVERT: W 126 GLU cc_start: 0.7642 (tt0) cc_final: 0.7349 (tt0) REVERT: W 217 ASP cc_start: 0.7967 (m-30) cc_final: 0.7476 (m-30) REVERT: W 236 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8545 (tp) REVERT: W 239 ASP cc_start: 0.8731 (t0) cc_final: 0.8398 (t0) REVERT: W 280 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8052 (mmm) REVERT: W 288 GLU cc_start: 0.8293 (mp0) cc_final: 0.7974 (mp0) REVERT: W 371 ARG cc_start: 0.8753 (mmt90) cc_final: 0.8510 (mmt90) REVERT: Y 89 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8678 (mm-40) REVERT: Y 213 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7440 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8013 (m-30) cc_final: 0.7619 (m-30) REVERT: Y 239 ASP cc_start: 0.8816 (t0) cc_final: 0.8491 (t0) REVERT: Y 280 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8220 (mmm) REVERT: Y 288 GLU cc_start: 0.8284 (mp0) cc_final: 0.7786 (mp0) REVERT: Y 292 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8108 (mt-10) REVERT: Y 318 ASN cc_start: 0.8508 (t0) cc_final: 0.8266 (t0) REVERT: 0 89 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8858 (mm-40) REVERT: 0 148 GLU cc_start: 0.7950 (pt0) cc_final: 0.7606 (mt-10) REVERT: 0 217 ASP cc_start: 0.7942 (m-30) cc_final: 0.7520 (m-30) REVERT: 0 225 GLU cc_start: 0.7944 (tp30) cc_final: 0.7632 (mm-30) REVERT: 0 239 ASP cc_start: 0.8609 (t0) cc_final: 0.8276 (t0) REVERT: 0 288 GLU cc_start: 0.8171 (mp0) cc_final: 0.7805 (mp0) REVERT: 0 318 ASN cc_start: 0.8492 (t0) cc_final: 0.8072 (t0) REVERT: 2 29 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7909 (mtm110) REVERT: 2 213 ARG cc_start: 0.8177 (mtp-110) cc_final: 0.7652 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7761 (m-30) cc_final: 0.7544 (m-30) REVERT: 2 239 ASP cc_start: 0.8649 (t0) cc_final: 0.8260 (t0) REVERT: 2 263 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7855 (mt-10) REVERT: 2 280 MET cc_start: 0.8846 (tpp) cc_final: 0.8545 (mmm) REVERT: 2 288 GLU cc_start: 0.8300 (mp0) cc_final: 0.7969 (mp0) REVERT: 2 318 ASN cc_start: 0.8532 (t0) cc_final: 0.8188 (t0) outliers start: 105 outliers final: 46 residues processed: 1257 average time/residue: 0.2633 time to fit residues: 542.2963 Evaluate side-chains 1102 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 1044 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 332 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain H residue 297 GLU 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 255 CYS 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 297 GLU Chi-restraints excluded: chain N residue 31 ILE 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 P residue 102 LEU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 332 LEU 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 255 CYS Chi-restraints excluded: chain U residue 376 VAL 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 190 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 427 optimal weight: 0.9990 chunk 510 optimal weight: 5.9990 chunk 395 optimal weight: 0.6980 chunk 344 optimal weight: 20.0000 chunk 558 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 227 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 553 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN H 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.095875 restraints weight = 64594.538| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.96 r_work: 0.2828 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 47672 Z= 0.148 Angle : 0.574 9.186 64860 Z= 0.294 Chirality : 0.042 0.158 7470 Planarity : 0.004 0.057 7980 Dihedral : 8.501 70.625 7255 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.76 % Allowed : 12.70 % Favored : 84.55 % 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: 0.36 (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 0.014 0.002 PHE F 275 TRP 0.009 0.001 TRP D 215 HIS 0.003 0.001 HIS J 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (47670) covalent geometry : angle 0.57383 / 0.29 (64860) hydrogen bonds : bond 0.03638 / 2.40 ( 1725) hydrogen bonds : angle 3.96542 / 2.70 ( 4995) Misc. bond : bond 0.00512 / 0.24 ( 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 1225 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1091 time to evaluate : 1.870 Fit side-chains revert: symmetry clash REVERT: B 7 SER cc_start: 0.9178 (t) cc_final: 0.8965 (m) REVERT: B 34 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8698 (pp) REVERT: B 53 ASP cc_start: 0.8937 (t0) cc_final: 0.8703 (t0) REVERT: B 129 GLN cc_start: 0.8343 (mt0) cc_final: 0.8131 (tm-30) REVERT: B 148 GLU cc_start: 0.7687 (pt0) cc_final: 0.7483 (mt-10) REVERT: B 213 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7404 (ttp80) REVERT: B 217 ASP cc_start: 0.7952 (m-30) cc_final: 0.7513 (m-30) REVERT: B 239 ASP cc_start: 0.8809 (t0) cc_final: 0.8523 (t0) REVERT: B 280 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8365 (mmm) REVERT: B 288 GLU cc_start: 0.8410 (mp0) cc_final: 0.7887 (mp0) REVERT: B 306 MET cc_start: 0.8471 (mtp) cc_final: 0.8216 (mtp) REVERT: B 318 ASN cc_start: 0.8696 (t0) cc_final: 0.8450 (t0) REVERT: A 103 GLU cc_start: 0.8366 (mp0) cc_final: 0.7966 (mp0) REVERT: A 115 THR cc_start: 0.8882 (p) cc_final: 0.8619 (t) REVERT: A 123 MET cc_start: 0.6227 (mmm) cc_final: 0.5622 (mmm) REVERT: A 164 ASN cc_start: 0.8732 (t0) cc_final: 0.8308 (t0) REVERT: A 213 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.7666 (ttp-110) REVERT: A 217 ASP cc_start: 0.7945 (m-30) cc_final: 0.7350 (m-30) REVERT: A 225 GLU cc_start: 0.8288 (tp30) cc_final: 0.7969 (mm-30) REVERT: A 280 MET cc_start: 0.8818 (mtm) cc_final: 0.8566 (mpp) REVERT: A 288 GLU cc_start: 0.8401 (mp0) cc_final: 0.7968 (mp0) REVERT: A 318 ASN cc_start: 0.8570 (t0) cc_final: 0.8296 (t0) REVERT: A 344 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8195 (mm-30) REVERT: D 82 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: D 103 GLU cc_start: 0.8440 (mp0) cc_final: 0.8083 (mp0) REVERT: D 123 MET cc_start: 0.5389 (mmt) cc_final: 0.4864 (mmm) REVERT: D 213 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7394 (ttp-110) REVERT: D 217 ASP cc_start: 0.7904 (m-30) cc_final: 0.7504 (m-30) REVERT: D 225 GLU cc_start: 0.8199 (tp30) cc_final: 0.7900 (mm-30) REVERT: D 239 ASP cc_start: 0.8831 (t0) cc_final: 0.8455 (t0) REVERT: D 280 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8327 (mmt) REVERT: D 288 GLU cc_start: 0.8350 (mp0) cc_final: 0.8004 (mp0) REVERT: F 12 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8331 (mttt) REVERT: F 57 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8109 (mtp180) REVERT: F 213 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7517 (ttp-110) REVERT: F 217 ASP cc_start: 0.7896 (m-30) cc_final: 0.7303 (m-30) REVERT: F 225 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7685 (mm-30) REVERT: F 239 ASP cc_start: 0.8603 (t0) cc_final: 0.8254 (t0) REVERT: H 53 ASP cc_start: 0.8809 (t0) cc_final: 0.8492 (t0) REVERT: H 213 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7781 (ttp-110) REVERT: H 239 ASP cc_start: 0.8633 (t0) cc_final: 0.8248 (t0) REVERT: H 280 MET cc_start: 0.8558 (mpp) cc_final: 0.8332 (mmm) REVERT: H 288 GLU cc_start: 0.8298 (mp0) cc_final: 0.8076 (mp0) REVERT: H 318 ASN cc_start: 0.8615 (t0) cc_final: 0.8304 (t0) REVERT: J 42 ASP cc_start: 0.8031 (p0) cc_final: 0.7442 (t0) REVERT: J 164 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8437 (t0) REVERT: J 213 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7619 (ttp-110) REVERT: J 217 ASP cc_start: 0.7831 (m-30) cc_final: 0.7418 (m-30) REVERT: J 225 GLU cc_start: 0.8229 (tp30) cc_final: 0.7793 (mm-30) REVERT: J 239 ASP cc_start: 0.8544 (t0) cc_final: 0.8267 (t0) REVERT: J 249 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8559 (ptm160) REVERT: J 263 GLU cc_start: 0.8078 (mp0) cc_final: 0.7718 (mp0) REVERT: J 288 GLU cc_start: 0.8435 (mp0) cc_final: 0.8054 (mp0) REVERT: J 318 ASN cc_start: 0.8577 (t0) cc_final: 0.8307 (t0) REVERT: J 375 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7790 (mptt) REVERT: L 102 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8366 (pp) REVERT: L 103 GLU cc_start: 0.8510 (mp0) cc_final: 0.8139 (mp0) REVERT: L 109 GLN cc_start: 0.8325 (pt0) cc_final: 0.7670 (mm-40) REVERT: L 213 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.7697 (ttp-110) REVERT: L 217 ASP cc_start: 0.8080 (m-30) cc_final: 0.7594 (m-30) REVERT: L 225 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7874 (mm-30) REVERT: L 239 ASP cc_start: 0.8864 (t0) cc_final: 0.8592 (t0) REVERT: L 393 LEU cc_start: 0.8276 (tt) cc_final: 0.7386 (mp) REVERT: N 31 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7334 (pp) REVERT: N 164 ASN cc_start: 0.8819 (t0) cc_final: 0.8533 (t0) REVERT: N 213 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7656 (ttp-110) REVERT: N 217 ASP cc_start: 0.8171 (m-30) cc_final: 0.7725 (m-30) REVERT: N 225 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7925 (mm-30) REVERT: N 239 ASP cc_start: 0.8790 (t0) cc_final: 0.8516 (t0) REVERT: N 249 ARG cc_start: 0.8821 (ppp-140) cc_final: 0.8619 (ptm160) REVERT: N 280 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8381 (mmm) REVERT: N 308 GLU cc_start: 0.8530 (pt0) cc_final: 0.8313 (pt0) REVERT: N 314 VAL cc_start: 0.9194 (p) cc_final: 0.8936 (t) REVERT: N 317 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7890 (mm-30) REVERT: P 32 LYS cc_start: 0.8271 (mttm) cc_final: 0.8031 (mmtt) REVERT: P 86 GLN cc_start: 0.8809 (mt0) cc_final: 0.8598 (mt0) REVERT: P 217 ASP cc_start: 0.7897 (m-30) cc_final: 0.7601 (m-30) REVERT: P 239 ASP cc_start: 0.8654 (t0) cc_final: 0.8226 (t0) REVERT: P 288 GLU cc_start: 0.8352 (mp0) cc_final: 0.7988 (mp0) REVERT: P 308 GLU cc_start: 0.8288 (pm20) cc_final: 0.7983 (pm20) REVERT: P 318 ASN cc_start: 0.8478 (t0) cc_final: 0.8182 (t0) REVERT: S 103 GLU cc_start: 0.8338 (mp0) cc_final: 0.8092 (mp0) REVERT: S 129 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: S 213 ARG cc_start: 0.8442 (ttm110) cc_final: 0.7493 (ttp-110) REVERT: S 217 ASP cc_start: 0.7958 (m-30) cc_final: 0.7561 (m-30) REVERT: S 239 ASP cc_start: 0.8695 (t0) cc_final: 0.8420 (t0) REVERT: S 241 LYS cc_start: 0.8915 (mttt) cc_final: 0.8517 (mmtt) REVERT: S 280 MET cc_start: 0.8604 (mtm) cc_final: 0.8301 (mmm) REVERT: S 318 ASN cc_start: 0.8627 (t0) cc_final: 0.8188 (t0) REVERT: U 103 GLU cc_start: 0.8457 (mp0) cc_final: 0.8030 (mp0) REVERT: U 213 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7316 (ttp80) REVERT: U 217 ASP cc_start: 0.7996 (m-30) cc_final: 0.7517 (m-30) REVERT: U 225 GLU cc_start: 0.8232 (tp30) cc_final: 0.7826 (mm-30) REVERT: U 239 ASP cc_start: 0.8742 (t0) cc_final: 0.8538 (t0) REVERT: U 271 LEU cc_start: 0.8580 (mt) cc_final: 0.8336 (mt) REVERT: U 280 MET cc_start: 0.8857 (tpp) cc_final: 0.8617 (tpp) REVERT: U 318 ASN cc_start: 0.8479 (t0) cc_final: 0.8254 (t0) REVERT: U 361 TYR cc_start: 0.9361 (m-80) cc_final: 0.9059 (m-80) REVERT: W 86 GLN cc_start: 0.8841 (mt0) cc_final: 0.8598 (mt0) REVERT: W 217 ASP cc_start: 0.8021 (m-30) cc_final: 0.7518 (m-30) REVERT: W 225 GLU cc_start: 0.8334 (tp30) cc_final: 0.8042 (mm-30) REVERT: W 239 ASP cc_start: 0.8755 (t0) cc_final: 0.8406 (t0) REVERT: W 280 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8171 (mmm) REVERT: W 288 GLU cc_start: 0.8358 (mp0) cc_final: 0.8021 (mp0) REVERT: W 342 GLU cc_start: 0.7382 (mp0) cc_final: 0.7167 (mp0) REVERT: W 371 ARG cc_start: 0.8733 (mmt90) cc_final: 0.8481 (mmt90) REVERT: Y 86 GLN cc_start: 0.8865 (mt0) cc_final: 0.8611 (mt0) REVERT: Y 99 ILE cc_start: 0.9186 (mm) cc_final: 0.8935 (tp) REVERT: Y 129 GLN cc_start: 0.8262 (mp10) cc_final: 0.8049 (mp10) REVERT: Y 208 GLU cc_start: 0.7505 (pm20) cc_final: 0.7121 (mp0) REVERT: Y 213 ARG cc_start: 0.8295 (ttp-110) cc_final: 0.7613 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8003 (m-30) cc_final: 0.7702 (m-30) REVERT: Y 225 GLU cc_start: 0.8091 (tp30) cc_final: 0.7883 (mm-30) REVERT: Y 239 ASP cc_start: 0.8734 (t0) cc_final: 0.8416 (t0) REVERT: Y 280 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8271 (mmm) REVERT: Y 288 GLU cc_start: 0.8304 (mp0) cc_final: 0.7952 (mp0) REVERT: Y 292 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8109 (mt-10) REVERT: Y 318 ASN cc_start: 0.8515 (t0) cc_final: 0.8238 (t0) REVERT: 0 86 GLN cc_start: 0.8788 (mt0) cc_final: 0.8578 (mt0) REVERT: 0 148 GLU cc_start: 0.7971 (pt0) cc_final: 0.7670 (mt-10) REVERT: 0 217 ASP cc_start: 0.7996 (m-30) cc_final: 0.7517 (m-30) REVERT: 0 239 ASP cc_start: 0.8651 (t0) cc_final: 0.8280 (t0) REVERT: 0 288 GLU cc_start: 0.8305 (mp0) cc_final: 0.7923 (mp0) REVERT: 0 318 ASN cc_start: 0.8500 (t0) cc_final: 0.8106 (t0) REVERT: 2 213 ARG cc_start: 0.8238 (mtp-110) cc_final: 0.7790 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7905 (m-30) cc_final: 0.7663 (m-30) REVERT: 2 239 ASP cc_start: 0.8662 (t0) cc_final: 0.8253 (t0) REVERT: 2 280 MET cc_start: 0.8908 (tpp) cc_final: 0.8560 (mmm) REVERT: 2 288 GLU cc_start: 0.8363 (mp0) cc_final: 0.8041 (mp0) REVERT: 2 318 ASN cc_start: 0.8505 (t0) cc_final: 0.8165 (t0) outliers start: 134 outliers final: 80 residues processed: 1161 average time/residue: 0.2843 time to fit residues: 539.0328 Evaluate side-chains 1116 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1022 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 375 LYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 82 GLU 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 44 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 355 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 34 ILE 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 258 ASP Chi-restraints excluded: chain N residue 280 MET Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU 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 255 CYS 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 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 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 102 LEU 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 355 SER Chi-restraints excluded: chain Y residue 375 LYS 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 380 LEU Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 149 ASN Chi-restraints excluded: chain 2 residue 255 CYS 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: 8.9990 chunk 501 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 350 optimal weight: 0.7980 chunk 351 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 415 optimal weight: 0.0770 chunk 266 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN H 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.100070 restraints weight = 64157.359| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.94 r_work: 0.2889 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 47672 Z= 0.101 Angle : 0.540 10.030 64860 Z= 0.274 Chirality : 0.040 0.151 7470 Planarity : 0.004 0.058 7980 Dihedral : 8.446 72.262 7249 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.65 % Allowed : 13.83 % Favored : 83.52 % 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: -0.04 (0.12), residues: 5625 helix: 0.11 (0.09), residues: 3180 sheet: 0.43 (0.28), residues: 375 loop : -0.07 (0.15), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 29 TYR 0.012 0.001 TYR A 312 PHE 0.016 0.001 PHE A 11 TRP 0.010 0.001 TRP D 215 HIS 0.003 0.001 HIS J 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (47670) covalent geometry : angle 0.53997 / 0.27 (64860) hydrogen bonds : bond 0.03212 / 2.12 ( 1725) hydrogen bonds : angle 3.79325 / 2.57 ( 4995) Misc. bond : bond 0.00202 / 0.10 ( 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 1281 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1152 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 SER cc_start: 0.9163 (t) cc_final: 0.8929 (m) REVERT: B 34 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8679 (pp) REVERT: B 129 GLN cc_start: 0.8333 (mt0) cc_final: 0.8114 (tm-30) REVERT: B 213 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7340 (ttp80) REVERT: B 217 ASP cc_start: 0.7913 (m-30) cc_final: 0.7460 (m-30) REVERT: B 239 ASP cc_start: 0.8682 (t0) cc_final: 0.8431 (t0) REVERT: B 306 MET cc_start: 0.8389 (mtp) cc_final: 0.8128 (mtp) REVERT: B 318 ASN cc_start: 0.8622 (t0) cc_final: 0.8358 (t0) REVERT: A 89 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8695 (mm-40) REVERT: A 103 GLU cc_start: 0.8296 (mp0) cc_final: 0.7971 (mp0) REVERT: A 115 THR cc_start: 0.8883 (p) cc_final: 0.8642 (t) REVERT: A 123 MET cc_start: 0.6323 (mmm) cc_final: 0.5531 (mmm) REVERT: A 164 ASN cc_start: 0.8705 (t0) cc_final: 0.8276 (t0) REVERT: A 213 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.7568 (ttp-110) REVERT: A 217 ASP cc_start: 0.7932 (m-30) cc_final: 0.7308 (m-30) REVERT: A 225 GLU cc_start: 0.8229 (tp30) cc_final: 0.7934 (mm-30) REVERT: A 280 MET cc_start: 0.8723 (mtm) cc_final: 0.8458 (mpp) REVERT: A 288 GLU cc_start: 0.8315 (mp0) cc_final: 0.8003 (mp0) REVERT: A 313 MET cc_start: 0.8731 (ptm) cc_final: 0.8512 (ptp) REVERT: A 318 ASN cc_start: 0.8450 (t0) cc_final: 0.8218 (t0) REVERT: A 344 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8161 (mm-30) REVERT: D 15 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8182 (ttmm) REVERT: D 103 GLU cc_start: 0.8414 (mp0) cc_final: 0.8006 (mp0) REVERT: D 213 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7545 (ttp-110) REVERT: D 217 ASP cc_start: 0.7804 (m-30) cc_final: 0.7389 (m-30) REVERT: D 225 GLU cc_start: 0.8114 (tp30) cc_final: 0.7879 (mm-30) REVERT: D 239 ASP cc_start: 0.8754 (t0) cc_final: 0.8315 (t0) REVERT: D 280 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8276 (tpp) REVERT: D 288 GLU cc_start: 0.8301 (mp0) cc_final: 0.8092 (mp0) REVERT: D 342 GLU cc_start: 0.7124 (mp0) cc_final: 0.6919 (mp0) REVERT: F 217 ASP cc_start: 0.7754 (m-30) cc_final: 0.7256 (m-30) REVERT: F 225 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7763 (mm-30) REVERT: F 239 ASP cc_start: 0.8494 (t0) cc_final: 0.8213 (t0) REVERT: H 213 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7761 (ttp-110) REVERT: H 239 ASP cc_start: 0.8567 (t0) cc_final: 0.8151 (t0) REVERT: J 15 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7619 (tptp) REVERT: J 164 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8396 (t0) REVERT: J 208 GLU cc_start: 0.7674 (pt0) cc_final: 0.7276 (mp0) REVERT: J 213 ARG cc_start: 0.8111 (ttp-110) cc_final: 0.7403 (ttp-110) REVERT: J 217 ASP cc_start: 0.7770 (m-30) cc_final: 0.7241 (m-30) REVERT: J 225 GLU cc_start: 0.8256 (tp30) cc_final: 0.7960 (mm-30) REVERT: J 239 ASP cc_start: 0.8503 (t0) cc_final: 0.8217 (t0) REVERT: J 263 GLU cc_start: 0.7935 (mp0) cc_final: 0.7512 (mp0) REVERT: J 280 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8119 (mpp) REVERT: J 288 GLU cc_start: 0.8467 (mp0) cc_final: 0.8147 (mp0) REVERT: J 344 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7788 (mm-30) REVERT: J 371 ARG cc_start: 0.8662 (mmt90) cc_final: 0.8429 (mmt90) REVERT: J 375 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7712 (mptt) REVERT: L 102 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8188 (pp) REVERT: L 103 GLU cc_start: 0.8450 (mp0) cc_final: 0.8153 (mp0) REVERT: L 109 GLN cc_start: 0.8311 (pt0) cc_final: 0.7676 (mm-40) REVERT: L 213 ARG cc_start: 0.8387 (ttp-110) cc_final: 0.7693 (ttp-110) REVERT: L 217 ASP cc_start: 0.7961 (m-30) cc_final: 0.7448 (m-30) REVERT: L 239 ASP cc_start: 0.8735 (t0) cc_final: 0.8466 (t0) REVERT: L 393 LEU cc_start: 0.8231 (tt) cc_final: 0.7269 (mp) REVERT: N 31 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6819 (pp) REVERT: N 148 GLU cc_start: 0.7848 (pt0) cc_final: 0.7516 (mt-10) REVERT: N 209 PHE cc_start: 0.8408 (m-10) cc_final: 0.8082 (m-10) REVERT: N 213 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7614 (ttp-110) REVERT: N 217 ASP cc_start: 0.8096 (m-30) cc_final: 0.7647 (m-30) REVERT: N 225 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7991 (mm-30) REVERT: N 263 GLU cc_start: 0.8117 (mp0) cc_final: 0.7625 (mp0) REVERT: N 280 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8239 (mmm) REVERT: N 314 VAL cc_start: 0.9106 (p) cc_final: 0.8856 (t) REVERT: N 317 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7900 (mm-30) REVERT: P 86 GLN cc_start: 0.8825 (mt0) cc_final: 0.8591 (mt0) REVERT: P 217 ASP cc_start: 0.7860 (m-30) cc_final: 0.7618 (m-30) REVERT: P 239 ASP cc_start: 0.8550 (t0) cc_final: 0.8274 (t0) REVERT: P 288 GLU cc_start: 0.8376 (mp0) cc_final: 0.8080 (mp0) REVERT: P 308 GLU cc_start: 0.8245 (pm20) cc_final: 0.7938 (pm20) REVERT: P 318 ASN cc_start: 0.8397 (t0) cc_final: 0.8083 (t0) REVERT: S 54 ARG cc_start: 0.8958 (mmt-90) cc_final: 0.8734 (mpt180) REVERT: S 103 GLU cc_start: 0.8357 (mp0) cc_final: 0.8128 (mp0) REVERT: S 129 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8073 (mp10) REVERT: S 213 ARG cc_start: 0.8480 (ttm110) cc_final: 0.7489 (ttp-110) REVERT: S 217 ASP cc_start: 0.7880 (m-30) cc_final: 0.7481 (m-30) REVERT: S 225 GLU cc_start: 0.8356 (tp30) cc_final: 0.8145 (mm-30) REVERT: S 280 MET cc_start: 0.8552 (mtm) cc_final: 0.8280 (mmm) REVERT: S 318 ASN cc_start: 0.8538 (t0) cc_final: 0.8119 (t0) REVERT: S 380 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7194 (tt) REVERT: U 103 GLU cc_start: 0.8457 (mp0) cc_final: 0.8097 (mp0) REVERT: U 213 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7377 (ttp80) REVERT: U 217 ASP cc_start: 0.7993 (m-30) cc_final: 0.7552 (m-30) REVERT: U 239 ASP cc_start: 0.8672 (t0) cc_final: 0.8463 (t0) REVERT: U 249 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8122 (ptp-170) REVERT: U 280 MET cc_start: 0.8741 (tpp) cc_final: 0.8527 (tpp) REVERT: U 361 TYR cc_start: 0.9342 (m-80) cc_final: 0.9039 (m-80) REVERT: W 129 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: W 217 ASP cc_start: 0.7932 (m-30) cc_final: 0.7423 (m-30) REVERT: W 288 GLU cc_start: 0.8343 (mp0) cc_final: 0.8136 (mp0) REVERT: Y 115 THR cc_start: 0.8844 (p) cc_final: 0.8546 (t) REVERT: Y 213 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.7533 (ttp-110) REVERT: Y 217 ASP cc_start: 0.7869 (m-30) cc_final: 0.7512 (m-30) REVERT: Y 239 ASP cc_start: 0.8636 (t0) cc_final: 0.8311 (t0) REVERT: Y 280 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8161 (mmm) REVERT: Y 288 GLU cc_start: 0.8237 (mp0) cc_final: 0.8032 (mp0) REVERT: Y 306 MET cc_start: 0.8476 (mtp) cc_final: 0.8137 (mtp) REVERT: Y 318 ASN cc_start: 0.8454 (t0) cc_final: 0.8123 (t0) REVERT: 0 89 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8870 (mm-40) REVERT: 0 115 THR cc_start: 0.8826 (p) cc_final: 0.8560 (t) REVERT: 0 148 GLU cc_start: 0.7898 (pt0) cc_final: 0.7647 (mt-10) REVERT: 0 213 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.7700 (ttp-110) REVERT: 0 217 ASP cc_start: 0.7912 (m-30) cc_final: 0.7420 (m-30) REVERT: 0 239 ASP cc_start: 0.8600 (t0) cc_final: 0.8296 (t0) REVERT: 0 288 GLU cc_start: 0.8287 (mp0) cc_final: 0.7968 (mp0) REVERT: 0 318 ASN cc_start: 0.8384 (t0) cc_final: 0.8031 (t0) REVERT: 2 53 ASP cc_start: 0.8740 (t0) cc_final: 0.8471 (t0) REVERT: 2 213 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7689 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7815 (m-30) cc_final: 0.7586 (m-30) REVERT: 2 239 ASP cc_start: 0.8582 (t0) cc_final: 0.8278 (t0) REVERT: 2 280 MET cc_start: 0.8806 (tpp) cc_final: 0.8531 (mmm) REVERT: 2 288 GLU cc_start: 0.8340 (mp0) cc_final: 0.8076 (mp0) REVERT: 2 318 ASN cc_start: 0.8412 (t0) cc_final: 0.8088 (t0) outliers start: 129 outliers final: 53 residues processed: 1226 average time/residue: 0.2901 time to fit residues: 580.2576 Evaluate side-chains 1117 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 1051 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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 A residue 102 LEU Chi-restraints excluded: chain A residue 258 ASP 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 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 342 GLU Chi-restraints excluded: chain H residue 34 ILE 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 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 280 MET Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain L residue 102 LEU 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 280 MET Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 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 375 LYS Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 129 GLN Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 380 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 249 ARG Chi-restraints excluded: chain U residue 252 GLU Chi-restraints excluded: chain U residue 255 CYS Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain Y residue 102 LEU 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 252 GLU Chi-restraints excluded: chain 0 residue 258 ASP Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 380 LEU Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 105 VAL Chi-restraints excluded: chain 2 residue 149 ASN Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 319 SER 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: 0.0070 chunk 107 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 334 optimal weight: 9.9990 chunk 435 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 541 optimal weight: 3.9990 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN F 305 GLN H 164 ASN H 318 ASN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.112834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.092128 restraints weight = 64840.586| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.94 r_work: 0.2777 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 47672 Z= 0.261 Angle : 0.640 8.242 64860 Z= 0.325 Chirality : 0.045 0.218 7470 Planarity : 0.005 0.065 7980 Dihedral : 8.310 69.768 7249 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.15 % Allowed : 14.59 % 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: -0.02 (0.12), residues: 5625 helix: 0.19 (0.09), residues: 3180 sheet: 0.44 (0.28), residues: 375 loop : -0.19 (0.15), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 231 TYR 0.018 0.002 TYR U 361 PHE 0.021 0.002 PHE 2 209 TRP 0.010 0.001 TRP H 215 HIS 0.003 0.001 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.26 (47670) covalent geometry : angle 0.63973 / 0.32 (64860) hydrogen bonds : bond 0.03808 / 2.50 ( 1725) hydrogen bonds : angle 3.91067 / 2.66 ( 4995) Misc. bond : bond 0.00566 / 0.27 ( 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 1206 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 1053 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 129 GLN cc_start: 0.8428 (mt0) cc_final: 0.8208 (tm-30) REVERT: B 213 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7476 (ttp80) REVERT: B 217 ASP cc_start: 0.7959 (m-30) cc_final: 0.7491 (m-30) REVERT: B 225 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 239 ASP cc_start: 0.8809 (t0) cc_final: 0.8504 (t0) REVERT: B 306 MET cc_start: 0.8571 (mtp) cc_final: 0.8277 (mtp) REVERT: A 103 GLU cc_start: 0.8436 (mp0) cc_final: 0.8074 (mp0) REVERT: A 115 THR cc_start: 0.8895 (p) cc_final: 0.8634 (t) REVERT: A 123 MET cc_start: 0.6343 (mmm) cc_final: 0.5381 (mmm) REVERT: A 164 ASN cc_start: 0.8751 (t0) cc_final: 0.8317 (t0) REVERT: A 208 GLU cc_start: 0.7745 (pt0) cc_final: 0.7503 (pm20) REVERT: A 213 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.7667 (ttp-110) REVERT: A 217 ASP cc_start: 0.7986 (m-30) cc_final: 0.7411 (m-30) REVERT: A 225 GLU cc_start: 0.8372 (tp30) cc_final: 0.8088 (mm-30) REVERT: A 280 MET cc_start: 0.8843 (mtm) cc_final: 0.8580 (mpp) REVERT: A 288 GLU cc_start: 0.8492 (mp0) cc_final: 0.8063 (mp0) REVERT: A 318 ASN cc_start: 0.8594 (t0) cc_final: 0.8348 (t0) REVERT: A 344 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8098 (mm-30) REVERT: D 103 GLU cc_start: 0.8510 (mp0) cc_final: 0.8191 (mp0) REVERT: D 123 MET cc_start: 0.5513 (mmt) cc_final: 0.4926 (mmm) REVERT: D 213 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7572 (ttp-110) REVERT: D 217 ASP cc_start: 0.7967 (m-30) cc_final: 0.7590 (m-30) REVERT: D 225 GLU cc_start: 0.8195 (tp30) cc_final: 0.7937 (mm-30) REVERT: D 239 ASP cc_start: 0.8845 (t0) cc_final: 0.8410 (t0) REVERT: D 280 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8426 (mmt) REVERT: D 288 GLU cc_start: 0.8372 (mp0) cc_final: 0.8073 (mp0) REVERT: F 12 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8270 (mttt) REVERT: F 57 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8214 (mtp180) REVERT: F 217 ASP cc_start: 0.7969 (m-30) cc_final: 0.7418 (m-30) REVERT: F 225 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7875 (mm-30) REVERT: F 239 ASP cc_start: 0.8606 (t0) cc_final: 0.8260 (t0) REVERT: F 280 MET cc_start: 0.8781 (mmm) cc_final: 0.8499 (mmt) REVERT: F 323 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8867 (ttmm) REVERT: H 12 LYS cc_start: 0.8314 (mmtt) cc_final: 0.8077 (mmtt) REVERT: H 109 GLN cc_start: 0.8327 (pt0) cc_final: 0.7648 (mm110) REVERT: H 213 ARG cc_start: 0.8328 (ttm110) cc_final: 0.7947 (ttp-110) REVERT: H 239 ASP cc_start: 0.8627 (t0) cc_final: 0.8223 (t0) REVERT: J 15 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7939 (tptp) REVERT: J 192 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: J 213 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7643 (ttp-110) REVERT: J 217 ASP cc_start: 0.7879 (m-30) cc_final: 0.7382 (m-30) REVERT: J 225 GLU cc_start: 0.8313 (tp30) cc_final: 0.7873 (mm-30) REVERT: J 239 ASP cc_start: 0.8563 (t0) cc_final: 0.8307 (t0) REVERT: J 280 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8222 (mpp) REVERT: J 375 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7745 (mptt) REVERT: L 103 GLU cc_start: 0.8541 (mp0) cc_final: 0.8140 (mp0) REVERT: L 213 ARG cc_start: 0.8434 (ttp-110) cc_final: 0.7810 (ttp-110) REVERT: L 217 ASP cc_start: 0.8040 (m-30) cc_final: 0.7582 (m-30) REVERT: L 239 ASP cc_start: 0.8802 (t0) cc_final: 0.8545 (t0) REVERT: L 393 LEU cc_start: 0.8357 (tt) cc_final: 0.7359 (mp) REVERT: N 31 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7253 (pp) REVERT: N 53 ASP cc_start: 0.8846 (t0) cc_final: 0.8629 (t0) REVERT: N 148 GLU cc_start: 0.7936 (pt0) cc_final: 0.7695 (mt-10) REVERT: N 203 ARG cc_start: 0.9090 (mtt180) cc_final: 0.8818 (mtt180) REVERT: N 209 PHE cc_start: 0.8645 (m-10) cc_final: 0.8345 (m-10) REVERT: N 225 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8151 (mm-30) REVERT: N 239 ASP cc_start: 0.8756 (t0) cc_final: 0.8541 (t0) REVERT: N 263 GLU cc_start: 0.8234 (mp0) cc_final: 0.7871 (mp0) REVERT: N 317 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8051 (mm-30) REVERT: P 217 ASP cc_start: 0.7932 (m-30) cc_final: 0.7684 (m-30) REVERT: P 233 MET cc_start: 0.9211 (mtm) cc_final: 0.8862 (mtp) REVERT: P 239 ASP cc_start: 0.8615 (t0) cc_final: 0.8208 (t0) REVERT: P 280 MET cc_start: 0.8931 (tpp) cc_final: 0.8723 (tpp) REVERT: P 288 GLU cc_start: 0.8496 (mp0) cc_final: 0.8144 (mp0) REVERT: P 308 GLU cc_start: 0.8244 (pm20) cc_final: 0.7943 (pm20) REVERT: P 318 ASN cc_start: 0.8535 (t0) cc_final: 0.8282 (t0) REVERT: S 54 ARG cc_start: 0.9004 (mmt-90) cc_final: 0.8773 (mpt180) REVERT: S 213 ARG cc_start: 0.8534 (ttm110) cc_final: 0.7690 (ttp-110) REVERT: S 217 ASP cc_start: 0.7978 (m-30) cc_final: 0.7664 (m-30) REVERT: S 239 ASP cc_start: 0.8854 (t0) cc_final: 0.8608 (t0) REVERT: S 249 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8564 (ptm160) REVERT: S 280 MET cc_start: 0.8719 (mtm) cc_final: 0.8494 (tpp) REVERT: S 317 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7788 (mm-30) REVERT: S 318 ASN cc_start: 0.8627 (t0) cc_final: 0.8245 (t0) REVERT: S 357 PHE cc_start: 0.8899 (t80) cc_final: 0.8549 (t80) REVERT: U 103 GLU cc_start: 0.8449 (mp0) cc_final: 0.8014 (mp0) REVERT: U 148 GLU cc_start: 0.7818 (pt0) cc_final: 0.7572 (mt-10) REVERT: U 213 ARG cc_start: 0.8307 (ttp-110) cc_final: 0.7374 (ttp80) REVERT: U 217 ASP cc_start: 0.8089 (m-30) cc_final: 0.7602 (m-30) REVERT: U 225 GLU cc_start: 0.8310 (tp30) cc_final: 0.7538 (mp0) REVERT: U 239 ASP cc_start: 0.8757 (t0) cc_final: 0.8530 (t0) REVERT: U 280 MET cc_start: 0.8913 (tpp) cc_final: 0.8677 (tpp) REVERT: U 361 TYR cc_start: 0.9395 (m-80) cc_final: 0.9150 (m-80) REVERT: W 15 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7744 (tptp) REVERT: W 129 GLN cc_start: 0.8283 (mp10) cc_final: 0.8029 (mp10) REVERT: W 164 ASN cc_start: 0.8846 (t0) cc_final: 0.8620 (t0) REVERT: W 192 GLU cc_start: 0.8066 (mp0) cc_final: 0.7853 (mt-10) REVERT: W 239 ASP cc_start: 0.8881 (t0) cc_final: 0.8596 (t0) REVERT: W 380 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7711 (tt) REVERT: Y 86 GLN cc_start: 0.8958 (mt0) cc_final: 0.8666 (mt0) REVERT: Y 115 THR cc_start: 0.8891 (p) cc_final: 0.8578 (t) REVERT: Y 129 GLN cc_start: 0.8295 (mp10) cc_final: 0.8054 (mp10) REVERT: Y 164 ASN cc_start: 0.8855 (t0) cc_final: 0.8554 (t0) REVERT: Y 213 ARG cc_start: 0.8297 (ttp-110) cc_final: 0.7729 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8071 (m-30) cc_final: 0.7805 (m-30) REVERT: Y 239 ASP cc_start: 0.8746 (t0) cc_final: 0.8361 (t0) REVERT: Y 263 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7838 (mt-10) REVERT: Y 280 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8184 (tpp) REVERT: Y 288 GLU cc_start: 0.8340 (mp0) cc_final: 0.7924 (mp0) REVERT: Y 318 ASN cc_start: 0.8551 (t0) cc_final: 0.8235 (t0) REVERT: Y 357 PHE cc_start: 0.8905 (t80) cc_final: 0.8692 (t80) REVERT: Y 361 TYR cc_start: 0.9359 (m-80) cc_final: 0.9066 (m-80) REVERT: Y 371 ARG cc_start: 0.8649 (mmt90) cc_final: 0.8413 (mmt90) REVERT: 0 86 GLN cc_start: 0.8875 (mt0) cc_final: 0.8674 (mt0) REVERT: 0 115 THR cc_start: 0.8872 (p) cc_final: 0.8567 (t) REVERT: 0 148 GLU cc_start: 0.8044 (pt0) cc_final: 0.7762 (mt-10) REVERT: 0 225 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7949 (mm-30) REVERT: 0 288 GLU cc_start: 0.8387 (mp0) cc_final: 0.7968 (mp0) REVERT: 0 318 ASN cc_start: 0.8575 (t0) cc_final: 0.8223 (t0) REVERT: 2 164 ASN cc_start: 0.8845 (t0) cc_final: 0.8155 (t0) REVERT: 2 213 ARG cc_start: 0.8307 (mtp-110) cc_final: 0.7875 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7895 (m-30) cc_final: 0.7643 (m-30) REVERT: 2 239 ASP cc_start: 0.8778 (t0) cc_final: 0.8392 (t0) REVERT: 2 280 MET cc_start: 0.8966 (tpp) cc_final: 0.8673 (mmm) REVERT: 2 288 GLU cc_start: 0.8452 (mp0) cc_final: 0.8115 (mp0) REVERT: 2 318 ASN cc_start: 0.8499 (t0) cc_final: 0.8216 (t0) REVERT: 2 363 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7451 (ttp-110) outliers start: 153 outliers final: 93 residues processed: 1135 average time/residue: 0.2652 time to fit residues: 490.9732 Evaluate side-chains 1096 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 991 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 94 ASP 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 49 SER 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 258 ASP 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 42 ASP Chi-restraints excluded: chain F residue 45 ILE 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 342 GLU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 94 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 367 GLU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 65 SER 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 355 SER 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 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 34 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 166 ILE Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 367 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 166 ILE Chi-restraints excluded: chain S residue 249 ARG Chi-restraints excluded: chain S residue 258 ASP Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 193 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 258 ASP Chi-restraints excluded: chain W residue 304 GLN 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 367 GLU 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 149 ASN Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 255 CYS 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 363 ARG Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 515 optimal weight: 4.9990 chunk 431 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 229 optimal weight: 0.0870 chunk 297 optimal weight: 0.9990 chunk 505 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 380 optimal weight: 10.0000 chunk 231 optimal weight: 0.9980 chunk 426 optimal weight: 0.9980 chunk 567 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 ASN D 305 GLN H 164 ASN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 GLN ** W 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 86 GLN 2 221 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.097537 restraints weight = 64298.955| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.96 r_work: 0.2855 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 47672 Z= 0.108 Angle : 0.560 9.926 64860 Z= 0.283 Chirality : 0.040 0.178 7470 Planarity : 0.004 0.059 7980 Dihedral : 8.321 71.788 7247 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.00 % Allowed : 15.97 % Favored : 82.04 % 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: 0.42 (0.12), residues: 5625 helix: 0.63 (0.10), residues: 3090 sheet: 0.40 (0.28), residues: 375 loop : -0.06 (0.15), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 213 TYR 0.011 0.001 TYR A 312 PHE 0.015 0.001 PHE D 275 TRP 0.011 0.001 TRP A 215 HIS 0.003 0.001 HIS J 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (47670) covalent geometry : angle 0.55966 / 0.28 (64860) hydrogen bonds : bond 0.03243 / 2.13 ( 1725) hydrogen bonds : angle 3.79903 / 2.58 ( 4995) Misc. bond : bond 0.00172 / 0.08 ( 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 1202 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 1105 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8686 (pp) REVERT: B 129 GLN cc_start: 0.8341 (mt0) cc_final: 0.8132 (tm-30) REVERT: B 213 ARG cc_start: 0.8128 (ttp-110) cc_final: 0.7363 (ttp80) REVERT: B 217 ASP cc_start: 0.7908 (m-30) cc_final: 0.7489 (m-30) REVERT: B 306 MET cc_start: 0.8460 (mtp) cc_final: 0.8191 (mtp) REVERT: A 103 GLU cc_start: 0.8380 (mp0) cc_final: 0.8049 (mp0) REVERT: A 123 MET cc_start: 0.6481 (mmm) cc_final: 0.5574 (mmm) REVERT: A 164 ASN cc_start: 0.8694 (t0) cc_final: 0.8283 (t0) REVERT: A 208 GLU cc_start: 0.7550 (pt0) cc_final: 0.7309 (pm20) REVERT: A 213 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.7465 (ttp-110) REVERT: A 217 ASP cc_start: 0.7918 (m-30) cc_final: 0.7291 (m-30) REVERT: A 225 GLU cc_start: 0.8282 (tp30) cc_final: 0.8015 (mm-30) REVERT: A 280 MET cc_start: 0.8769 (mtm) cc_final: 0.8515 (mpp) REVERT: A 288 GLU cc_start: 0.8468 (mp0) cc_final: 0.8143 (mp0) REVERT: A 313 MET cc_start: 0.8782 (ptm) cc_final: 0.8514 (ptp) REVERT: A 318 ASN cc_start: 0.8446 (t0) cc_final: 0.8228 (t0) REVERT: D 103 GLU cc_start: 0.8505 (mp0) cc_final: 0.8100 (mp0) REVERT: D 123 MET cc_start: 0.5506 (mmt) cc_final: 0.4996 (mmm) REVERT: D 164 ASN cc_start: 0.8804 (t0) cc_final: 0.8485 (t0) REVERT: D 213 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7517 (ttp-110) REVERT: D 217 ASP cc_start: 0.7797 (m-30) cc_final: 0.7378 (m-30) REVERT: D 225 GLU cc_start: 0.8170 (tp30) cc_final: 0.7954 (mm-30) REVERT: D 239 ASP cc_start: 0.8738 (t0) cc_final: 0.8279 (t0) REVERT: D 280 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8312 (mmt) REVERT: D 342 GLU cc_start: 0.7153 (mp0) cc_final: 0.6951 (mp0) REVERT: F 209 PHE cc_start: 0.8475 (m-10) cc_final: 0.8269 (m-10) REVERT: F 217 ASP cc_start: 0.7850 (m-30) cc_final: 0.7359 (m-30) REVERT: F 225 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7882 (mm-30) REVERT: F 239 ASP cc_start: 0.8546 (t0) cc_final: 0.8225 (t0) REVERT: F 323 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8801 (ttmm) REVERT: H 213 ARG cc_start: 0.8264 (ttm110) cc_final: 0.7848 (ttp-110) REVERT: H 225 GLU cc_start: 0.8118 (tp30) cc_final: 0.7520 (mm-30) REVERT: H 239 ASP cc_start: 0.8575 (t0) cc_final: 0.8149 (t0) REVERT: J 15 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7850 (tptp) REVERT: J 192 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: J 208 GLU cc_start: 0.7509 (pt0) cc_final: 0.7144 (mp0) REVERT: J 213 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.7475 (ttp-110) REVERT: J 217 ASP cc_start: 0.7778 (m-30) cc_final: 0.7173 (m-30) REVERT: J 239 ASP cc_start: 0.8566 (t0) cc_final: 0.8352 (t0) REVERT: J 263 GLU cc_start: 0.7986 (mp0) cc_final: 0.7601 (mp0) REVERT: J 375 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7632 (mptt) REVERT: L 103 GLU cc_start: 0.8510 (mp0) cc_final: 0.8181 (mp0) REVERT: L 213 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.7749 (ttp-110) REVERT: L 217 ASP cc_start: 0.7944 (m-30) cc_final: 0.7457 (m-30) REVERT: L 239 ASP cc_start: 0.8715 (t0) cc_final: 0.8472 (t0) REVERT: L 393 LEU cc_start: 0.8246 (tt) cc_final: 0.7344 (mp) REVERT: N 31 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6947 (pp) REVERT: N 164 ASN cc_start: 0.8824 (t0) cc_final: 0.8516 (t0) REVERT: N 192 GLU cc_start: 0.8168 (mp0) cc_final: 0.7895 (mt-10) REVERT: N 225 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8077 (mm-30) REVERT: N 317 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8071 (mm-30) REVERT: P 86 GLN cc_start: 0.8865 (mt0) cc_final: 0.8635 (mt0) REVERT: P 213 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.7818 (ttp-110) REVERT: P 217 ASP cc_start: 0.7899 (m-30) cc_final: 0.7671 (m-30) REVERT: P 239 ASP cc_start: 0.8548 (t0) cc_final: 0.8300 (t0) REVERT: P 288 GLU cc_start: 0.8507 (mp0) cc_final: 0.8263 (mp0) REVERT: P 308 GLU cc_start: 0.8232 (pm20) cc_final: 0.7924 (pm20) REVERT: P 318 ASN cc_start: 0.8410 (t0) cc_final: 0.8139 (t0) REVERT: S 54 ARG cc_start: 0.8984 (mmt-90) cc_final: 0.8776 (mpt180) REVERT: S 213 ARG cc_start: 0.8485 (ttm110) cc_final: 0.7627 (ttp-110) REVERT: S 217 ASP cc_start: 0.7933 (m-30) cc_final: 0.7575 (m-30) REVERT: S 318 ASN cc_start: 0.8448 (t0) cc_final: 0.8058 (t0) REVERT: U 103 GLU cc_start: 0.8470 (mp0) cc_final: 0.8061 (mp0) REVERT: U 164 ASN cc_start: 0.8911 (t0) cc_final: 0.8565 (t0) REVERT: U 213 ARG cc_start: 0.8240 (ttp-110) cc_final: 0.7387 (ttp80) REVERT: U 217 ASP cc_start: 0.8021 (m-30) cc_final: 0.7546 (m-30) REVERT: U 225 GLU cc_start: 0.8305 (tp30) cc_final: 0.7552 (mp0) REVERT: U 239 ASP cc_start: 0.8689 (t0) cc_final: 0.8476 (t0) REVERT: U 280 MET cc_start: 0.8830 (tpp) cc_final: 0.8588 (tpp) REVERT: U 337 MET cc_start: 0.9260 (mmp) cc_final: 0.8977 (mmp) REVERT: U 361 TYR cc_start: 0.9362 (m-80) cc_final: 0.9106 (m-80) REVERT: W 15 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7567 (tptp) REVERT: W 86 GLN cc_start: 0.8813 (mt0) cc_final: 0.8604 (mt0) REVERT: W 129 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: W 192 GLU cc_start: 0.8002 (mp0) cc_final: 0.7777 (mt-10) REVERT: W 225 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8058 (mm-30) REVERT: W 239 ASP cc_start: 0.8871 (t0) cc_final: 0.8549 (t0) REVERT: W 280 MET cc_start: 0.8806 (tpp) cc_final: 0.8591 (mmm) REVERT: Y 86 GLN cc_start: 0.8895 (mt0) cc_final: 0.8581 (mt0) REVERT: Y 115 THR cc_start: 0.8875 (p) cc_final: 0.8566 (t) REVERT: Y 164 ASN cc_start: 0.8815 (t0) cc_final: 0.8490 (t0) REVERT: Y 213 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7666 (ttp-110) REVERT: Y 217 ASP cc_start: 0.7954 (m-30) cc_final: 0.7660 (m-30) REVERT: Y 225 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7942 (mm-30) REVERT: Y 239 ASP cc_start: 0.8680 (t0) cc_final: 0.8371 (t0) REVERT: Y 263 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7895 (mt-10) REVERT: Y 280 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8143 (mmm) REVERT: Y 288 GLU cc_start: 0.8242 (mp0) cc_final: 0.8015 (mp0) REVERT: Y 318 ASN cc_start: 0.8462 (t0) cc_final: 0.8133 (t0) REVERT: Y 371 ARG cc_start: 0.8613 (mmt90) cc_final: 0.8394 (mmt90) REVERT: 0 89 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8884 (mm-40) REVERT: 0 115 THR cc_start: 0.8848 (p) cc_final: 0.8571 (t) REVERT: 0 213 ARG cc_start: 0.8431 (ttp-110) cc_final: 0.7816 (ttp-110) REVERT: 0 217 ASP cc_start: 0.7991 (m-30) cc_final: 0.7479 (m-30) REVERT: 0 288 GLU cc_start: 0.8322 (mp0) cc_final: 0.7953 (mp0) REVERT: 0 318 ASN cc_start: 0.8399 (t0) cc_final: 0.8084 (t0) REVERT: 2 213 ARG cc_start: 0.8250 (mtp-110) cc_final: 0.7793 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7794 (m-30) cc_final: 0.7519 (m-30) REVERT: 2 239 ASP cc_start: 0.8731 (t0) cc_final: 0.8505 (t0) REVERT: 2 280 MET cc_start: 0.8859 (tpp) cc_final: 0.8626 (mmm) REVERT: 2 288 GLU cc_start: 0.8355 (mp0) cc_final: 0.8119 (mp0) REVERT: 2 318 ASN cc_start: 0.8415 (t0) cc_final: 0.8128 (t0) outliers start: 97 outliers final: 60 residues processed: 1160 average time/residue: 0.2475 time to fit residues: 469.9522 Evaluate side-chains 1081 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1013 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 A residue 102 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 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 342 GLU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 102 LEU 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 367 GLU Chi-restraints excluded: chain J residue 102 LEU 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 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 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 102 LEU Chi-restraints excluded: chain N residue 332 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 355 SER 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 U residue 102 LEU Chi-restraints excluded: chain U residue 255 CYS Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 304 GLN Chi-restraints excluded: chain W residue 343 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 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 255 CYS Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 51 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 562 optimal weight: 3.9990 chunk 424 optimal weight: 8.9990 chunk 318 optimal weight: 2.9990 chunk 563 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 449 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN H 164 ASN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.114816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.094278 restraints weight = 64717.514| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.95 r_work: 0.2812 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 47672 Z= 0.183 Angle : 0.599 11.057 64860 Z= 0.303 Chirality : 0.043 0.161 7470 Planarity : 0.004 0.062 7980 Dihedral : 8.220 71.260 7247 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.41 % Allowed : 16.11 % Favored : 81.48 % 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: 0.46 (0.12), residues: 5625 helix: 0.73 (0.10), residues: 3075 sheet: 0.34 (0.28), residues: 375 loop : -0.14 (0.15), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 213 TYR 0.015 0.001 TYR 0 361 PHE 0.021 0.002 PHE S 209 TRP 0.010 0.001 TRP A 215 HIS 0.003 0.001 HIS W 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (47670) covalent geometry : angle 0.59940 / 0.30 (64860) hydrogen bonds : bond 0.03449 / 2.27 ( 1725) hydrogen bonds : angle 3.78795 / 2.57 ( 4995) Misc. bond : bond 0.00278 / 0.13 ( 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 1153 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1036 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8737 (pp) REVERT: B 129 GLN cc_start: 0.8399 (mt0) cc_final: 0.8149 (tm-30) REVERT: B 164 ASN cc_start: 0.8838 (t0) cc_final: 0.8229 (t0) REVERT: B 213 ARG cc_start: 0.8173 (ttp-110) cc_final: 0.7396 (ttp80) REVERT: B 217 ASP cc_start: 0.7959 (m-30) cc_final: 0.7467 (m-30) REVERT: B 225 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7983 (mm-30) REVERT: B 306 MET cc_start: 0.8588 (mtp) cc_final: 0.8316 (mtp) REVERT: A 103 GLU cc_start: 0.8402 (mp0) cc_final: 0.8136 (mp0) REVERT: A 123 MET cc_start: 0.6488 (mmm) cc_final: 0.5600 (mmm) REVERT: A 129 GLN cc_start: 0.8354 (mt0) cc_final: 0.8140 (tm-30) REVERT: A 164 ASN cc_start: 0.8742 (t0) cc_final: 0.8317 (t0) REVERT: A 208 GLU cc_start: 0.7661 (pt0) cc_final: 0.7444 (pm20) REVERT: A 217 ASP cc_start: 0.7938 (m-30) cc_final: 0.7319 (m-30) REVERT: A 225 GLU cc_start: 0.8342 (tp30) cc_final: 0.8069 (mm-30) REVERT: A 280 MET cc_start: 0.8791 (mtm) cc_final: 0.8499 (mpp) REVERT: A 288 GLU cc_start: 0.8486 (mp0) cc_final: 0.8088 (mp0) REVERT: A 318 ASN cc_start: 0.8566 (t0) cc_final: 0.8340 (t0) REVERT: D 103 GLU cc_start: 0.8518 (mp0) cc_final: 0.8170 (mp0) REVERT: D 123 MET cc_start: 0.5528 (mmt) cc_final: 0.4994 (mmm) REVERT: D 164 ASN cc_start: 0.8851 (t0) cc_final: 0.8536 (t0) REVERT: D 213 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7545 (ttp-110) REVERT: D 217 ASP cc_start: 0.7883 (m-30) cc_final: 0.7484 (m-30) REVERT: D 225 GLU cc_start: 0.8210 (tp30) cc_final: 0.7932 (mm-30) REVERT: D 239 ASP cc_start: 0.8701 (t0) cc_final: 0.8250 (t0) REVERT: D 342 GLU cc_start: 0.7300 (mp0) cc_final: 0.7061 (mp0) REVERT: F 12 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8348 (mmtt) REVERT: F 217 ASP cc_start: 0.7922 (m-30) cc_final: 0.7449 (m-30) REVERT: F 225 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7893 (mm-30) REVERT: F 239 ASP cc_start: 0.8569 (t0) cc_final: 0.8249 (t0) REVERT: F 323 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8860 (ttmm) REVERT: H 12 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7918 (mmtt) REVERT: H 213 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7846 (ttp-110) REVERT: H 225 GLU cc_start: 0.8155 (tp30) cc_final: 0.7699 (mm-30) REVERT: H 239 ASP cc_start: 0.8564 (t0) cc_final: 0.8162 (t0) REVERT: J 192 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: J 213 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.7603 (ttp-110) REVERT: J 217 ASP cc_start: 0.7853 (m-30) cc_final: 0.7256 (m-30) REVERT: J 239 ASP cc_start: 0.8572 (t0) cc_final: 0.8348 (t0) REVERT: J 375 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7654 (mptt) REVERT: L 103 GLU cc_start: 0.8451 (mp0) cc_final: 0.8177 (mp0) REVERT: L 164 ASN cc_start: 0.8824 (t0) cc_final: 0.8445 (t0) REVERT: L 213 ARG cc_start: 0.8438 (ttp-110) cc_final: 0.7852 (ttp-110) REVERT: L 217 ASP cc_start: 0.7971 (m-30) cc_final: 0.7509 (m-30) REVERT: L 225 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7814 (mm-30) REVERT: L 239 ASP cc_start: 0.8771 (t0) cc_final: 0.8542 (t0) REVERT: L 393 LEU cc_start: 0.8336 (tt) cc_final: 0.7393 (mp) REVERT: N 164 ASN cc_start: 0.8894 (t0) cc_final: 0.8581 (t0) REVERT: N 192 GLU cc_start: 0.8235 (mp0) cc_final: 0.7962 (mt-10) REVERT: N 225 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8138 (mm-30) REVERT: N 239 ASP cc_start: 0.8720 (t0) cc_final: 0.8508 (t0) REVERT: N 317 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8090 (mm-30) REVERT: N 342 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: P 32 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8165 (mmtp) REVERT: P 213 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.7858 (ttp-110) REVERT: P 217 ASP cc_start: 0.7942 (m-30) cc_final: 0.7697 (m-30) REVERT: P 239 ASP cc_start: 0.8602 (t0) cc_final: 0.8360 (t0) REVERT: P 308 GLU cc_start: 0.8271 (pm20) cc_final: 0.7923 (pm20) REVERT: P 318 ASN cc_start: 0.8501 (t0) cc_final: 0.8236 (t0) REVERT: S 54 ARG cc_start: 0.9005 (mmt-90) cc_final: 0.8769 (mpt180) REVERT: S 213 ARG cc_start: 0.8511 (ttm110) cc_final: 0.7627 (ttp-110) REVERT: S 217 ASP cc_start: 0.7967 (m-30) cc_final: 0.7584 (m-30) REVERT: S 225 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8284 (mm-30) REVERT: S 280 MET cc_start: 0.8919 (tpp) cc_final: 0.8632 (mmm) REVERT: S 317 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7763 (mm-30) REVERT: S 318 ASN cc_start: 0.8484 (t0) cc_final: 0.8120 (t0) REVERT: U 103 GLU cc_start: 0.8469 (mp0) cc_final: 0.8054 (mp0) REVERT: U 164 ASN cc_start: 0.8937 (t0) cc_final: 0.8585 (t0) REVERT: U 213 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.7381 (ttp80) REVERT: U 217 ASP cc_start: 0.8061 (m-30) cc_final: 0.7596 (m-30) REVERT: U 225 GLU cc_start: 0.8367 (tp30) cc_final: 0.8006 (mm-30) REVERT: U 239 ASP cc_start: 0.8736 (t0) cc_final: 0.8512 (t0) REVERT: U 280 MET cc_start: 0.8882 (tpp) cc_final: 0.8632 (tpp) REVERT: U 361 TYR cc_start: 0.9387 (m-80) cc_final: 0.9131 (m-80) REVERT: W 129 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: W 164 ASN cc_start: 0.8874 (t0) cc_final: 0.8627 (t0) REVERT: W 192 GLU cc_start: 0.8019 (mp0) cc_final: 0.7793 (mt-10) REVERT: W 225 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8010 (mm-30) REVERT: W 239 ASP cc_start: 0.8875 (t0) cc_final: 0.8546 (t0) REVERT: W 342 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: W 380 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7692 (tt) REVERT: Y 86 GLN cc_start: 0.8943 (mt0) cc_final: 0.8663 (mt0) REVERT: Y 115 THR cc_start: 0.8904 (p) cc_final: 0.8595 (t) REVERT: Y 213 ARG cc_start: 0.8259 (ttp-110) cc_final: 0.7850 (ttp-110) REVERT: Y 217 ASP cc_start: 0.8012 (m-30) cc_final: 0.7774 (m-30) REVERT: Y 239 ASP cc_start: 0.8746 (t0) cc_final: 0.8399 (t0) REVERT: Y 280 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8123 (tpp) REVERT: Y 288 GLU cc_start: 0.8292 (mp0) cc_final: 0.7949 (mp0) REVERT: Y 318 ASN cc_start: 0.8499 (t0) cc_final: 0.8174 (t0) REVERT: Y 371 ARG cc_start: 0.8608 (mmt90) cc_final: 0.8404 (mmt90) REVERT: 0 115 THR cc_start: 0.8876 (p) cc_final: 0.8584 (t) REVERT: 0 288 GLU cc_start: 0.8336 (mp0) cc_final: 0.7932 (mp0) REVERT: 0 318 ASN cc_start: 0.8481 (t0) cc_final: 0.8168 (t0) REVERT: 2 53 ASP cc_start: 0.8792 (t0) cc_final: 0.8530 (t0) REVERT: 2 123 MET cc_start: 0.7093 (mmt) cc_final: 0.6650 (mmt) REVERT: 2 164 ASN cc_start: 0.8838 (t0) cc_final: 0.8408 (t0) REVERT: 2 213 ARG cc_start: 0.8282 (mtp-110) cc_final: 0.7854 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7854 (m-30) cc_final: 0.7602 (m-30) REVERT: 2 239 ASP cc_start: 0.8759 (t0) cc_final: 0.8509 (t0) REVERT: 2 280 MET cc_start: 0.8929 (tpp) cc_final: 0.8628 (mmm) REVERT: 2 288 GLU cc_start: 0.8358 (mp0) cc_final: 0.8096 (mp0) REVERT: 2 318 ASN cc_start: 0.8449 (t0) cc_final: 0.8155 (t0) outliers start: 117 outliers final: 84 residues processed: 1105 average time/residue: 0.2147 time to fit residues: 390.3337 Evaluate side-chains 1103 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1010 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 42 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 193 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 332 LEU Chi-restraints excluded: chain D residue 355 SER 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 342 GLU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 94 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 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 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 42 ASP 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 367 GLU Chi-restraints excluded: chain N residue 15 LYS 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 367 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 355 SER Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 102 LEU 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 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 U residue 369 VAL Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 304 GLN Chi-restraints excluded: chain W residue 342 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 355 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 105 VAL 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 369 VAL 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 304 GLN Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Chi-restraints excluded: chain 2 residue 342 GLU Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 322 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 478 optimal weight: 4.9990 chunk 555 optimal weight: 1.9990 chunk 418 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 257 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 GLN ** W 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3266 r_free = 0.3266 target = 0.118636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.098450 restraints weight = 64066.877| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.92 r_work: 0.2861 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47672 Z= 0.120 Angle : 0.568 11.289 64860 Z= 0.287 Chirality : 0.041 0.161 7470 Planarity : 0.004 0.061 7980 Dihedral : 8.250 72.194 7247 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.14 % Allowed : 16.79 % Favored : 81.07 % 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: 0.81 (0.10), residues: 3090 sheet: 0.26 (0.28), residues: 375 loop : -0.01 (0.15), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG N 392 TYR 0.013 0.001 TYR 0 361 PHE 0.022 0.001 PHE U 209 TRP 0.011 0.001 TRP A 215 HIS 0.003 0.001 HIS S 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (47670) covalent geometry : angle 0.56769 / 0.29 (64860) hydrogen bonds : bond 0.03153 / 2.08 ( 1725) hydrogen bonds : angle 3.72722 / 2.53 ( 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 1199 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 1095 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8710 (pp) REVERT: B 92 THR cc_start: 0.8486 (m) cc_final: 0.8255 (m) REVERT: B 129 GLN cc_start: 0.8326 (mt0) cc_final: 0.8118 (tm-30) REVERT: B 213 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7360 (ttp80) REVERT: B 217 ASP cc_start: 0.7908 (m-30) cc_final: 0.7398 (m-30) REVERT: B 306 MET cc_start: 0.8432 (mtp) cc_final: 0.8147 (mtp) REVERT: A 103 GLU cc_start: 0.8323 (mp0) cc_final: 0.8035 (mp0) REVERT: A 123 MET cc_start: 0.6375 (mmm) cc_final: 0.5470 (mmm) REVERT: A 129 GLN cc_start: 0.8309 (mt0) cc_final: 0.8090 (tm-30) REVERT: A 213 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.7464 (ttp-110) REVERT: A 217 ASP cc_start: 0.7878 (m-30) cc_final: 0.7220 (m-30) REVERT: A 225 GLU cc_start: 0.8271 (tp30) cc_final: 0.7967 (mm-30) REVERT: A 280 MET cc_start: 0.8700 (mtm) cc_final: 0.8440 (mpp) REVERT: A 288 GLU cc_start: 0.8493 (mp0) cc_final: 0.8131 (mp0) REVERT: A 318 ASN cc_start: 0.8490 (t0) cc_final: 0.8251 (t0) REVERT: A 342 GLU cc_start: 0.7553 (mp0) cc_final: 0.6122 (mt-10) REVERT: D 103 GLU cc_start: 0.8527 (mp0) cc_final: 0.8124 (mp0) REVERT: D 123 MET cc_start: 0.5497 (mmt) cc_final: 0.4951 (mmm) REVERT: D 164 ASN cc_start: 0.8827 (t0) cc_final: 0.8516 (t0) REVERT: D 213 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7516 (ttp-110) REVERT: D 217 ASP cc_start: 0.7779 (m-30) cc_final: 0.7350 (m-30) REVERT: D 225 GLU cc_start: 0.8175 (tp30) cc_final: 0.7941 (mm-30) REVERT: D 239 ASP cc_start: 0.8615 (t0) cc_final: 0.8402 (t70) REVERT: F 217 ASP cc_start: 0.7806 (m-30) cc_final: 0.7314 (m-30) REVERT: F 225 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7836 (mm-30) REVERT: F 239 ASP cc_start: 0.8495 (t0) cc_final: 0.8170 (t0) REVERT: F 280 MET cc_start: 0.8752 (mmm) cc_final: 0.8447 (mmt) REVERT: F 323 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8833 (ttmm) REVERT: H 213 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7901 (ttp-110) REVERT: H 225 GLU cc_start: 0.8172 (tp30) cc_final: 0.7653 (mm-30) REVERT: H 239 ASP cc_start: 0.8552 (t0) cc_final: 0.8237 (t0) REVERT: H 241 LYS cc_start: 0.8892 (mttm) cc_final: 0.8646 (mmtt) REVERT: J 192 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: J 208 GLU cc_start: 0.7556 (pt0) cc_final: 0.7164 (mp0) REVERT: J 213 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.7538 (ttp-110) REVERT: J 217 ASP cc_start: 0.7723 (m-30) cc_final: 0.7089 (m-30) REVERT: J 239 ASP cc_start: 0.8539 (t0) cc_final: 0.8309 (t0) REVERT: J 263 GLU cc_start: 0.8046 (mp0) cc_final: 0.7628 (mp0) REVERT: J 375 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7584 (mptt) REVERT: L 15 LYS cc_start: 0.8285 (ttmt) cc_final: 0.8033 (ttmt) REVERT: L 103 GLU cc_start: 0.8488 (mp0) cc_final: 0.8176 (mp0) REVERT: L 213 ARG cc_start: 0.8410 (ttp-110) cc_final: 0.7716 (ttp-110) REVERT: L 217 ASP cc_start: 0.7905 (m-30) cc_final: 0.7406 (m-30) REVERT: L 225 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7748 (mm-30) REVERT: L 239 ASP cc_start: 0.8715 (t0) cc_final: 0.8483 (t0) REVERT: L 393 LEU cc_start: 0.8292 (tt) cc_final: 0.7375 (mp) REVERT: N 192 GLU cc_start: 0.8201 (mp0) cc_final: 0.7900 (mt-10) REVERT: N 225 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8081 (mm-30) REVERT: N 317 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8014 (mm-30) REVERT: N 342 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: P 86 GLN cc_start: 0.8879 (mt0) cc_final: 0.8633 (mt0) REVERT: P 213 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.7772 (ttp-110) REVERT: P 217 ASP cc_start: 0.7930 (m-30) cc_final: 0.7672 (m-30) REVERT: P 239 ASP cc_start: 0.8494 (t0) cc_final: 0.8264 (t0) REVERT: P 288 GLU cc_start: 0.8547 (mp0) cc_final: 0.8190 (mp0) REVERT: P 308 GLU cc_start: 0.8197 (pm20) cc_final: 0.7805 (pm20) REVERT: P 318 ASN cc_start: 0.8437 (t0) cc_final: 0.8176 (t0) REVERT: S 12 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8207 (mmtt) REVERT: S 54 ARG cc_start: 0.8975 (mmt-90) cc_final: 0.8749 (mpt180) REVERT: S 213 ARG cc_start: 0.8493 (ttm110) cc_final: 0.7681 (ttp-110) REVERT: S 217 ASP cc_start: 0.7919 (m-30) cc_final: 0.7584 (m-30) REVERT: S 225 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8259 (mm-30) REVERT: S 317 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7796 (mm-30) REVERT: U 67 PRO cc_start: 0.8550 (Cg_exo) cc_final: 0.8268 (Cg_endo) REVERT: U 103 GLU cc_start: 0.8460 (mp0) cc_final: 0.8034 (mp0) REVERT: U 164 ASN cc_start: 0.8877 (t0) cc_final: 0.8466 (t0) REVERT: U 213 ARG cc_start: 0.8230 (ttp-110) cc_final: 0.7345 (ttp80) REVERT: U 217 ASP cc_start: 0.8039 (m-30) cc_final: 0.7558 (m-30) REVERT: U 225 GLU cc_start: 0.8281 (tp30) cc_final: 0.7886 (mm-30) REVERT: U 239 ASP cc_start: 0.8686 (t0) cc_final: 0.8471 (t0) REVERT: U 280 MET cc_start: 0.8793 (tpp) cc_final: 0.8546 (tpp) REVERT: U 337 MET cc_start: 0.9207 (mmp) cc_final: 0.8929 (mmp) REVERT: U 361 TYR cc_start: 0.9348 (m-80) cc_final: 0.9083 (m-80) REVERT: W 103 GLU cc_start: 0.8578 (mp0) cc_final: 0.8186 (mp0) REVERT: W 129 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: W 164 ASN cc_start: 0.8877 (t0) cc_final: 0.8597 (t0) REVERT: W 192 GLU cc_start: 0.7996 (mp0) cc_final: 0.7735 (mt-10) REVERT: W 217 ASP cc_start: 0.8005 (m-30) cc_final: 0.7595 (m-30) REVERT: W 225 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7843 (mm-30) REVERT: W 239 ASP cc_start: 0.8822 (t0) cc_final: 0.8510 (t0) REVERT: W 342 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: W 380 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7616 (tt) REVERT: Y 86 GLN cc_start: 0.8921 (mt0) cc_final: 0.8637 (mt0) REVERT: Y 115 THR cc_start: 0.8872 (p) cc_final: 0.8563 (t) REVERT: Y 213 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7575 (ttp-110) REVERT: Y 217 ASP cc_start: 0.7945 (m-30) cc_final: 0.7670 (m-30) REVERT: Y 225 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7990 (mm-30) REVERT: Y 239 ASP cc_start: 0.8720 (t0) cc_final: 0.8515 (t0) REVERT: Y 263 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7821 (mt-10) REVERT: Y 280 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8070 (mmm) REVERT: Y 288 GLU cc_start: 0.8188 (mp0) cc_final: 0.7823 (mp0) REVERT: Y 318 ASN cc_start: 0.8425 (t0) cc_final: 0.8108 (t0) REVERT: Y 371 ARG cc_start: 0.8544 (mmt90) cc_final: 0.8344 (mmt90) REVERT: 0 32 LYS cc_start: 0.8392 (mttm) cc_final: 0.8140 (mttt) REVERT: 0 115 THR cc_start: 0.8814 (p) cc_final: 0.8510 (t) REVERT: 0 217 ASP cc_start: 0.7963 (m-30) cc_final: 0.7514 (m-30) REVERT: 0 288 GLU cc_start: 0.8290 (mp0) cc_final: 0.7956 (mp0) REVERT: 0 318 ASN cc_start: 0.8408 (t0) cc_final: 0.8083 (t0) REVERT: 2 53 ASP cc_start: 0.8713 (t0) cc_final: 0.8448 (t0) REVERT: 2 123 MET cc_start: 0.7042 (mmt) cc_final: 0.6617 (mmt) REVERT: 2 213 ARG cc_start: 0.8153 (mtp-110) cc_final: 0.7714 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7784 (m-30) cc_final: 0.7501 (m-30) REVERT: 2 239 ASP cc_start: 0.8707 (t0) cc_final: 0.8462 (t0) REVERT: 2 280 MET cc_start: 0.8831 (tpp) cc_final: 0.8540 (mmm) REVERT: 2 288 GLU cc_start: 0.8282 (mp0) cc_final: 0.8067 (mp0) REVERT: 2 318 ASN cc_start: 0.8392 (t0) cc_final: 0.8120 (t0) REVERT: 2 371 ARG cc_start: 0.8477 (mmt90) cc_final: 0.7641 (ptm160) outliers start: 104 outliers final: 70 residues processed: 1167 average time/residue: 0.1746 time to fit residues: 338.2129 Evaluate side-chains 1117 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1038 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain A residue 42 ASP 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 332 LEU Chi-restraints excluded: chain F residue 42 ASP 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 367 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 102 LEU 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 102 LEU Chi-restraints excluded: chain J residue 192 GLU 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 105 VAL 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 15 LYS 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 304 GLN Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 255 CYS Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 304 GLN Chi-restraints excluded: chain W residue 342 GLU Chi-restraints excluded: chain W residue 343 LEU 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 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 42 ASP 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 342 GLU Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 87 optimal weight: 8.9990 chunk 361 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 528 optimal weight: 0.9990 chunk 476 optimal weight: 0.7980 chunk 345 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 323 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN W 86 GLN ** W 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.119975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.099738 restraints weight = 64370.853| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.93 r_work: 0.2868 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 47672 Z= 0.113 Angle : 0.565 11.580 64860 Z= 0.285 Chirality : 0.041 0.146 7470 Planarity : 0.004 0.064 7980 Dihedral : 8.206 73.108 7247 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.71 % Allowed : 17.45 % Favored : 80.84 % 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: 0.56 (0.12), residues: 5625 helix: 0.79 (0.10), residues: 3165 sheet: 0.12 (0.28), residues: 375 loop : -0.03 (0.15), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG N 392 TYR 0.012 0.001 TYR Y 361 PHE 0.013 0.001 PHE B 163 TRP 0.011 0.001 TRP A 215 HIS 0.004 0.001 HIS S 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (47670) covalent geometry : angle 0.56477 / 0.28 (64860) hydrogen bonds : bond 0.03042 / 2.01 ( 1725) hydrogen bonds : angle 3.67407 / 2.49 ( 4995) Misc. bond : bond 0.00158 / 0.08 ( 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 1189 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1106 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8675 (pp) REVERT: B 92 THR cc_start: 0.8419 (m) cc_final: 0.8174 (m) REVERT: B 213 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7406 (ttp80) REVERT: B 217 ASP cc_start: 0.7890 (m-30) cc_final: 0.7430 (m-30) REVERT: A 123 MET cc_start: 0.6415 (mmm) cc_final: 0.5507 (mmm) REVERT: A 129 GLN cc_start: 0.8276 (mt0) cc_final: 0.8072 (tm-30) REVERT: A 164 ASN cc_start: 0.8679 (t0) cc_final: 0.8281 (t0) REVERT: A 213 ARG cc_start: 0.8295 (ttp-110) cc_final: 0.7473 (ttp-110) REVERT: A 217 ASP cc_start: 0.7825 (m-30) cc_final: 0.7217 (m-30) REVERT: A 225 GLU cc_start: 0.8240 (tp30) cc_final: 0.7958 (mm-30) REVERT: A 280 MET cc_start: 0.8656 (mtm) cc_final: 0.8435 (mpp) REVERT: A 288 GLU cc_start: 0.8490 (mp0) cc_final: 0.7951 (mp0) REVERT: A 318 ASN cc_start: 0.8466 (t0) cc_final: 0.8253 (t0) REVERT: D 103 GLU cc_start: 0.8539 (mp0) cc_final: 0.8101 (mp0) REVERT: D 123 MET cc_start: 0.5500 (mmt) cc_final: 0.4954 (mmm) REVERT: D 164 ASN cc_start: 0.8828 (t0) cc_final: 0.8517 (t0) REVERT: D 213 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7486 (ttp-110) REVERT: D 217 ASP cc_start: 0.7758 (m-30) cc_final: 0.7313 (m-30) REVERT: D 225 GLU cc_start: 0.8217 (tp30) cc_final: 0.7960 (mm-30) REVERT: D 239 ASP cc_start: 0.8596 (t0) cc_final: 0.8384 (t70) REVERT: F 217 ASP cc_start: 0.7811 (m-30) cc_final: 0.7300 (m-30) REVERT: F 225 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7828 (mm-30) REVERT: F 239 ASP cc_start: 0.8489 (t0) cc_final: 0.8168 (t0) REVERT: F 323 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8819 (ttmm) REVERT: H 213 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7834 (ttp-110) REVERT: H 225 GLU cc_start: 0.8110 (tp30) cc_final: 0.7558 (mm-30) REVERT: H 280 MET cc_start: 0.8487 (tpp) cc_final: 0.8267 (mmm) REVERT: J 28 ILE cc_start: 0.9160 (mt) cc_final: 0.8954 (mt) REVERT: J 192 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: J 208 GLU cc_start: 0.7562 (pt0) cc_final: 0.7174 (mp0) REVERT: J 209 PHE cc_start: 0.8250 (m-10) cc_final: 0.8049 (m-10) REVERT: J 213 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7553 (ttp-110) REVERT: J 217 ASP cc_start: 0.7698 (m-30) cc_final: 0.7059 (m-30) REVERT: J 239 ASP cc_start: 0.8514 (t0) cc_final: 0.8282 (t0) REVERT: J 263 GLU cc_start: 0.8031 (mp0) cc_final: 0.7637 (mp0) REVERT: J 371 ARG cc_start: 0.8562 (mmt90) cc_final: 0.8311 (mmt90) REVERT: J 375 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7510 (mptt) REVERT: L 103 GLU cc_start: 0.8504 (mp0) cc_final: 0.8303 (mp0) REVERT: L 164 ASN cc_start: 0.8799 (t0) cc_final: 0.8403 (t0) REVERT: L 213 ARG cc_start: 0.8412 (ttp-110) cc_final: 0.7729 (ttp-110) REVERT: L 217 ASP cc_start: 0.7877 (m-30) cc_final: 0.7389 (m-30) REVERT: L 225 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7750 (mm-30) REVERT: L 239 ASP cc_start: 0.8693 (t0) cc_final: 0.8431 (t0) REVERT: L 393 LEU cc_start: 0.8269 (tt) cc_final: 0.7346 (mp) REVERT: N 15 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7957 (ttmm) REVERT: N 53 ASP cc_start: 0.8735 (t0) cc_final: 0.8484 (t0) REVERT: N 192 GLU cc_start: 0.8224 (mp0) cc_final: 0.7906 (mt-10) REVERT: N 217 ASP cc_start: 0.8094 (m-30) cc_final: 0.7596 (m-30) REVERT: N 225 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8104 (mm-30) REVERT: N 317 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8006 (mm-30) REVERT: N 342 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: N 371 ARG cc_start: 0.8534 (mmt90) cc_final: 0.8329 (mmt90) REVERT: P 86 GLN cc_start: 0.8859 (mt0) cc_final: 0.8602 (mt0) REVERT: P 213 ARG cc_start: 0.8204 (ttp-110) cc_final: 0.7763 (ttp-110) REVERT: P 217 ASP cc_start: 0.7904 (m-30) cc_final: 0.7637 (m-30) REVERT: P 288 GLU cc_start: 0.8525 (mp0) cc_final: 0.8201 (mp0) REVERT: P 308 GLU cc_start: 0.8275 (pm20) cc_final: 0.7882 (pm20) REVERT: P 318 ASN cc_start: 0.8449 (t0) cc_final: 0.8174 (t0) REVERT: P 323 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8607 (ttmm) REVERT: S 12 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8200 (mmtt) REVERT: S 54 ARG cc_start: 0.8949 (mmt-90) cc_final: 0.8714 (mpt180) REVERT: S 67 PRO cc_start: 0.8582 (Cg_exo) cc_final: 0.8325 (Cg_endo) REVERT: S 208 GLU cc_start: 0.7223 (pt0) cc_final: 0.6958 (pm20) REVERT: S 213 ARG cc_start: 0.8470 (ttm110) cc_final: 0.7650 (ttp-110) REVERT: S 217 ASP cc_start: 0.7960 (m-30) cc_final: 0.7601 (m-30) REVERT: S 225 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8142 (mm-30) REVERT: S 317 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7770 (mm-30) REVERT: U 103 GLU cc_start: 0.8462 (mp0) cc_final: 0.8082 (mp0) REVERT: U 164 ASN cc_start: 0.8846 (t0) cc_final: 0.8427 (t0) REVERT: U 213 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7358 (ttp80) REVERT: U 217 ASP cc_start: 0.8012 (m-30) cc_final: 0.7517 (m-30) REVERT: U 225 GLU cc_start: 0.8291 (tp30) cc_final: 0.7889 (mm-30) REVERT: U 239 ASP cc_start: 0.8689 (t0) cc_final: 0.8446 (t0) REVERT: U 280 MET cc_start: 0.8761 (tpp) cc_final: 0.8525 (tpp) REVERT: U 337 MET cc_start: 0.9176 (mmp) cc_final: 0.8926 (mmp) REVERT: U 342 GLU cc_start: 0.7262 (mp0) cc_final: 0.6967 (mp0) REVERT: U 361 TYR cc_start: 0.9348 (m-80) cc_final: 0.9061 (m-80) REVERT: W 53 ASP cc_start: 0.8715 (t0) cc_final: 0.8482 (t0) REVERT: W 86 GLN cc_start: 0.8851 (mt0) cc_final: 0.8641 (mt0) REVERT: W 129 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: W 164 ASN cc_start: 0.8880 (t0) cc_final: 0.8570 (t0) REVERT: W 192 GLU cc_start: 0.7985 (mp0) cc_final: 0.7714 (mt-10) REVERT: W 209 PHE cc_start: 0.7943 (m-10) cc_final: 0.7626 (m-80) REVERT: W 217 ASP cc_start: 0.8033 (m-30) cc_final: 0.7659 (m-30) REVERT: W 225 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7740 (mm-30) REVERT: W 239 ASP cc_start: 0.8790 (t0) cc_final: 0.8500 (t0) REVERT: W 280 MET cc_start: 0.8756 (tpp) cc_final: 0.8492 (mmm) REVERT: W 361 TYR cc_start: 0.9330 (m-80) cc_final: 0.9037 (m-80) REVERT: W 380 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7598 (tt) REVERT: Y 86 GLN cc_start: 0.8918 (mt0) cc_final: 0.8639 (mt0) REVERT: Y 115 THR cc_start: 0.8864 (p) cc_final: 0.8552 (t) REVERT: Y 129 GLN cc_start: 0.8301 (mp10) cc_final: 0.8014 (mp10) REVERT: Y 209 PHE cc_start: 0.8148 (m-10) cc_final: 0.7889 (m-80) REVERT: Y 213 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7646 (ttp-110) REVERT: Y 217 ASP cc_start: 0.7937 (m-30) cc_final: 0.7654 (m-30) REVERT: Y 225 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8024 (mm-30) REVERT: Y 239 ASP cc_start: 0.8718 (t0) cc_final: 0.8487 (t0) REVERT: Y 263 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7861 (mt-10) REVERT: Y 280 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8069 (mmm) REVERT: Y 288 GLU cc_start: 0.8154 (mp0) cc_final: 0.7854 (mp0) REVERT: 0 32 LYS cc_start: 0.8344 (mttm) cc_final: 0.8099 (mttt) REVERT: 0 115 THR cc_start: 0.8811 (p) cc_final: 0.8508 (t) REVERT: 0 217 ASP cc_start: 0.7945 (m-30) cc_final: 0.7473 (m-30) REVERT: 0 288 GLU cc_start: 0.8264 (mp0) cc_final: 0.7954 (mp0) REVERT: 0 318 ASN cc_start: 0.8435 (t0) cc_final: 0.8037 (t0) REVERT: 2 53 ASP cc_start: 0.8678 (t0) cc_final: 0.8395 (t0) REVERT: 2 123 MET cc_start: 0.7076 (mmt) cc_final: 0.6657 (mmt) REVERT: 2 164 ASN cc_start: 0.8808 (t0) cc_final: 0.8361 (t0) REVERT: 2 213 ARG cc_start: 0.8114 (mtp-110) cc_final: 0.7641 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7804 (m-30) cc_final: 0.7516 (m-30) REVERT: 2 239 ASP cc_start: 0.8676 (t0) cc_final: 0.8419 (t0) REVERT: 2 280 MET cc_start: 0.8793 (tpp) cc_final: 0.8526 (mmm) REVERT: 2 308 GLU cc_start: 0.8054 (pm20) cc_final: 0.7765 (pm20) REVERT: 2 318 ASN cc_start: 0.8341 (t0) cc_final: 0.7988 (t0) REVERT: 2 371 ARG cc_start: 0.8465 (mmt90) cc_final: 0.7624 (ptm160) outliers start: 83 outliers final: 64 residues processed: 1160 average time/residue: 0.1684 time to fit residues: 324.8905 Evaluate side-chains 1104 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 1031 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 A residue 42 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 355 SER 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 255 CYS Chi-restraints excluded: chain H residue 288 GLU 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 102 LEU Chi-restraints excluded: chain J residue 192 GLU 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 105 VAL Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain N residue 15 LYS 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 304 GLN 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 U residue 102 LEU Chi-restraints excluded: chain U residue 252 GLU Chi-restraints excluded: chain U residue 255 CYS Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 304 GLN Chi-restraints excluded: chain W residue 342 GLU Chi-restraints excluded: chain W residue 343 LEU 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 355 SER Chi-restraints excluded: chain Y residue 375 LYS 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 319 SER Chi-restraints excluded: chain 2 residue 342 GLU Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 233 optimal weight: 3.9990 chunk 302 optimal weight: 8.9990 chunk 563 optimal weight: 0.7980 chunk 546 optimal weight: 8.9990 chunk 377 optimal weight: 0.6980 chunk 458 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 548 optimal weight: 6.9990 chunk 249 optimal weight: 0.8980 chunk 463 optimal weight: 6.9990 chunk 413 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.098364 restraints weight = 64478.944| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.93 r_work: 0.2856 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 47672 Z= 0.132 Angle : 0.579 11.450 64860 Z= 0.292 Chirality : 0.041 0.145 7470 Planarity : 0.004 0.064 7980 Dihedral : 8.161 72.657 7247 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.91 % Allowed : 17.67 % Favored : 80.41 % 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: 0.61 (0.12), residues: 5625 helix: 0.84 (0.10), residues: 3180 sheet: 0.09 (0.28), residues: 375 loop : -0.03 (0.15), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 392 TYR 0.015 0.001 TYR U 260 PHE 0.019 0.001 PHE U 209 TRP 0.010 0.001 TRP A 215 HIS 0.003 0.001 HIS S 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (47670) covalent geometry : angle 0.57854 / 0.29 (64860) hydrogen bonds : bond 0.03071 / 2.02 ( 1725) hydrogen bonds : angle 3.65333 / 2.48 ( 4995) Misc. bond : bond 0.00150 / 0.07 ( 2) =============================================================================== Job complete usr+sys time: 12481.08 seconds wall clock time: 213 minutes 8.57 seconds (12788.57 seconds total)