Starting phenix.real_space_refine on Tue Aug 26 23:47:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h05_0108/08_2025/6h05_0108.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h05_0108/08_2025/6h05_0108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6h05_0108/08_2025/6h05_0108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h05_0108/08_2025/6h05_0108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6h05_0108/08_2025/6h05_0108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h05_0108/08_2025/6h05_0108.map" } resolution = 2.9 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= 0.002 sd= 0.189 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: 4 Type Number sf(0) Gaussians S 288 5.16 5 C 28080 2.51 5 N 8016 2.21 5 O 8160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 216 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44544 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 4.07, per 1000 atoms: 0.09 Number of scatterers: 44544 At special positions: 0 Unit cell: (155.967, 158.089, 155.967, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 288 16.00 O 8160 8.00 N 8016 7.00 C 28080 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10608 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 72 sheets defined 44.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 271 Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE B 167 " --> pdb=" O MET B 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.609A pdb=" N HIS B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 271 Processing helix chain 'C' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE C 368 " --> pdb=" O GLU C 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL C 376 " --> pdb=" O ILE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 Processing helix chain 'D' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS D 199 " --> pdb=" O MET D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 208 Processing helix chain 'D' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 271 Processing helix chain 'D' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 376 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 194 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS E 199 " --> pdb=" O MET E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 208 Processing helix chain 'E' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU E 225 " --> pdb=" O SER E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN E 232 " --> pdb=" O GLN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 271 Processing helix chain 'E' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET E 297 " --> pdb=" O ALA E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL E 376 " --> pdb=" O ILE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE F 167 " --> pdb=" O MET F 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 194 Processing helix chain 'F' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS F 199 " --> pdb=" O MET F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 208 Processing helix chain 'F' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU F 225 " --> pdb=" O SER F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 4.075A pdb=" N ASN F 232 " --> pdb=" O GLN F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 271 Processing helix chain 'F' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET F 297 " --> pdb=" O ALA F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL F 376 " --> pdb=" O ILE F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA G 168 " --> pdb=" O ARG G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 194 Processing helix chain 'G' and resid 194 through 199 removed outlier: 3.609A pdb=" N HIS G 199 " --> pdb=" O MET G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 208 Processing helix chain 'G' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU G 225 " --> pdb=" O SER G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 271 Processing helix chain 'G' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS G 286 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 289 " --> pdb=" O GLU G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET G 297 " --> pdb=" O ALA G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE G 368 " --> pdb=" O GLU G 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL G 376 " --> pdb=" O ILE G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU G 384 " --> pdb=" O ARG G 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE H 167 " --> pdb=" O MET H 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA H 168 " --> pdb=" O ARG H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 194 Processing helix chain 'H' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS H 199 " --> pdb=" O MET H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 208 Processing helix chain 'H' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU H 225 " --> pdb=" O SER H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN H 232 " --> pdb=" O GLN H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 271 Processing helix chain 'H' and resid 274 through 289 removed outlier: 3.609A pdb=" N LYS H 286 " --> pdb=" O GLU H 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 289 " --> pdb=" O GLU H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET H 297 " --> pdb=" O ALA H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE H 368 " --> pdb=" O GLU H 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL H 376 " --> pdb=" O ILE H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU H 384 " --> pdb=" O ARG H 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 172 removed outlier: 3.869A pdb=" N ILE I 167 " --> pdb=" O MET I 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA I 168 " --> pdb=" O ARG I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 194 Processing helix chain 'I' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS I 199 " --> pdb=" O MET I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 208 Processing helix chain 'I' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU I 225 " --> pdb=" O SER I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 271 Processing helix chain 'I' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS I 286 " --> pdb=" O GLU I 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS I 289 " --> pdb=" O GLU I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET I 297 " --> pdb=" O ALA I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE I 368 " --> pdb=" O GLU I 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL I 376 " --> pdb=" O ILE I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU I 384 " --> pdb=" O ARG I 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE J 167 " --> pdb=" O MET J 163 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA J 168 " --> pdb=" O ARG J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 194 Processing helix chain 'J' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS J 199 " --> pdb=" O MET J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 208 Processing helix chain 'J' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU J 225 " --> pdb=" O SER J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN J 232 " --> pdb=" O GLN J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 271 Processing helix chain 'J' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS J 286 " --> pdb=" O GLU J 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS J 289 " --> pdb=" O GLU J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET J 297 " --> pdb=" O ALA J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE J 368 " --> pdb=" O GLU J 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL J 376 " --> pdb=" O ILE J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU J 384 " --> pdb=" O ARG J 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE K 167 " --> pdb=" O MET K 163 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA K 168 " --> pdb=" O ARG K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 194 Processing helix chain 'K' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS K 199 " --> pdb=" O MET K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 208 Processing helix chain 'K' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU K 225 " --> pdb=" O SER K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN K 232 " --> pdb=" O GLN K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 271 Processing helix chain 'K' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS K 286 " --> pdb=" O GLU K 282 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS K 289 " --> pdb=" O GLU K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET K 297 " --> pdb=" O ALA K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE K 368 " --> pdb=" O GLU K 364 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL K 376 " --> pdb=" O ILE K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU K 384 " --> pdb=" O ARG K 380 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 172 removed outlier: 3.869A pdb=" N ILE L 167 " --> pdb=" O MET L 163 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 194 Processing helix chain 'L' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS L 199 " --> pdb=" O MET L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 208 Processing helix chain 'L' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU L 225 " --> pdb=" O SER L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN L 232 " --> pdb=" O GLN L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 271 Processing helix chain 'L' and resid 274 through 289 removed outlier: 3.609A pdb=" N LYS L 286 " --> pdb=" O GLU L 282 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS L 289 " --> pdb=" O GLU L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET L 297 " --> pdb=" O ALA L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE L 368 " --> pdb=" O GLU L 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL L 376 " --> pdb=" O ILE L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU L 384 " --> pdb=" O ARG L 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE M 167 " --> pdb=" O MET M 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA M 168 " --> pdb=" O ARG M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 194 Processing helix chain 'M' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS M 199 " --> pdb=" O MET M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 208 Processing helix chain 'M' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU M 225 " --> pdb=" O SER M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN M 232 " --> pdb=" O GLN M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 271 Processing helix chain 'M' and resid 274 through 289 removed outlier: 3.609A pdb=" N LYS M 286 " --> pdb=" O GLU M 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS M 289 " --> pdb=" O GLU M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE M 368 " --> pdb=" O GLU M 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL M 376 " --> pdb=" O ILE M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU M 384 " --> pdb=" O ARG M 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE N 167 " --> pdb=" O MET N 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA N 168 " --> pdb=" O ARG N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 189 through 194 Processing helix chain 'N' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS N 199 " --> pdb=" O MET N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 208 Processing helix chain 'N' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU N 225 " --> pdb=" O SER N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN N 232 " --> pdb=" O GLN N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 271 Processing helix chain 'N' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS N 286 " --> pdb=" O GLU N 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS N 289 " --> pdb=" O GLU N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET N 297 " --> pdb=" O ALA N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 362 through 378 removed outlier: 4.072A pdb=" N PHE N 368 " --> pdb=" O GLU N 364 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL N 376 " --> pdb=" O ILE N 372 " (cutoff:3.500A) Processing helix chain 'N' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU N 384 " --> pdb=" O ARG N 380 " (cutoff:3.500A) Processing helix chain 'O' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE O 167 " --> pdb=" O MET O 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA O 168 " --> pdb=" O ARG O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 194 Processing helix chain 'O' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS O 199 " --> pdb=" O MET O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 199 through 208 Processing helix chain 'O' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU O 225 " --> pdb=" O SER O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN O 232 " --> pdb=" O GLN O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 268 through 271 Processing helix chain 'O' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS O 286 " --> pdb=" O GLU O 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS O 289 " --> pdb=" O GLU O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET O 297 " --> pdb=" O ALA O 293 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE O 368 " --> pdb=" O GLU O 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL O 376 " --> pdb=" O ILE O 372 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU O 384 " --> pdb=" O ARG O 380 " (cutoff:3.500A) Processing helix chain 'P' and resid 161 through 172 removed outlier: 3.869A pdb=" N ILE P 167 " --> pdb=" O MET P 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA P 168 " --> pdb=" O ARG P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 194 Processing helix chain 'P' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS P 199 " --> pdb=" O MET P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 199 through 208 Processing helix chain 'P' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU P 225 " --> pdb=" O SER P 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN P 232 " --> pdb=" O GLN P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 271 Processing helix chain 'P' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS P 286 " --> pdb=" O GLU P 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS P 289 " --> pdb=" O GLU P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET P 297 " --> pdb=" O ALA P 293 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE P 368 " --> pdb=" O GLU P 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL P 376 " --> pdb=" O ILE P 372 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU P 384 " --> pdb=" O ARG P 380 " (cutoff:3.500A) Processing helix chain 'Q' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE Q 167 " --> pdb=" O MET Q 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA Q 168 " --> pdb=" O ARG Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 194 Processing helix chain 'Q' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS Q 199 " --> pdb=" O MET Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 199 through 208 Processing helix chain 'Q' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU Q 225 " --> pdb=" O SER Q 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN Q 232 " --> pdb=" O GLN Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 268 through 271 Processing helix chain 'Q' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS Q 286 " --> pdb=" O GLU Q 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS Q 289 " --> pdb=" O GLU Q 285 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET Q 297 " --> pdb=" O ALA Q 293 " (cutoff:3.500A) Processing helix chain 'Q' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE Q 368 " --> pdb=" O GLU Q 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL Q 376 " --> pdb=" O ILE Q 372 " (cutoff:3.500A) Processing helix chain 'Q' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU Q 384 " --> pdb=" O ARG Q 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE R 167 " --> pdb=" O MET R 163 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA R 168 " --> pdb=" O ARG R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 194 Processing helix chain 'R' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS R 199 " --> pdb=" O MET R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 208 Processing helix chain 'R' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU R 225 " --> pdb=" O SER R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN R 232 " --> pdb=" O GLN R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 271 Processing helix chain 'R' and resid 274 through 289 removed outlier: 3.611A pdb=" N LYS R 286 " --> pdb=" O GLU R 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS R 289 " --> pdb=" O GLU R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE R 368 " --> pdb=" O GLU R 364 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL R 376 " --> pdb=" O ILE R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU R 384 " --> pdb=" O ARG R 380 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE S 167 " --> pdb=" O MET S 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA S 168 " --> pdb=" O ARG S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 189 through 194 Processing helix chain 'S' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS S 199 " --> pdb=" O MET S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 199 through 208 Processing helix chain 'S' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU S 225 " --> pdb=" O SER S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN S 232 " --> pdb=" O GLN S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 268 through 271 Processing helix chain 'S' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS S 286 " --> pdb=" O GLU S 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS S 289 " --> pdb=" O GLU S 285 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET S 297 " --> pdb=" O ALA S 293 " (cutoff:3.500A) Processing helix chain 'S' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE S 368 " --> pdb=" O GLU S 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL S 376 " --> pdb=" O ILE S 372 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU S 384 " --> pdb=" O ARG S 380 " (cutoff:3.500A) Processing helix chain 'T' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE T 167 " --> pdb=" O MET T 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 189 through 194 Processing helix chain 'T' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS T 199 " --> pdb=" O MET T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 199 through 208 Processing helix chain 'T' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU T 225 " --> pdb=" O SER T 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 228 through 233 removed outlier: 4.073A pdb=" N ASN T 232 " --> pdb=" O GLN T 228 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 271 Processing helix chain 'T' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS T 286 " --> pdb=" O GLU T 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS T 289 " --> pdb=" O GLU T 285 " (cutoff:3.500A) Processing helix chain 'T' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET T 297 " --> pdb=" O ALA T 293 " (cutoff:3.500A) Processing helix chain 'T' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE T 368 " --> pdb=" O GLU T 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL T 376 " --> pdb=" O ILE T 372 " (cutoff:3.500A) Processing helix chain 'T' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU T 384 " --> pdb=" O ARG T 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE U 167 " --> pdb=" O MET U 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA U 168 " --> pdb=" O ARG U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 189 through 194 Processing helix chain 'U' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS U 199 " --> pdb=" O MET U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 199 through 208 Processing helix chain 'U' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU U 225 " --> pdb=" O SER U 221 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 233 removed outlier: 4.073A pdb=" N ASN U 232 " --> pdb=" O GLN U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 268 through 271 Processing helix chain 'U' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS U 286 " --> pdb=" O GLU U 282 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS U 289 " --> pdb=" O GLU U 285 " (cutoff:3.500A) Processing helix chain 'U' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET U 297 " --> pdb=" O ALA U 293 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE U 368 " --> pdb=" O GLU U 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL U 376 " --> pdb=" O ILE U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU U 384 " --> pdb=" O ARG U 380 " (cutoff:3.500A) Processing helix chain 'V' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE V 167 " --> pdb=" O MET V 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA V 168 " --> pdb=" O ARG V 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 189 through 194 Processing helix chain 'V' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS V 199 " --> pdb=" O MET V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 199 through 208 Processing helix chain 'V' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU V 225 " --> pdb=" O SER V 221 " (cutoff:3.500A) Processing helix chain 'V' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN V 232 " --> pdb=" O GLN V 228 " (cutoff:3.500A) Processing helix chain 'V' and resid 268 through 271 Processing helix chain 'V' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS V 286 " --> pdb=" O GLU V 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS V 289 " --> pdb=" O GLU V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET V 297 " --> pdb=" O ALA V 293 " (cutoff:3.500A) Processing helix chain 'V' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE V 368 " --> pdb=" O GLU V 364 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL V 376 " --> pdb=" O ILE V 372 " (cutoff:3.500A) Processing helix chain 'V' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU V 384 " --> pdb=" O ARG V 380 " (cutoff:3.500A) Processing helix chain 'W' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE W 167 " --> pdb=" O MET W 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA W 168 " --> pdb=" O ARG W 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 189 through 194 Processing helix chain 'W' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS W 199 " --> pdb=" O MET W 195 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 208 Processing helix chain 'W' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU W 225 " --> pdb=" O SER W 221 " (cutoff:3.500A) Processing helix chain 'W' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN W 232 " --> pdb=" O GLN W 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 268 through 271 Processing helix chain 'W' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS W 289 " --> pdb=" O GLU W 285 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET W 297 " --> pdb=" O ALA W 293 " (cutoff:3.500A) Processing helix chain 'W' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE W 368 " --> pdb=" O GLU W 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL W 376 " --> pdb=" O ILE W 372 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU W 384 " --> pdb=" O ARG W 380 " (cutoff:3.500A) Processing helix chain 'X' and resid 161 through 172 removed outlier: 3.869A pdb=" N ILE X 167 " --> pdb=" O MET X 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA X 168 " --> pdb=" O ARG X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 189 through 194 Processing helix chain 'X' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS X 199 " --> pdb=" O MET X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 199 through 208 Processing helix chain 'X' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU X 225 " --> pdb=" O SER X 221 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN X 232 " --> pdb=" O GLN X 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 268 through 271 Processing helix chain 'X' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS X 286 " --> pdb=" O GLU X 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS X 289 " --> pdb=" O GLU X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE X 368 " --> pdb=" O GLU X 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL X 376 " --> pdb=" O ILE X 372 " (cutoff:3.500A) Processing helix chain 'X' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU X 384 " --> pdb=" O ARG X 380 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR A 350 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY A 331 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA A 352 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET A 329 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR A 354 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU A 327 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP A 356 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA A 325 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 303 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET A 329 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER A 305 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY A 331 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE A 304 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 251 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN A 306 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU A 241 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 254 through 256 Processing sheet with id=4, first strand: chain 'B' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR B 350 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY B 331 " --> pdb=" O TYR B 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA B 352 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET B 329 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR B 354 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU B 327 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP B 356 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 325 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR B 303 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET B 329 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER B 305 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY B 331 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE B 304 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER B 251 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN B 306 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU B 241 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 254 through 256 Processing sheet with id=7, first strand: chain 'C' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR C 350 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY C 331 " --> pdb=" O TYR C 350 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA C 352 " --> pdb=" O MET C 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET C 329 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR C 354 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU C 327 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP C 356 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA C 325 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR C 303 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET C 329 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER C 305 " --> pdb=" O MET C 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY C 331 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ILE C 304 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER C 251 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN C 306 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU C 241 " --> pdb=" O ASP C 236 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 254 through 256 Processing sheet with id=10, first strand: chain 'D' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR D 350 " --> pdb=" O GLY D 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY D 331 " --> pdb=" O TYR D 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA D 352 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET D 329 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR D 354 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU D 327 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP D 356 " --> pdb=" O ALA D 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA D 325 " --> pdb=" O ASP D 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR D 303 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET D 329 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER D 305 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY D 331 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE D 304 " --> pdb=" O ASP D 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER D 251 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN D 306 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'D' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU D 241 " --> pdb=" O ASP D 236 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'D' and resid 254 through 256 Processing sheet with id=13, first strand: chain 'E' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR E 350 " --> pdb=" O GLY E 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY E 331 " --> pdb=" O TYR E 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA E 352 " --> pdb=" O MET E 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET E 329 " --> pdb=" O ALA E 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR E 354 " --> pdb=" O LEU E 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU E 327 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP E 356 " --> pdb=" O ALA E 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA E 325 " --> pdb=" O ASP E 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR E 303 " --> pdb=" O LEU E 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET E 329 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER E 305 " --> pdb=" O MET E 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY E 331 " --> pdb=" O SER E 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE E 304 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER E 251 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN E 306 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'E' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU E 241 " --> pdb=" O ASP E 236 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'E' and resid 254 through 256 Processing sheet with id=16, first strand: chain 'F' and resid 180 through 188 removed outlier: 4.338A pdb=" N TYR F 350 " --> pdb=" O GLY F 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY F 331 " --> pdb=" O TYR F 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA F 352 " --> pdb=" O MET F 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET F 329 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR F 354 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU F 327 " --> pdb=" O THR F 354 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP F 356 " --> pdb=" O ALA F 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA F 325 " --> pdb=" O ASP F 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR F 303 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET F 329 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER F 305 " --> pdb=" O MET F 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY F 331 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE F 304 " --> pdb=" O ASP F 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER F 251 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN F 306 " --> pdb=" O SER F 251 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'F' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU F 241 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'F' and resid 254 through 256 Processing sheet with id=19, first strand: chain 'G' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR G 350 " --> pdb=" O GLY G 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY G 331 " --> pdb=" O TYR G 350 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA G 352 " --> pdb=" O MET G 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET G 329 " --> pdb=" O ALA G 352 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR G 354 " --> pdb=" O LEU G 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU G 327 " --> pdb=" O THR G 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP G 356 " --> pdb=" O ALA G 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA G 325 " --> pdb=" O ASP G 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR G 303 " --> pdb=" O LEU G 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET G 329 " --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER G 305 " --> pdb=" O MET G 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY G 331 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE G 304 " --> pdb=" O ASP G 249 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER G 251 " --> pdb=" O ILE G 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN G 306 " --> pdb=" O SER G 251 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'G' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU G 241 " --> pdb=" O ASP G 236 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'G' and resid 254 through 256 Processing sheet with id=22, first strand: chain 'H' and resid 180 through 188 removed outlier: 4.338A pdb=" N TYR H 350 " --> pdb=" O GLY H 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY H 331 " --> pdb=" O TYR H 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA H 352 " --> pdb=" O MET H 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET H 329 " --> pdb=" O ALA H 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR H 354 " --> pdb=" O LEU H 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU H 327 " --> pdb=" O THR H 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP H 356 " --> pdb=" O ALA H 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA H 325 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR H 303 " --> pdb=" O LEU H 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET H 329 " --> pdb=" O THR H 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER H 305 " --> pdb=" O MET H 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY H 331 " --> pdb=" O SER H 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE H 304 " --> pdb=" O ASP H 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER H 251 " --> pdb=" O ILE H 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN H 306 " --> pdb=" O SER H 251 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'H' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU H 241 " --> pdb=" O ASP H 236 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'H' and resid 254 through 256 Processing sheet with id=25, first strand: chain 'I' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR I 350 " --> pdb=" O GLY I 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY I 331 " --> pdb=" O TYR I 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA I 352 " --> pdb=" O MET I 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET I 329 " --> pdb=" O ALA I 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR I 354 " --> pdb=" O LEU I 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU I 327 " --> pdb=" O THR I 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP I 356 " --> pdb=" O ALA I 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA I 325 " --> pdb=" O ASP I 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR I 303 " --> pdb=" O LEU I 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET I 329 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER I 305 " --> pdb=" O MET I 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY I 331 " --> pdb=" O SER I 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE I 304 " --> pdb=" O ASP I 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER I 251 " --> pdb=" O ILE I 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN I 306 " --> pdb=" O SER I 251 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'I' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU I 241 " --> pdb=" O ASP I 236 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'I' and resid 254 through 256 Processing sheet with id=28, first strand: chain 'J' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR J 350 " --> pdb=" O GLY J 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY J 331 " --> pdb=" O TYR J 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA J 352 " --> pdb=" O MET J 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET J 329 " --> pdb=" O ALA J 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR J 354 " --> pdb=" O LEU J 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU J 327 " --> pdb=" O THR J 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP J 356 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA J 325 " --> pdb=" O ASP J 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR J 303 " --> pdb=" O LEU J 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET J 329 " --> pdb=" O THR J 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER J 305 " --> pdb=" O MET J 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY J 331 " --> pdb=" O SER J 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE J 304 " --> pdb=" O ASP J 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER J 251 " --> pdb=" O ILE J 304 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN J 306 " --> pdb=" O SER J 251 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'J' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU J 241 " --> pdb=" O ASP J 236 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'J' and resid 254 through 256 Processing sheet with id=31, first strand: chain 'K' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR K 350 " --> pdb=" O GLY K 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY K 331 " --> pdb=" O TYR K 350 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA K 352 " --> pdb=" O MET K 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET K 329 " --> pdb=" O ALA K 352 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR K 354 " --> pdb=" O LEU K 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU K 327 " --> pdb=" O THR K 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP K 356 " --> pdb=" O ALA K 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA K 325 " --> pdb=" O ASP K 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR K 303 " --> pdb=" O LEU K 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET K 329 " --> pdb=" O THR K 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER K 305 " --> pdb=" O MET K 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY K 331 " --> pdb=" O SER K 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE K 304 " --> pdb=" O ASP K 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER K 251 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN K 306 " --> pdb=" O SER K 251 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'K' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU K 241 " --> pdb=" O ASP K 236 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'K' and resid 254 through 256 Processing sheet with id=34, first strand: chain 'L' and resid 180 through 188 removed outlier: 4.338A pdb=" N TYR L 350 " --> pdb=" O GLY L 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY L 331 " --> pdb=" O TYR L 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA L 352 " --> pdb=" O MET L 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET L 329 " --> pdb=" O ALA L 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR L 354 " --> pdb=" O LEU L 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU L 327 " --> pdb=" O THR L 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP L 356 " --> pdb=" O ALA L 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA L 325 " --> pdb=" O ASP L 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR L 303 " --> pdb=" O LEU L 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET L 329 " --> pdb=" O THR L 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER L 305 " --> pdb=" O MET L 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY L 331 " --> pdb=" O SER L 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE L 304 " --> pdb=" O ASP L 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER L 251 " --> pdb=" O ILE L 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN L 306 " --> pdb=" O SER L 251 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'L' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU L 241 " --> pdb=" O ASP L 236 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'L' and resid 254 through 256 Processing sheet with id=37, first strand: chain 'M' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR M 350 " --> pdb=" O GLY M 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY M 331 " --> pdb=" O TYR M 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA M 352 " --> pdb=" O MET M 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET M 329 " --> pdb=" O ALA M 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR M 354 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU M 327 " --> pdb=" O THR M 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP M 356 " --> pdb=" O ALA M 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA M 325 " --> pdb=" O ASP M 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR M 303 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET M 329 " --> pdb=" O THR M 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER M 305 " --> pdb=" O MET M 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY M 331 " --> pdb=" O SER M 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE M 304 " --> pdb=" O ASP M 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER M 251 " --> pdb=" O ILE M 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN M 306 " --> pdb=" O SER M 251 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'M' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU M 241 " --> pdb=" O ASP M 236 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'M' and resid 254 through 256 Processing sheet with id=40, first strand: chain 'N' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR N 350 " --> pdb=" O GLY N 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY N 331 " --> pdb=" O TYR N 350 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA N 352 " --> pdb=" O MET N 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET N 329 " --> pdb=" O ALA N 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR N 354 " --> pdb=" O LEU N 327 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU N 327 " --> pdb=" O THR N 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP N 356 " --> pdb=" O ALA N 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA N 325 " --> pdb=" O ASP N 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR N 303 " --> pdb=" O LEU N 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET N 329 " --> pdb=" O THR N 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER N 305 " --> pdb=" O MET N 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY N 331 " --> pdb=" O SER N 305 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE N 304 " --> pdb=" O ASP N 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER N 251 " --> pdb=" O ILE N 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN N 306 " --> pdb=" O SER N 251 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'N' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU N 241 " --> pdb=" O ASP N 236 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'N' and resid 254 through 256 Processing sheet with id=43, first strand: chain 'O' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR O 350 " --> pdb=" O GLY O 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY O 331 " --> pdb=" O TYR O 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA O 352 " --> pdb=" O MET O 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET O 329 " --> pdb=" O ALA O 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR O 354 " --> pdb=" O LEU O 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU O 327 " --> pdb=" O THR O 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP O 356 " --> pdb=" O ALA O 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA O 325 " --> pdb=" O ASP O 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR O 303 " --> pdb=" O LEU O 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET O 329 " --> pdb=" O THR O 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER O 305 " --> pdb=" O MET O 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY O 331 " --> pdb=" O SER O 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE O 304 " --> pdb=" O ASP O 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER O 251 " --> pdb=" O ILE O 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN O 306 " --> pdb=" O SER O 251 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'O' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU O 241 " --> pdb=" O ASP O 236 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'O' and resid 254 through 256 Processing sheet with id=46, first strand: chain 'P' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR P 350 " --> pdb=" O GLY P 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY P 331 " --> pdb=" O TYR P 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA P 352 " --> pdb=" O MET P 329 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N MET P 329 " --> pdb=" O ALA P 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR P 354 " --> pdb=" O LEU P 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU P 327 " --> pdb=" O THR P 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP P 356 " --> pdb=" O ALA P 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA P 325 " --> pdb=" O ASP P 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR P 303 " --> pdb=" O LEU P 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET P 329 " --> pdb=" O THR P 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER P 305 " --> pdb=" O MET P 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY P 331 " --> pdb=" O SER P 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE P 304 " --> pdb=" O ASP P 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER P 251 " --> pdb=" O ILE P 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN P 306 " --> pdb=" O SER P 251 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'P' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU P 241 " --> pdb=" O ASP P 236 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'P' and resid 254 through 256 Processing sheet with id=49, first strand: chain 'Q' and resid 180 through 188 removed outlier: 4.338A pdb=" N TYR Q 350 " --> pdb=" O GLY Q 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY Q 331 " --> pdb=" O TYR Q 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA Q 352 " --> pdb=" O MET Q 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET Q 329 " --> pdb=" O ALA Q 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR Q 354 " --> pdb=" O LEU Q 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU Q 327 " --> pdb=" O THR Q 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP Q 356 " --> pdb=" O ALA Q 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA Q 325 " --> pdb=" O ASP Q 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR Q 303 " --> pdb=" O LEU Q 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET Q 329 " --> pdb=" O THR Q 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER Q 305 " --> pdb=" O MET Q 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY Q 331 " --> pdb=" O SER Q 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE Q 304 " --> pdb=" O ASP Q 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER Q 251 " --> pdb=" O ILE Q 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN Q 306 " --> pdb=" O SER Q 251 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'Q' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU Q 241 " --> pdb=" O ASP Q 236 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'Q' and resid 254 through 256 Processing sheet with id=52, first strand: chain 'R' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR R 350 " --> pdb=" O GLY R 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY R 331 " --> pdb=" O TYR R 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA R 352 " --> pdb=" O MET R 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET R 329 " --> pdb=" O ALA R 352 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR R 354 " --> pdb=" O LEU R 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU R 327 " --> pdb=" O THR R 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP R 356 " --> pdb=" O ALA R 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA R 325 " --> pdb=" O ASP R 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR R 303 " --> pdb=" O LEU R 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET R 329 " --> pdb=" O THR R 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER R 305 " --> pdb=" O MET R 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY R 331 " --> pdb=" O SER R 305 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE R 304 " --> pdb=" O ASP R 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER R 251 " --> pdb=" O ILE R 304 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN R 306 " --> pdb=" O SER R 251 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'R' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU R 241 " --> pdb=" O ASP R 236 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'R' and resid 254 through 256 Processing sheet with id=55, first strand: chain 'S' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR S 350 " --> pdb=" O GLY S 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY S 331 " --> pdb=" O TYR S 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA S 352 " --> pdb=" O MET S 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET S 329 " --> pdb=" O ALA S 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR S 354 " --> pdb=" O LEU S 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU S 327 " --> pdb=" O THR S 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP S 356 " --> pdb=" O ALA S 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA S 325 " --> pdb=" O ASP S 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR S 303 " --> pdb=" O LEU S 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET S 329 " --> pdb=" O THR S 303 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER S 305 " --> pdb=" O MET S 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY S 331 " --> pdb=" O SER S 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE S 304 " --> pdb=" O ASP S 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER S 251 " --> pdb=" O ILE S 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN S 306 " --> pdb=" O SER S 251 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'S' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU S 241 " --> pdb=" O ASP S 236 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'S' and resid 254 through 256 Processing sheet with id=58, first strand: chain 'T' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR T 350 " --> pdb=" O GLY T 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY T 331 " --> pdb=" O TYR T 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA T 352 " --> pdb=" O MET T 329 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N MET T 329 " --> pdb=" O ALA T 352 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR T 354 " --> pdb=" O LEU T 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU T 327 " --> pdb=" O THR T 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP T 356 " --> pdb=" O ALA T 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA T 325 " --> pdb=" O ASP T 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR T 303 " --> pdb=" O LEU T 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET T 329 " --> pdb=" O THR T 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER T 305 " --> pdb=" O MET T 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY T 331 " --> pdb=" O SER T 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE T 304 " --> pdb=" O ASP T 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER T 251 " --> pdb=" O ILE T 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN T 306 " --> pdb=" O SER T 251 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'T' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU T 241 " --> pdb=" O ASP T 236 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'T' and resid 254 through 256 Processing sheet with id=61, first strand: chain 'U' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR U 350 " --> pdb=" O GLY U 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY U 331 " --> pdb=" O TYR U 350 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA U 352 " --> pdb=" O MET U 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET U 329 " --> pdb=" O ALA U 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR U 354 " --> pdb=" O LEU U 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU U 327 " --> pdb=" O THR U 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP U 356 " --> pdb=" O ALA U 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA U 325 " --> pdb=" O ASP U 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR U 303 " --> pdb=" O LEU U 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET U 329 " --> pdb=" O THR U 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER U 305 " --> pdb=" O MET U 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY U 331 " --> pdb=" O SER U 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE U 304 " --> pdb=" O ASP U 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER U 251 " --> pdb=" O ILE U 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN U 306 " --> pdb=" O SER U 251 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'U' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU U 241 " --> pdb=" O ASP U 236 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'U' and resid 254 through 256 Processing sheet with id=64, first strand: chain 'V' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR V 350 " --> pdb=" O GLY V 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY V 331 " --> pdb=" O TYR V 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA V 352 " --> pdb=" O MET V 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET V 329 " --> pdb=" O ALA V 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR V 354 " --> pdb=" O LEU V 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU V 327 " --> pdb=" O THR V 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP V 356 " --> pdb=" O ALA V 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA V 325 " --> pdb=" O ASP V 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR V 303 " --> pdb=" O LEU V 327 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET V 329 " --> pdb=" O THR V 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER V 305 " --> pdb=" O MET V 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY V 331 " --> pdb=" O SER V 305 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE V 304 " --> pdb=" O ASP V 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER V 251 " --> pdb=" O ILE V 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN V 306 " --> pdb=" O SER V 251 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'V' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU V 241 " --> pdb=" O ASP V 236 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'V' and resid 254 through 256 Processing sheet with id=67, first strand: chain 'W' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR W 350 " --> pdb=" O GLY W 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY W 331 " --> pdb=" O TYR W 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA W 352 " --> pdb=" O MET W 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET W 329 " --> pdb=" O ALA W 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR W 354 " --> pdb=" O LEU W 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU W 327 " --> pdb=" O THR W 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP W 356 " --> pdb=" O ALA W 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA W 325 " --> pdb=" O ASP W 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR W 303 " --> pdb=" O LEU W 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET W 329 " --> pdb=" O THR W 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER W 305 " --> pdb=" O MET W 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY W 331 " --> pdb=" O SER W 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE W 304 " --> pdb=" O ASP W 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER W 251 " --> pdb=" O ILE W 304 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN W 306 " --> pdb=" O SER W 251 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'W' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU W 241 " --> pdb=" O ASP W 236 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'W' and resid 254 through 256 Processing sheet with id=70, first strand: chain 'X' and resid 180 through 188 removed outlier: 4.338A pdb=" N TYR X 350 " --> pdb=" O GLY X 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY X 331 " --> pdb=" O TYR X 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA X 352 " --> pdb=" O MET X 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET X 329 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR X 354 " --> pdb=" O LEU X 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU X 327 " --> pdb=" O THR X 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP X 356 " --> pdb=" O ALA X 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA X 325 " --> pdb=" O ASP X 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR X 303 " --> pdb=" O LEU X 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET X 329 " --> pdb=" O THR X 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER X 305 " --> pdb=" O MET X 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY X 331 " --> pdb=" O SER X 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE X 304 " --> pdb=" O ASP X 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER X 251 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN X 306 " --> pdb=" O SER X 251 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'X' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU X 241 " --> pdb=" O ASP X 236 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'X' and resid 254 through 256 1752 hydrogen bonds defined for protein. 4968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.41 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 15033 1.33 - 1.45: 6647 1.45 - 1.57: 22984 1.57 - 1.69: 0 1.69 - 1.80: 552 Bond restraints: 45216 Sorted by residual: bond pdb=" CG LEU N 353 " pdb=" CD2 LEU N 353 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.51e+00 bond pdb=" CG LEU Q 353 " pdb=" CD2 LEU Q 353 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.49e+00 bond pdb=" CG LEU T 353 " pdb=" CD2 LEU T 353 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.48e+00 bond pdb=" CG LEU I 353 " pdb=" CD2 LEU I 353 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.46e+00 bond pdb=" CG LEU E 353 " pdb=" CD2 LEU E 353 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.46e+00 ... (remaining 45211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 57440 2.22 - 4.44: 3194 4.44 - 6.66: 277 6.66 - 8.89: 1 8.89 - 11.11: 24 Bond angle restraints: 60936 Sorted by residual: angle pdb=" C HIS N 207 " pdb=" N ASN N 208 " pdb=" CA ASN N 208 " ideal model delta sigma weight residual 122.82 128.23 -5.41 1.42e+00 4.96e-01 1.45e+01 angle pdb=" C HIS M 207 " pdb=" N ASN M 208 " pdb=" CA ASN M 208 " ideal model delta sigma weight residual 122.82 128.23 -5.41 1.42e+00 4.96e-01 1.45e+01 angle pdb=" C HIS D 207 " pdb=" N ASN D 208 " pdb=" CA ASN D 208 " ideal model delta sigma weight residual 122.82 128.20 -5.38 1.42e+00 4.96e-01 1.44e+01 angle pdb=" C HIS J 207 " pdb=" N ASN J 208 " pdb=" CA ASN J 208 " ideal model delta sigma weight residual 122.82 128.20 -5.38 1.42e+00 4.96e-01 1.44e+01 angle pdb=" C HIS G 207 " pdb=" N ASN G 208 " pdb=" CA ASN G 208 " ideal model delta sigma weight residual 122.82 128.20 -5.38 1.42e+00 4.96e-01 1.44e+01 ... (remaining 60931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 26910 16.89 - 33.77: 858 33.77 - 50.65: 144 50.65 - 67.54: 0 67.54 - 84.42: 48 Dihedral angle restraints: 27960 sinusoidal: 11616 harmonic: 16344 Sorted by residual: dihedral pdb=" CA ASN C 320 " pdb=" C ASN C 320 " pdb=" N PRO C 321 " pdb=" CA PRO C 321 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASN K 320 " pdb=" C ASN K 320 " pdb=" N PRO K 321 " pdb=" CA PRO K 321 " ideal model delta harmonic sigma weight residual 180.00 -155.45 -24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASN R 320 " pdb=" C ASN R 320 " pdb=" N PRO R 321 " pdb=" CA PRO R 321 " ideal model delta harmonic sigma weight residual 180.00 -155.45 -24.55 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 27957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4156 0.054 - 0.109: 2172 0.109 - 0.163: 440 0.163 - 0.218: 168 0.218 - 0.272: 48 Chirality restraints: 6984 Sorted by residual: chirality pdb=" CB VAL D 351 " pdb=" CA VAL D 351 " pdb=" CG1 VAL D 351 " pdb=" CG2 VAL D 351 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL M 351 " pdb=" CA VAL M 351 " pdb=" CG1 VAL M 351 " pdb=" CG2 VAL M 351 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL J 351 " pdb=" CA VAL J 351 " pdb=" CG1 VAL J 351 " pdb=" CG2 VAL J 351 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 6981 not shown) Planarity restraints: 7968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 262 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO R 263 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO R 263 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 263 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL U 262 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO U 263 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO U 263 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO U 263 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 262 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO H 263 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 263 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 263 " -0.033 5.00e-02 4.00e+02 ... (remaining 7965 not shown) Histogram of nonbonded interaction distances: 0.43 - 1.32: 84 1.32 - 2.22: 408 2.22 - 3.11: 36942 3.11 - 4.01: 108628 4.01 - 4.90: 211568 Warning: very small nonbonded interaction distances. Nonbonded interactions: 357630 Sorted by model distance: nonbonded pdb=" CD2 LEU L 383 " pdb=" CA LEU X 383 " model vdw 0.426 3.890 nonbonded pdb=" CD2 LEU F 383 " pdb=" CA LEU Q 383 " model vdw 0.426 3.890 nonbonded pdb=" CD2 LEU E 383 " pdb=" CA LEU K 383 " model vdw 0.426 3.890 nonbonded pdb=" CA LEU A 383 " pdb=" CD2 LEU G 383 " model vdw 0.426 3.890 nonbonded pdb=" CD2 LEU B 383 " pdb=" CA LEU T 383 " model vdw 0.426 3.890 ... (remaining 357625 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 0.010 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.630 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 36.410 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1339 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 : 0.016 0.206 45240 Z= 0.795 Angle : 1.093 11.108 60936 Z= 0.597 Chirality : 0.067 0.272 6984 Planarity : 0.007 0.060 7968 Dihedral : 9.736 84.423 17352 Min Nonbonded Distance : 0.426 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.50 (0.09), residues: 5616 helix: -4.41 (0.07), residues: 1992 sheet: -2.89 (0.13), residues: 1464 loop : -3.10 (0.10), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 258 TYR 0.020 0.003 TYR H 355 PHE 0.033 0.004 PHE W 314 HIS 0.013 0.004 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.01581 (45216) covalent geometry : angle 1.09341 (60936) hydrogen bonds : bond 0.30281 ( 1752) hydrogen bonds : angle 12.05509 ( 4968) Misc. bond : bond 0.20577 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 838 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 242 VAL cc_start: 0.2363 (t) cc_final: 0.2136 (m) REVERT: J 163 MET cc_start: 0.1082 (mmt) cc_final: 0.0567 (tmt) REVERT: J 172 LYS cc_start: 0.3194 (mmmt) cc_final: 0.2025 (mmmt) REVERT: J 302 PHE cc_start: 0.0805 (t80) cc_final: -0.0364 (t80) REVERT: Q 169 GLN cc_start: 0.2397 (mm110) cc_final: 0.1724 (mp10) outliers start: 0 outliers final: 4 residues processed: 838 average time/residue: 0.8824 time to fit residues: 890.4700 Evaluate side-chains 532 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 528 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain K residue 175 GLN Chi-restraints excluded: chain V residue 188 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 394 optimal weight: 0.7980 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 0.7980 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 0.0050 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 207 HIS C 175 GLN C 193 GLN C 228 GLN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS D 357 HIS E 357 HIS F 193 GLN F 228 GLN ** F 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS H 267 ASN I 207 HIS ** I 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 357 HIS J 193 GLN J 207 HIS J 228 GLN K 185 ASN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 228 GLN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN ** N 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN O 207 HIS ** P 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 228 GLN Q 199 HIS Q 228 GLN ** Q 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 GLN ** R 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 ASN S 357 HIS T 228 GLN ** T 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 175 GLN U 199 HIS U 228 GLN V 357 HIS ** W 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 357 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5597 r_free = 0.5597 target = 0.327470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5487 r_free = 0.5487 target = 0.311312 restraints weight = 75048.016| |-----------------------------------------------------------------------------| r_work (start): 0.5461 rms_B_bonded: 3.03 r_work: 0.5389 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.5389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2470 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 45240 Z= 0.177 Angle : 0.792 18.065 60936 Z= 0.408 Chirality : 0.048 0.312 6984 Planarity : 0.006 0.085 7968 Dihedral : 7.862 117.039 6226 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.62 % Allowed : 9.80 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.59 (0.10), residues: 5616 helix: -2.57 (0.10), residues: 2064 sheet: -2.05 (0.14), residues: 1344 loop : -2.13 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 170 TYR 0.026 0.002 TYR J 350 PHE 0.034 0.002 PHE I 273 HIS 0.014 0.001 HIS G 199 Details of bonding type rmsd covalent geometry : bond 0.00379 (45216) covalent geometry : angle 0.79221 (60936) hydrogen bonds : bond 0.04503 ( 1752) hydrogen bonds : angle 6.75825 ( 4968) Misc. bond : bond 0.00196 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 652 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7187 (mm110) REVERT: A 180 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8084 (mpp) REVERT: A 214 MET cc_start: 0.7330 (tpt) cc_final: 0.7121 (tpt) REVERT: A 223 PHE cc_start: 0.7816 (t80) cc_final: 0.7300 (t80) REVERT: A 249 ASP cc_start: 0.7716 (p0) cc_final: 0.7512 (p0) REVERT: B 349 MET cc_start: 0.1281 (pmm) cc_final: 0.0553 (pmm) REVERT: B 380 ARG cc_start: 0.2749 (mtm180) cc_final: 0.1994 (ptm160) REVERT: C 355 TYR cc_start: 0.0946 (p90) cc_final: 0.0496 (p90) REVERT: D 175 GLN cc_start: 0.1906 (mt0) cc_final: 0.1501 (tm-30) REVERT: D 348 MET cc_start: 0.2049 (tpp) cc_final: 0.1818 (tpp) REVERT: F 163 MET cc_start: -0.1004 (tmm) cc_final: -0.1404 (mmt) REVERT: H 160 MET cc_start: 0.2872 (mpt) cc_final: 0.2606 (mpt) REVERT: J 163 MET cc_start: 0.1656 (mmt) cc_final: 0.0766 (tmt) REVERT: J 166 ARG cc_start: 0.0664 (OUTLIER) cc_final: -0.0187 (mmp-170) REVERT: J 244 TYR cc_start: 0.0227 (OUTLIER) cc_final: -0.1824 (m-80) REVERT: J 302 PHE cc_start: 0.0268 (t80) cc_final: -0.1093 (t80) REVERT: K 180 MET cc_start: 0.2048 (tmt) cc_final: 0.1712 (tmm) REVERT: K 214 MET cc_start: 0.3625 (tmm) cc_final: 0.2670 (ttt) REVERT: K 297 MET cc_start: 0.0029 (OUTLIER) cc_final: -0.0487 (mmm) REVERT: L 171 LEU cc_start: -0.2698 (tt) cc_final: -0.2998 (tt) REVERT: L 349 MET cc_start: -0.0663 (mmm) cc_final: -0.2804 (ppp) REVERT: P 155 GLU cc_start: 0.0186 (pt0) cc_final: -0.0708 (tm-30) REVERT: P 271 MET cc_start: 0.3899 (ttm) cc_final: 0.3597 (ttm) REVERT: Q 195 MET cc_start: 0.2981 (tpp) cc_final: 0.2611 (tpt) REVERT: Q 204 LEU cc_start: 0.6333 (pp) cc_final: 0.6120 (pp) REVERT: Q 348 MET cc_start: 0.0938 (mmt) cc_final: -0.1155 (mtp) REVERT: Q 349 MET cc_start: 0.0373 (ppp) cc_final: -0.0616 (ttt) REVERT: R 189 MET cc_start: 0.2363 (mmm) cc_final: 0.1466 (mtt) REVERT: R 203 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.5240 (m-80) REVERT: S 276 ILE cc_start: 0.1230 (OUTLIER) cc_final: 0.0439 (tt) REVERT: S 357 HIS cc_start: 0.1842 (t70) cc_final: 0.0013 (t70) REVERT: T 163 MET cc_start: 0.0390 (OUTLIER) cc_final: 0.0049 (tpt) REVERT: T 297 MET cc_start: -0.0786 (ttt) cc_final: -0.1174 (ttp) REVERT: W 163 MET cc_start: 0.5542 (mpt) cc_final: 0.4788 (pmm) REVERT: W 271 MET cc_start: -0.0396 (ptt) cc_final: -0.0600 (mtp) REVERT: X 160 MET cc_start: -0.3983 (OUTLIER) cc_final: -0.4208 (ptt) REVERT: X 170 ARG cc_start: 0.3226 (mmp80) cc_final: 0.2962 (mmp80) REVERT: X 269 GLU cc_start: 0.0154 (mm-30) cc_final: -0.0677 (mp0) outliers start: 125 outliers final: 30 residues processed: 716 average time/residue: 0.7835 time to fit residues: 683.5558 Evaluate side-chains 535 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 496 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain J residue 166 ARG Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain K residue 297 MET Chi-restraints excluded: chain L residue 189 MET Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain N residue 160 MET Chi-restraints excluded: chain N residue 244 TYR Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain S residue 195 MET Chi-restraints excluded: chain S residue 223 PHE Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 163 MET Chi-restraints excluded: chain T residue 235 ILE Chi-restraints excluded: chain V residue 326 ILE Chi-restraints excluded: chain W residue 339 ILE Chi-restraints excluded: chain X residue 160 MET Chi-restraints excluded: chain X residue 228 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 158 optimal weight: 5.9990 chunk 225 optimal weight: 0.0970 chunk 426 optimal weight: 4.9990 chunk 255 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 394 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 549 optimal weight: 0.1980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN D 267 ASN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 ASN F 193 GLN F 199 HIS F 323 GLN ** F 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 ASN H 185 ASN H 228 GLN H 323 GLN I 228 GLN I 323 GLN ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 323 GLN L 161 ASN ** L 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 GLN ** N 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 323 GLN P 175 GLN P 267 ASN P 323 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 357 HIS R 323 GLN ** R 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN T 228 GLN T 323 GLN ** T 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 175 GLN U 228 GLN ** V 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 185 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5517 r_free = 0.5517 target = 0.316414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5358 r_free = 0.5358 target = 0.293587 restraints weight = 72818.654| |-----------------------------------------------------------------------------| r_work (start): 0.5338 rms_B_bonded: 3.16 r_work: 0.5259 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.5259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3492 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 45240 Z= 0.195 Angle : 0.808 14.407 60936 Z= 0.416 Chirality : 0.049 0.244 6984 Planarity : 0.006 0.083 7968 Dihedral : 6.756 72.941 6216 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.56 % Allowed : 12.67 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.10), residues: 5616 helix: -2.03 (0.10), residues: 2064 sheet: -1.91 (0.13), residues: 1416 loop : -1.45 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 358 TYR 0.023 0.002 TYR M 355 PHE 0.028 0.003 PHE L 314 HIS 0.014 0.002 HIS W 357 Details of bonding type rmsd covalent geometry : bond 0.00430 (45216) covalent geometry : angle 0.80834 (60936) hydrogen bonds : bond 0.04422 ( 1752) hydrogen bonds : angle 6.24861 ( 4968) Misc. bond : bond 0.00316 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 652 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8694 (tppt) cc_final: 0.8370 (tptp) REVERT: A 163 MET cc_start: 0.8123 (mmp) cc_final: 0.7481 (pmm) REVERT: A 169 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7722 (mp10) REVERT: A 170 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7703 (pmm-80) REVERT: A 180 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8223 (mtp) REVERT: A 246 ASP cc_start: 0.7315 (p0) cc_final: 0.7067 (p0) REVERT: B 163 MET cc_start: 0.4165 (mtp) cc_final: 0.3802 (pp-130) REVERT: B 327 LEU cc_start: 0.4393 (tp) cc_final: 0.4161 (tp) REVERT: C 195 MET cc_start: 0.2116 (mtt) cc_final: 0.1328 (tpp) REVERT: C 355 TYR cc_start: 0.0863 (p90) cc_final: -0.0018 (p90) REVERT: D 160 MET cc_start: 0.0684 (mtt) cc_final: 0.0421 (mtp) REVERT: D 175 GLN cc_start: 0.2512 (mt0) cc_final: 0.1527 (tp40) REVERT: D 342 LYS cc_start: 0.8529 (mptp) cc_final: 0.8164 (mmmt) REVERT: E 217 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6284 (t80) REVERT: E 243 VAL cc_start: 0.6661 (t) cc_final: 0.5785 (m) REVERT: E 271 MET cc_start: 0.4443 (ppp) cc_final: 0.4016 (ppp) REVERT: E 297 MET cc_start: 0.5458 (tmm) cc_final: 0.5071 (tmm) REVERT: E 342 LYS cc_start: 0.7095 (pptt) cc_final: 0.6806 (pptt) REVERT: E 344 GLU cc_start: 0.7950 (pm20) cc_final: 0.7195 (pm20) REVERT: G 163 MET cc_start: 0.3123 (tpt) cc_final: 0.2667 (tmm) REVERT: G 348 MET cc_start: 0.1119 (tpp) cc_final: -0.0352 (mmm) REVERT: H 291 GLU cc_start: 0.4401 (OUTLIER) cc_final: 0.3971 (pm20) REVERT: H 297 MET cc_start: 0.2882 (mmp) cc_final: 0.2545 (mmp) REVERT: I 160 MET cc_start: -0.0639 (pmm) cc_final: -0.1117 (ptt) REVERT: I 176 ASN cc_start: 0.4633 (m-40) cc_final: 0.4357 (m110) REVERT: I 335 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7626 (ttm170) REVERT: J 163 MET cc_start: 0.1695 (mmt) cc_final: 0.0576 (tmt) REVERT: J 166 ARG cc_start: 0.0883 (OUTLIER) cc_final: 0.0337 (mmp-170) REVERT: J 172 LYS cc_start: 0.3663 (mmmt) cc_final: 0.3414 (ptpp) REVERT: J 244 TYR cc_start: 0.0509 (OUTLIER) cc_final: -0.1562 (m-80) REVERT: J 302 PHE cc_start: 0.1759 (t80) cc_final: -0.0471 (t80) REVERT: J 336 PRO cc_start: 0.2780 (Cg_endo) cc_final: 0.2334 (Cg_exo) REVERT: K 163 MET cc_start: 0.0876 (mmm) cc_final: 0.0065 (ptp) REVERT: K 180 MET cc_start: 0.1597 (tmt) cc_final: 0.1267 (tmt) REVERT: K 195 MET cc_start: 0.0293 (OUTLIER) cc_final: -0.0946 (mmt) REVERT: K 214 MET cc_start: 0.3904 (tmm) cc_final: 0.2958 (ttp) REVERT: K 297 MET cc_start: 0.0502 (mmm) cc_final: 0.0062 (mmm) REVERT: K 358 ARG cc_start: 0.2289 (OUTLIER) cc_final: 0.1665 (mtm-85) REVERT: M 350 TYR cc_start: 0.7757 (m-80) cc_final: 0.7230 (m-80) REVERT: N 195 MET cc_start: 0.7250 (ttt) cc_final: 0.7046 (ttp) REVERT: N 214 MET cc_start: 0.4375 (tpt) cc_final: 0.3074 (pmm) REVERT: N 297 MET cc_start: 0.4652 (tpt) cc_final: 0.2099 (mpp) REVERT: O 302 PHE cc_start: 0.1322 (t80) cc_final: -0.1346 (t80) REVERT: P 155 GLU cc_start: 0.0642 (pt0) cc_final: -0.0613 (tm-30) REVERT: P 163 MET cc_start: 0.0204 (OUTLIER) cc_final: -0.0081 (tpt) REVERT: P 189 MET cc_start: 0.3611 (mmm) cc_final: 0.3090 (mpp) REVERT: Q 160 MET cc_start: 0.0438 (mtt) cc_final: 0.0237 (mtt) REVERT: Q 163 MET cc_start: 0.3176 (mmm) cc_final: 0.2780 (mmp) REVERT: Q 200 LYS cc_start: 0.7795 (ptmm) cc_final: 0.7561 (ptpp) REVERT: Q 297 MET cc_start: 0.2713 (mmt) cc_final: 0.2011 (mpt) REVERT: R 180 MET cc_start: 0.0117 (OUTLIER) cc_final: -0.0384 (mtm) REVERT: R 204 LEU cc_start: 0.8327 (mm) cc_final: 0.8015 (mt) REVERT: R 205 LYS cc_start: 0.7960 (pttt) cc_final: 0.7450 (mmmt) REVERT: R 382 LEU cc_start: 0.7441 (mt) cc_final: 0.7229 (mm) REVERT: S 180 MET cc_start: -0.0116 (tmt) cc_final: -0.2921 (mmm) REVERT: T 163 MET cc_start: 0.1637 (OUTLIER) cc_final: 0.1325 (tpt) REVERT: T 189 MET cc_start: 0.3037 (mmm) cc_final: 0.2419 (mpp) REVERT: T 214 MET cc_start: 0.4544 (tpt) cc_final: 0.3484 (tmm) REVERT: T 297 MET cc_start: -0.1523 (ttt) cc_final: -0.2055 (ttp) REVERT: U 214 MET cc_start: 0.2726 (tpt) cc_final: 0.2165 (tmm) REVERT: U 286 LYS cc_start: 0.3999 (tttt) cc_final: 0.3615 (ttpp) REVERT: W 163 MET cc_start: 0.4860 (mpt) cc_final: 0.4571 (pmm) REVERT: W 185 ASN cc_start: 0.7275 (m-40) cc_final: 0.6868 (m-40) REVERT: W 189 MET cc_start: 0.4740 (mpp) cc_final: 0.4540 (mpp) REVERT: W 276 ILE cc_start: 0.1931 (OUTLIER) cc_final: 0.1706 (tt) REVERT: W 319 ILE cc_start: 0.1834 (tt) cc_final: 0.1541 (tp) REVERT: X 163 MET cc_start: 0.1887 (tpt) cc_final: 0.0837 (ppp) REVERT: X 180 MET cc_start: 0.1993 (ttp) cc_final: 0.1659 (tmm) REVERT: X 327 LEU cc_start: 0.5099 (OUTLIER) cc_final: 0.4796 (tm) REVERT: X 353 LEU cc_start: 0.6826 (tp) cc_final: 0.6594 (mp) outliers start: 170 outliers final: 38 residues processed: 747 average time/residue: 0.8059 time to fit residues: 735.5778 Evaluate side-chains 549 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 496 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 349 MET Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain I residue 335 ARG Chi-restraints excluded: chain J residue 166 ARG Chi-restraints excluded: chain J residue 203 PHE Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain K residue 195 MET Chi-restraints excluded: chain K residue 323 GLN Chi-restraints excluded: chain K residue 348 MET Chi-restraints excluded: chain K residue 358 ARG Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain N residue 244 TYR Chi-restraints excluded: chain P residue 163 MET Chi-restraints excluded: chain P residue 357 HIS Chi-restraints excluded: chain Q residue 339 ILE Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 323 GLN Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 163 MET Chi-restraints excluded: chain T residue 235 ILE Chi-restraints excluded: chain T residue 278 ARG Chi-restraints excluded: chain T residue 378 ASP Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain W residue 276 ILE Chi-restraints excluded: chain X residue 327 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 466 optimal weight: 8.9990 chunk 476 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 249 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 0.0030 chunk 149 optimal weight: 0.3980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 175 GLN A 323 GLN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN ** F 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN G 185 ASN G 199 HIS G 323 GLN ** H 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN I 165 GLN I 208 ASN J 193 GLN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 GLN ** N 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 272 ASN S 165 GLN T 357 HIS U 175 GLN U 199 HIS ** V 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 191 ASN ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 357 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5517 r_free = 0.5517 target = 0.316176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5356 r_free = 0.5356 target = 0.293529 restraints weight = 73021.247| |-----------------------------------------------------------------------------| r_work (start): 0.5336 rms_B_bonded: 3.34 r_work: 0.5251 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.5251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3503 moved from start: 0.7786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 45240 Z= 0.127 Angle : 0.669 13.121 60936 Z= 0.340 Chirality : 0.045 0.196 6984 Planarity : 0.005 0.064 7968 Dihedral : 6.058 72.138 6216 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.18 % Allowed : 16.31 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.11), residues: 5616 helix: -1.35 (0.11), residues: 1992 sheet: -1.79 (0.13), residues: 1392 loop : -1.28 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 288 TYR 0.015 0.001 TYR U 244 PHE 0.033 0.002 PHE M 273 HIS 0.015 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00275 (45216) covalent geometry : angle 0.66869 (60936) hydrogen bonds : bond 0.03324 ( 1752) hydrogen bonds : angle 5.59369 ( 4968) Misc. bond : bond 0.00181 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 562 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8118 (mmp) cc_final: 0.7855 (tpp) REVERT: A 166 ARG cc_start: 0.7839 (tpt170) cc_final: 0.7603 (tpm-80) REVERT: A 223 PHE cc_start: 0.7628 (t80) cc_final: 0.7333 (t80) REVERT: B 180 MET cc_start: 0.1555 (mmm) cc_final: 0.0399 (mmm) REVERT: B 349 MET cc_start: 0.0905 (OUTLIER) cc_final: -0.0007 (mpm) REVERT: C 189 MET cc_start: 0.4032 (tpp) cc_final: 0.3832 (mmm) REVERT: C 214 MET cc_start: 0.3684 (OUTLIER) cc_final: 0.3147 (pp-130) REVERT: C 355 TYR cc_start: 0.0928 (p90) cc_final: -0.0054 (p90) REVERT: D 160 MET cc_start: 0.0673 (mtt) cc_final: 0.0395 (mtp) REVERT: D 163 MET cc_start: 0.5741 (mmp) cc_final: 0.4785 (mpm) REVERT: D 175 GLN cc_start: 0.2262 (mt0) cc_final: 0.1527 (tp40) REVERT: D 286 LYS cc_start: 0.4332 (ttmt) cc_final: 0.3551 (ptpt) REVERT: D 292 LEU cc_start: 0.3352 (tp) cc_final: 0.2538 (pt) REVERT: D 297 MET cc_start: 0.3939 (tpt) cc_final: 0.3005 (mmt) REVERT: E 217 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.6491 (t80) REVERT: E 271 MET cc_start: 0.4320 (ppp) cc_final: 0.3198 (ptp) REVERT: E 344 GLU cc_start: 0.7920 (pm20) cc_final: 0.7697 (pm20) REVERT: E 378 ASP cc_start: 0.7116 (p0) cc_final: 0.6741 (p0) REVERT: E 385 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6559 (t70) REVERT: G 163 MET cc_start: 0.3434 (tpt) cc_final: 0.3197 (tmm) REVERT: I 160 MET cc_start: -0.0709 (pmm) cc_final: -0.1123 (ptm) REVERT: I 335 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7853 (ttm170) REVERT: I 344 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: J 163 MET cc_start: 0.1449 (mmt) cc_final: 0.0549 (tmt) REVERT: J 166 ARG cc_start: 0.1332 (OUTLIER) cc_final: 0.0945 (mmp-170) REVERT: J 244 TYR cc_start: 0.0119 (OUTLIER) cc_final: -0.1913 (m-80) REVERT: K 189 MET cc_start: 0.3407 (mpp) cc_final: 0.3011 (mpp) REVERT: K 195 MET cc_start: -0.0067 (OUTLIER) cc_final: -0.1185 (mmt) REVERT: K 297 MET cc_start: 0.0445 (OUTLIER) cc_final: 0.0102 (mmm) REVERT: L 195 MET cc_start: 0.3355 (tpp) cc_final: 0.2276 (tpt) REVERT: L 266 ARG cc_start: 0.3874 (OUTLIER) cc_final: 0.3553 (mtt-85) REVERT: L 271 MET cc_start: 0.4141 (tpp) cc_final: 0.3881 (mmp) REVERT: M 176 ASN cc_start: 0.6381 (p0) cc_final: 0.6081 (m-40) REVERT: M 350 TYR cc_start: 0.7822 (m-80) cc_final: 0.6997 (m-80) REVERT: N 378 ASP cc_start: 0.7825 (p0) cc_final: 0.7469 (p0) REVERT: N 385 ASP cc_start: 0.7082 (t70) cc_final: 0.6789 (t70) REVERT: O 163 MET cc_start: 0.0473 (OUTLIER) cc_final: 0.0040 (mmm) REVERT: O 189 MET cc_start: 0.1492 (tpp) cc_final: 0.0300 (ttp) REVERT: O 214 MET cc_start: 0.3158 (tpt) cc_final: 0.2530 (pmm) REVERT: P 155 GLU cc_start: 0.0425 (pt0) cc_final: -0.0650 (tm-30) REVERT: P 189 MET cc_start: 0.3080 (mmm) cc_final: 0.2864 (mpp) REVERT: Q 180 MET cc_start: 0.2917 (OUTLIER) cc_final: 0.1891 (mtm) REVERT: Q 210 LYS cc_start: 0.6482 (tppt) cc_final: 0.5941 (tmmt) REVERT: Q 297 MET cc_start: 0.2676 (mmt) cc_final: 0.1967 (mpt) REVERT: Q 349 MET cc_start: 0.2513 (ppp) cc_final: -0.0334 (mpp) REVERT: R 163 MET cc_start: 0.4550 (mpm) cc_final: 0.4156 (mpp) REVERT: R 180 MET cc_start: -0.0039 (pmm) cc_final: -0.0733 (mtm) REVERT: R 200 LYS cc_start: 0.7257 (mmmm) cc_final: 0.6898 (mmtt) REVERT: R 204 LEU cc_start: 0.8022 (mm) cc_final: 0.7697 (mt) REVERT: R 205 LYS cc_start: 0.7932 (pttt) cc_final: 0.7309 (mmmt) REVERT: R 260 LEU cc_start: 0.1785 (OUTLIER) cc_final: 0.0976 (pp) REVERT: R 377 GLU cc_start: 0.6645 (pt0) cc_final: 0.6310 (pt0) REVERT: R 382 LEU cc_start: 0.7431 (mt) cc_final: 0.7176 (mm) REVERT: S 180 MET cc_start: -0.0205 (tmt) cc_final: -0.0560 (tmt) REVERT: T 163 MET cc_start: 0.1993 (mmp) cc_final: 0.1779 (tpt) REVERT: T 214 MET cc_start: 0.4340 (tpt) cc_final: 0.3058 (tmm) REVERT: U 214 MET cc_start: 0.2861 (tpt) cc_final: 0.2657 (tpt) REVERT: U 286 LYS cc_start: 0.4184 (tttt) cc_final: 0.3802 (ttpp) REVERT: V 273 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6212 (t80) REVERT: V 303 THR cc_start: 0.8800 (t) cc_final: 0.8557 (m) REVERT: W 209 LEU cc_start: 0.2387 (OUTLIER) cc_final: 0.1308 (mt) REVERT: W 258 ARG cc_start: 0.1572 (pmt170) cc_final: 0.1353 (tmm-80) REVERT: W 276 ILE cc_start: 0.1834 (OUTLIER) cc_final: 0.1602 (tt) REVERT: W 334 ASP cc_start: 0.7992 (m-30) cc_final: 0.7774 (m-30) REVERT: W 378 ASP cc_start: 0.7402 (p0) cc_final: 0.6608 (p0) REVERT: X 163 MET cc_start: 0.1448 (tpt) cc_final: 0.0667 (ppp) REVERT: X 180 MET cc_start: 0.1473 (ttp) cc_final: 0.1194 (tmm) outliers start: 152 outliers final: 46 residues processed: 652 average time/residue: 0.8475 time to fit residues: 672.9411 Evaluate side-chains 552 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 489 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 335 ARG Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain J residue 166 ARG Chi-restraints excluded: chain J residue 188 ASP Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain K residue 195 MET Chi-restraints excluded: chain K residue 297 MET Chi-restraints excluded: chain K residue 358 ARG Chi-restraints excluded: chain L residue 266 ARG Chi-restraints excluded: chain L residue 349 MET Chi-restraints excluded: chain M residue 160 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain N residue 244 TYR Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 318 ILE Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain Q residue 180 MET Chi-restraints excluded: chain Q residue 339 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 273 PHE Chi-restraints excluded: chain R residue 335 ARG Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 278 ARG Chi-restraints excluded: chain T residue 378 ASP Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain U residue 312 SER Chi-restraints excluded: chain V residue 204 LEU Chi-restraints excluded: chain V residue 273 PHE Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain W residue 209 LEU Chi-restraints excluded: chain W residue 276 ILE Chi-restraints excluded: chain W residue 316 THR Chi-restraints excluded: chain W residue 359 LEU Chi-restraints excluded: chain X residue 228 GLN Chi-restraints excluded: chain X residue 326 ILE Chi-restraints excluded: chain X residue 349 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 522 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 335 optimal weight: 20.0000 chunk 299 optimal weight: 2.9990 chunk 376 optimal weight: 9.9990 chunk 196 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS C 207 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 GLN F 207 HIS ** F 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN J 228 GLN J 330 HIS K 228 GLN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 GLN L 199 HIS ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 GLN N 267 ASN N 357 HIS O 193 GLN ** O 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 165 GLN P 175 GLN P 199 HIS P 357 HIS ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN S 176 ASN T 199 HIS T 267 ASN ** V 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 193 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5417 r_free = 0.5417 target = 0.303038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.277271 restraints weight = 71631.130| |-----------------------------------------------------------------------------| r_work (start): 0.5177 rms_B_bonded: 3.40 r_work: 0.5078 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.5078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4116 moved from start: 0.9943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.168 45240 Z= 0.203 Angle : 0.823 16.557 60936 Z= 0.423 Chirality : 0.049 0.226 6984 Planarity : 0.006 0.239 7968 Dihedral : 6.414 89.456 6216 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.81 % Allowed : 17.42 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.10), residues: 5616 helix: -1.52 (0.11), residues: 2016 sheet: -1.15 (0.16), residues: 888 loop : -1.69 (0.11), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 358 TYR 0.029 0.003 TYR M 355 PHE 0.068 0.003 PHE R 273 HIS 0.025 0.002 HIS L 330 Details of bonding type rmsd covalent geometry : bond 0.00454 (45216) covalent geometry : angle 0.82259 (60936) hydrogen bonds : bond 0.04340 ( 1752) hydrogen bonds : angle 6.17555 ( 4968) Misc. bond : bond 0.00163 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 651 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8054 (mmp) cc_final: 0.7472 (tmm) REVERT: A 170 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7340 (mpp80) REVERT: A 349 MET cc_start: 0.9107 (ttm) cc_final: 0.8907 (ttm) REVERT: B 180 MET cc_start: 0.1710 (mmm) cc_final: -0.0034 (ttp) REVERT: B 342 LYS cc_start: 0.7066 (pptt) cc_final: 0.6799 (pptt) REVERT: B 344 GLU cc_start: 0.7162 (pt0) cc_final: 0.6865 (pm20) REVERT: B 370 ARG cc_start: 0.3135 (OUTLIER) cc_final: 0.2211 (mmp80) REVERT: C 214 MET cc_start: 0.3332 (OUTLIER) cc_final: 0.2615 (pp-130) REVERT: C 329 MET cc_start: 0.3389 (mpt) cc_final: 0.2826 (mmt) REVERT: C 335 ARG cc_start: 0.3819 (OUTLIER) cc_final: 0.2087 (mmm-85) REVERT: C 357 HIS cc_start: 0.1676 (OUTLIER) cc_final: -0.0162 (t70) REVERT: D 160 MET cc_start: 0.2574 (mtt) cc_final: 0.2127 (mtp) REVERT: D 163 MET cc_start: 0.5797 (mmp) cc_final: 0.4872 (mpm) REVERT: D 170 ARG cc_start: 0.3545 (OUTLIER) cc_final: 0.3099 (mmt90) REVERT: D 177 THR cc_start: 0.3470 (p) cc_final: 0.3263 (p) REVERT: D 180 MET cc_start: 0.1339 (ptp) cc_final: 0.0966 (tmt) REVERT: D 292 LEU cc_start: 0.3426 (tp) cc_final: 0.2324 (pt) REVERT: D 297 MET cc_start: 0.3870 (tpt) cc_final: 0.2955 (mmt) REVERT: D 344 GLU cc_start: 0.8102 (pm20) cc_final: 0.7848 (pm20) REVERT: D 349 MET cc_start: 0.2396 (OUTLIER) cc_final: 0.0799 (pp-130) REVERT: E 160 MET cc_start: 0.1060 (mpp) cc_final: 0.0804 (mtp) REVERT: E 271 MET cc_start: 0.4687 (ppp) cc_final: 0.4104 (ptp) REVERT: E 277 GLU cc_start: 0.5735 (tp30) cc_final: 0.5163 (mm-30) REVERT: E 361 ASP cc_start: 0.7593 (t70) cc_final: 0.6933 (m-30) REVERT: E 383 LEU cc_start: 0.4718 (OUTLIER) cc_final: 0.4264 (mt) REVERT: F 189 MET cc_start: 0.3437 (mmt) cc_final: 0.3157 (mmm) REVERT: F 214 MET cc_start: 0.5086 (OUTLIER) cc_final: 0.3974 (pmm) REVERT: G 163 MET cc_start: 0.3589 (tpt) cc_final: 0.3358 (tmm) REVERT: G 249 ASP cc_start: 0.5563 (p0) cc_final: 0.5303 (p0) REVERT: G 348 MET cc_start: 0.1600 (tpp) cc_final: -0.1442 (mtp) REVERT: H 158 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7013 (pp20) REVERT: H 172 LYS cc_start: 0.5127 (mmmt) cc_final: 0.4106 (mmtt) REVERT: I 160 MET cc_start: -0.0416 (pmm) cc_final: -0.0897 (ptt) REVERT: I 194 GLU cc_start: 0.8027 (pp20) cc_final: 0.7820 (pp20) REVERT: I 208 ASN cc_start: 0.8353 (p0) cc_final: 0.8144 (p0) REVERT: I 344 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: J 166 ARG cc_start: 0.1786 (OUTLIER) cc_final: 0.1298 (mmp-170) REVERT: J 214 MET cc_start: 0.3986 (tpt) cc_final: 0.3387 (pp-130) REVERT: J 217 PHE cc_start: 0.4004 (m-10) cc_final: 0.3774 (m-80) REVERT: J 244 TYR cc_start: 0.0779 (OUTLIER) cc_final: -0.1526 (m-80) REVERT: J 350 TYR cc_start: 0.1767 (OUTLIER) cc_final: 0.1340 (m-80) REVERT: K 214 MET cc_start: 0.5020 (mmm) cc_final: 0.3408 (ttp) REVERT: K 297 MET cc_start: 0.0573 (mmm) cc_final: 0.0155 (mmm) REVERT: K 348 MET cc_start: 0.3199 (mpp) cc_final: 0.2596 (mtp) REVERT: K 357 HIS cc_start: 0.4883 (OUTLIER) cc_final: 0.4513 (t70) REVERT: L 195 MET cc_start: 0.4020 (tpp) cc_final: 0.3004 (ttt) REVERT: L 266 ARG cc_start: 0.4491 (OUTLIER) cc_final: 0.4006 (mtt-85) REVERT: L 271 MET cc_start: 0.3838 (tpp) cc_final: 0.3050 (mpm) REVERT: L 329 MET cc_start: 0.0613 (mmt) cc_final: 0.0365 (mmt) REVERT: L 330 HIS cc_start: 0.1195 (OUTLIER) cc_final: -0.0752 (m90) REVERT: M 201 GLU cc_start: 0.7407 (pm20) cc_final: 0.7021 (pm20) REVERT: N 200 LYS cc_start: 0.6534 (mmmm) cc_final: 0.6289 (mtpp) REVERT: N 297 MET cc_start: 0.4645 (tpt) cc_final: 0.4427 (tpt) REVERT: N 335 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7360 (ttm170) REVERT: O 160 MET cc_start: -0.4732 (OUTLIER) cc_final: -0.5231 (mtt) REVERT: O 163 MET cc_start: 0.0295 (OUTLIER) cc_final: -0.0051 (tmm) REVERT: O 195 MET cc_start: 0.5437 (mtt) cc_final: 0.5217 (mtp) REVERT: O 271 MET cc_start: 0.1739 (OUTLIER) cc_final: 0.0985 (ttp) REVERT: O 302 PHE cc_start: 0.1903 (t80) cc_final: -0.0595 (t80) REVERT: P 189 MET cc_start: 0.3777 (mmm) cc_final: 0.3150 (mpp) REVERT: P 214 MET cc_start: 0.4189 (tmm) cc_final: 0.3931 (mpt) REVERT: P 263 PRO cc_start: 0.5440 (Cg_endo) cc_final: 0.5213 (Cg_exo) REVERT: P 277 GLU cc_start: 0.5505 (pt0) cc_final: 0.4417 (pp20) REVERT: P 297 MET cc_start: -0.0335 (tpp) cc_final: -0.0710 (mmm) REVERT: P 342 LYS cc_start: 0.8437 (mptt) cc_final: 0.8106 (mptp) REVERT: P 348 MET cc_start: 0.1975 (mtt) cc_final: 0.0829 (ttm) REVERT: P 357 HIS cc_start: 0.5167 (OUTLIER) cc_final: 0.4659 (m90) REVERT: Q 160 MET cc_start: 0.0820 (mtt) cc_final: 0.0511 (mtt) REVERT: Q 180 MET cc_start: 0.2790 (OUTLIER) cc_final: 0.1826 (mtm) REVERT: Q 201 GLU cc_start: 0.7526 (pm20) cc_final: 0.7293 (pm20) REVERT: Q 205 LYS cc_start: 0.7743 (tmmt) cc_final: 0.7344 (ptpt) REVERT: Q 209 LEU cc_start: 0.3546 (OUTLIER) cc_final: 0.3203 (pp) REVERT: Q 210 LYS cc_start: 0.6732 (tppt) cc_final: 0.6467 (tmmt) REVERT: Q 271 MET cc_start: 0.2392 (OUTLIER) cc_final: 0.1344 (tmt) REVERT: Q 329 MET cc_start: -0.0267 (OUTLIER) cc_final: -0.1091 (mmt) REVERT: Q 342 LYS cc_start: 0.8774 (pmtt) cc_final: 0.8365 (pptt) REVERT: R 180 MET cc_start: 0.0209 (pmm) cc_final: -0.0974 (mtm) REVERT: R 205 LYS cc_start: 0.8043 (pttt) cc_final: 0.7577 (mmmt) REVERT: R 260 LEU cc_start: 0.1591 (OUTLIER) cc_final: 0.0734 (pp) REVERT: R 276 ILE cc_start: 0.4748 (mm) cc_final: 0.4223 (mt) REVERT: S 180 MET cc_start: 0.0120 (tmt) cc_final: -0.0499 (tmt) REVERT: S 297 MET cc_start: 0.3301 (mtt) cc_final: 0.3000 (mmt) REVERT: S 329 MET cc_start: 0.2017 (mmp) cc_final: 0.1233 (mpp) REVERT: S 351 VAL cc_start: 0.3028 (p) cc_final: 0.2708 (t) REVERT: T 163 MET cc_start: 0.2953 (OUTLIER) cc_final: 0.2497 (mmm) REVERT: T 189 MET cc_start: 0.3433 (mmm) cc_final: 0.2121 (mpp) REVERT: T 245 ARG cc_start: 0.2574 (mpt180) cc_final: 0.0750 (ptp-170) REVERT: T 271 MET cc_start: 0.1817 (OUTLIER) cc_final: 0.1518 (ttt) REVERT: T 292 LEU cc_start: 0.0701 (OUTLIER) cc_final: 0.0359 (mm) REVERT: T 297 MET cc_start: -0.0742 (mmm) cc_final: -0.3407 (ttp) REVERT: V 297 MET cc_start: 0.6806 (mmm) cc_final: 0.6574 (mmm) REVERT: W 160 MET cc_start: 0.1094 (mpp) cc_final: 0.0771 (mtp) REVERT: W 214 MET cc_start: 0.6521 (tpp) cc_final: 0.6199 (tpp) REVERT: W 217 PHE cc_start: 0.6381 (OUTLIER) cc_final: 0.5128 (t80) REVERT: W 219 LYS cc_start: 0.4534 (ttmm) cc_final: 0.4251 (tppt) REVERT: W 258 ARG cc_start: 0.2511 (pmt170) cc_final: 0.2243 (tmm-80) REVERT: W 378 ASP cc_start: 0.7651 (p0) cc_final: 0.7118 (p0) REVERT: X 163 MET cc_start: 0.1349 (tpt) cc_final: 0.0474 (ppp) REVERT: X 373 LYS cc_start: 0.3219 (OUTLIER) cc_final: 0.2329 (pttt) outliers start: 182 outliers final: 50 residues processed: 765 average time/residue: 0.8182 time to fit residues: 762.9134 Evaluate side-chains 593 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 511 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 166 ARG Chi-restraints excluded: chain J residue 188 ASP Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain J residue 350 TYR Chi-restraints excluded: chain K residue 357 HIS Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain L residue 266 ARG Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain M residue 160 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain N residue 244 TYR Chi-restraints excluded: chain N residue 318 ILE Chi-restraints excluded: chain N residue 335 ARG Chi-restraints excluded: chain O residue 160 MET Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 271 MET Chi-restraints excluded: chain O residue 351 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 357 HIS Chi-restraints excluded: chain Q residue 180 MET Chi-restraints excluded: chain Q residue 209 LEU Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain Q residue 329 MET Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain S residue 250 ILE Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 163 MET Chi-restraints excluded: chain T residue 271 MET Chi-restraints excluded: chain T residue 278 ARG Chi-restraints excluded: chain T residue 292 LEU Chi-restraints excluded: chain T residue 378 ASP Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain U residue 188 ASP Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain W residue 217 PHE Chi-restraints excluded: chain W residue 316 THR Chi-restraints excluded: chain W residue 359 LEU Chi-restraints excluded: chain X residue 326 ILE Chi-restraints excluded: chain X residue 373 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 504 optimal weight: 0.9980 chunk 277 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 237 optimal weight: 0.1980 chunk 443 optimal weight: 2.9990 chunk 452 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 455 optimal weight: 0.9990 chunk 400 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS E 175 GLN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 GLN J 330 HIS ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 207 HIS N 228 GLN O 176 ASN O 228 GLN P 165 GLN P 199 HIS P 357 HIS ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 191 ASN ** R 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 199 HIS T 323 GLN ** V 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 199 HIS V 226 GLN V 228 GLN ** V 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 228 GLN W 330 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5425 r_free = 0.5425 target = 0.303915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.277458 restraints weight = 70964.045| |-----------------------------------------------------------------------------| r_work (start): 0.5185 rms_B_bonded: 3.28 r_work: 0.5091 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.5091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4103 moved from start: 1.0195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 45240 Z= 0.135 Angle : 0.702 14.945 60936 Z= 0.355 Chirality : 0.045 0.268 6984 Planarity : 0.005 0.062 7968 Dihedral : 5.806 87.258 6216 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.95 % Allowed : 20.44 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.11), residues: 5616 helix: -0.97 (0.11), residues: 1992 sheet: -0.97 (0.16), residues: 888 loop : -1.40 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 198 TYR 0.019 0.001 TYR X 350 PHE 0.030 0.002 PHE N 314 HIS 0.016 0.001 HIS P 357 Details of bonding type rmsd covalent geometry : bond 0.00301 (45216) covalent geometry : angle 0.70173 (60936) hydrogen bonds : bond 0.03353 ( 1752) hydrogen bonds : angle 5.59216 ( 4968) Misc. bond : bond 0.00299 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 547 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7984 (mmp) cc_final: 0.7506 (tmm) REVERT: A 166 ARG cc_start: 0.8030 (tpt170) cc_final: 0.7652 (mmm160) REVERT: A 170 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7399 (pmm-80) REVERT: B 163 MET cc_start: 0.4056 (pp-130) cc_final: 0.3818 (tmt) REVERT: B 180 MET cc_start: 0.1633 (mmm) cc_final: 0.0828 (ttp) REVERT: B 297 MET cc_start: -0.0079 (mtm) cc_final: -0.0724 (mtt) REVERT: B 314 PHE cc_start: 0.1200 (p90) cc_final: 0.0001 (p90) REVERT: B 327 LEU cc_start: 0.5084 (tp) cc_final: 0.4666 (tp) REVERT: B 342 LYS cc_start: 0.7011 (pptt) cc_final: 0.6232 (pptt) REVERT: B 344 GLU cc_start: 0.7417 (pt0) cc_final: 0.7096 (pm20) REVERT: B 349 MET cc_start: 0.2499 (OUTLIER) cc_final: 0.1109 (mpp) REVERT: B 353 LEU cc_start: 0.4462 (tp) cc_final: 0.4163 (mp) REVERT: C 214 MET cc_start: 0.3300 (OUTLIER) cc_final: 0.2816 (pp-130) REVERT: C 271 MET cc_start: 0.2182 (ptt) cc_final: 0.1976 (ptt) REVERT: C 329 MET cc_start: 0.2944 (mpt) cc_final: 0.2378 (mmp) REVERT: D 160 MET cc_start: 0.1557 (mtt) cc_final: 0.1194 (mtp) REVERT: D 163 MET cc_start: 0.5856 (mmp) cc_final: 0.4947 (mpm) REVERT: D 292 LEU cc_start: 0.3325 (tp) cc_final: 0.2302 (pt) REVERT: D 297 MET cc_start: 0.3789 (tpt) cc_final: 0.2914 (mmt) REVERT: D 344 GLU cc_start: 0.8158 (pm20) cc_final: 0.7903 (pm20) REVERT: D 349 MET cc_start: 0.2168 (pp-130) cc_final: 0.1079 (pp-130) REVERT: E 160 MET cc_start: 0.1287 (mpp) cc_final: 0.1034 (mtp) REVERT: E 206 LYS cc_start: 0.3366 (pttt) cc_final: 0.3042 (pttt) REVERT: E 271 MET cc_start: 0.4802 (ppp) cc_final: 0.4397 (ptp) REVERT: E 361 ASP cc_start: 0.7783 (t70) cc_final: 0.7415 (m-30) REVERT: F 189 MET cc_start: 0.3181 (mmt) cc_final: 0.2907 (mmm) REVERT: F 214 MET cc_start: 0.6308 (tpt) cc_final: 0.5089 (mpt) REVERT: G 348 MET cc_start: 0.1302 (tpp) cc_final: -0.1350 (mtp) REVERT: H 172 LYS cc_start: 0.5205 (mmmt) cc_final: 0.3877 (mmtt) REVERT: H 191 ASN cc_start: 0.8536 (t0) cc_final: 0.8294 (t0) REVERT: H 210 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7935 (mmmt) REVERT: J 166 ARG cc_start: 0.1756 (OUTLIER) cc_final: 0.1335 (mmp-170) REVERT: J 214 MET cc_start: 0.4088 (tpt) cc_final: 0.3418 (pmt) REVERT: J 244 TYR cc_start: 0.0543 (OUTLIER) cc_final: -0.1613 (m-80) REVERT: K 180 MET cc_start: -0.0312 (tmt) cc_final: -0.1232 (tmt) REVERT: K 214 MET cc_start: 0.4659 (mmm) cc_final: 0.3507 (tpt) REVERT: K 297 MET cc_start: 0.0169 (OUTLIER) cc_final: -0.0121 (mmm) REVERT: L 195 MET cc_start: 0.3957 (tpp) cc_final: 0.3690 (mtm) REVERT: L 266 ARG cc_start: 0.4453 (OUTLIER) cc_final: 0.3944 (mtt-85) REVERT: L 271 MET cc_start: 0.3862 (tpp) cc_final: 0.3217 (mpm) REVERT: L 330 HIS cc_start: 0.1812 (p-80) cc_final: -0.0806 (m90) REVERT: L 348 MET cc_start: 0.0033 (mmt) cc_final: -0.0246 (ttp) REVERT: M 163 MET cc_start: 0.4993 (mmp) cc_final: 0.4778 (ppp) REVERT: M 201 GLU cc_start: 0.7490 (pm20) cc_final: 0.7232 (pm20) REVERT: M 205 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8317 (ttpt) REVERT: M 342 LYS cc_start: 0.8916 (ptmt) cc_final: 0.8633 (pptt) REVERT: M 377 GLU cc_start: 0.7799 (tt0) cc_final: 0.7569 (tt0) REVERT: O 160 MET cc_start: -0.4430 (OUTLIER) cc_final: -0.4922 (mtt) REVERT: O 163 MET cc_start: 0.0174 (OUTLIER) cc_final: -0.0070 (tmm) REVERT: O 214 MET cc_start: 0.3083 (tpt) cc_final: 0.2476 (pmm) REVERT: O 271 MET cc_start: 0.1187 (OUTLIER) cc_final: 0.0590 (ttp) REVERT: O 302 PHE cc_start: 0.1265 (t80) cc_final: -0.1207 (t80) REVERT: P 155 GLU cc_start: 0.1955 (pt0) cc_final: 0.0390 (tm-30) REVERT: P 172 LYS cc_start: 0.1499 (tppt) cc_final: -0.0222 (mmtt) REVERT: P 189 MET cc_start: 0.3905 (mmm) cc_final: 0.2833 (mpp) REVERT: P 263 PRO cc_start: 0.5188 (Cg_endo) cc_final: 0.4914 (Cg_exo) REVERT: P 297 MET cc_start: -0.0293 (tpp) cc_final: -0.0588 (mmm) REVERT: P 348 MET cc_start: 0.2224 (mtt) cc_final: 0.1085 (ttm) REVERT: P 357 HIS cc_start: 0.4702 (OUTLIER) cc_final: 0.3957 (m90) REVERT: Q 160 MET cc_start: 0.1086 (mtt) cc_final: 0.0794 (mtt) REVERT: Q 180 MET cc_start: 0.3152 (OUTLIER) cc_final: 0.1846 (mtm) REVERT: Q 205 LYS cc_start: 0.7693 (tmmt) cc_final: 0.7346 (ptpt) REVERT: Q 210 LYS cc_start: 0.6748 (tppt) cc_final: 0.6454 (tmmt) REVERT: Q 230 VAL cc_start: -0.1969 (OUTLIER) cc_final: -0.2295 (m) REVERT: Q 271 MET cc_start: 0.2540 (OUTLIER) cc_final: 0.1145 (pp-130) REVERT: Q 297 MET cc_start: 0.2816 (mmt) cc_final: 0.2517 (mmt) REVERT: Q 329 MET cc_start: -0.0088 (OUTLIER) cc_final: -0.0694 (mpp) REVERT: R 163 MET cc_start: 0.5024 (mmm) cc_final: 0.4478 (mpp) REVERT: R 180 MET cc_start: -0.0062 (pmm) cc_final: -0.0725 (mtp) REVERT: R 205 LYS cc_start: 0.8064 (pttt) cc_final: 0.7574 (mmmt) REVERT: R 333 PHE cc_start: 0.3208 (m-80) cc_final: 0.2886 (m-80) REVERT: S 180 MET cc_start: -0.0207 (tmt) cc_final: -0.0694 (tmt) REVERT: S 297 MET cc_start: 0.3542 (mtt) cc_final: 0.3175 (mmt) REVERT: S 329 MET cc_start: 0.1968 (mmp) cc_final: 0.0144 (tpp) REVERT: T 163 MET cc_start: 0.2630 (mmp) cc_final: 0.2217 (mmm) REVERT: T 172 LYS cc_start: 0.1875 (tppt) cc_final: -0.0361 (mmtt) REVERT: T 245 ARG cc_start: 0.2362 (mpt180) cc_final: 0.0943 (ptp-170) REVERT: T 292 LEU cc_start: 0.0663 (mt) cc_final: 0.0363 (mm) REVERT: T 297 MET cc_start: -0.0690 (mmm) cc_final: -0.3341 (ttp) REVERT: T 348 MET cc_start: 0.3318 (mtt) cc_final: 0.1460 (ttm) REVERT: U 163 MET cc_start: 0.5149 (mmm) cc_final: 0.4635 (mpp) REVERT: U 173 GLU cc_start: 0.7136 (pp20) cc_final: 0.6853 (pp20) REVERT: V 297 MET cc_start: 0.7157 (mmm) cc_final: 0.6858 (mmm) REVERT: V 303 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8610 (m) REVERT: W 160 MET cc_start: 0.1003 (mpp) cc_final: 0.0695 (mtp) REVERT: W 175 GLN cc_start: 0.4354 (OUTLIER) cc_final: 0.1541 (pm20) REVERT: W 219 LYS cc_start: 0.4686 (ttmm) cc_final: 0.4181 (mttm) REVERT: W 271 MET cc_start: 0.0246 (pmm) cc_final: -0.0783 (ptp) REVERT: W 329 MET cc_start: 0.7632 (mpp) cc_final: 0.7419 (mpp) REVERT: X 163 MET cc_start: 0.1331 (tpt) cc_final: 0.0440 (ppp) REVERT: X 180 MET cc_start: 0.1700 (ttp) cc_final: 0.1490 (tmm) REVERT: X 186 GLU cc_start: -0.1077 (OUTLIER) cc_final: -0.2242 (mm-30) REVERT: X 370 ARG cc_start: 0.3153 (OUTLIER) cc_final: 0.2041 (ppt-90) outliers start: 141 outliers final: 47 residues processed: 638 average time/residue: 0.8140 time to fit residues: 635.2679 Evaluate side-chains 560 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 494 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain J residue 166 ARG Chi-restraints excluded: chain J residue 188 ASP Chi-restraints excluded: chain J residue 203 PHE Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain J residue 348 MET Chi-restraints excluded: chain K residue 297 MET Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain L residue 266 ARG Chi-restraints excluded: chain M residue 160 MET Chi-restraints excluded: chain M residue 208 ASN Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 244 TYR Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain N residue 318 ILE Chi-restraints excluded: chain O residue 160 MET Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 271 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 357 HIS Chi-restraints excluded: chain Q residue 180 MET Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain Q residue 329 MET Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain S residue 223 PHE Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 278 ARG Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain V residue 303 THR Chi-restraints excluded: chain W residue 175 GLN Chi-restraints excluded: chain W residue 182 THR Chi-restraints excluded: chain W residue 223 PHE Chi-restraints excluded: chain W residue 316 THR Chi-restraints excluded: chain W residue 359 LEU Chi-restraints excluded: chain X residue 186 GLU Chi-restraints excluded: chain X residue 228 GLN Chi-restraints excluded: chain X residue 326 ILE Chi-restraints excluded: chain X residue 370 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 482 optimal weight: 0.9990 chunk 502 optimal weight: 9.9990 chunk 535 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 527 optimal weight: 0.9990 chunk 515 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 386 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN B 228 GLN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 HIS H 191 ASN I 226 GLN ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 272 ASN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 207 HIS ** S 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 226 GLN V 228 GLN ** V 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5385 r_free = 0.5385 target = 0.298766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5176 r_free = 0.5176 target = 0.271210 restraints weight = 69689.935| |-----------------------------------------------------------------------------| r_work (start): 0.5136 rms_B_bonded: 3.24 r_work: 0.5035 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.5035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4283 moved from start: 1.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 45240 Z= 0.153 Angle : 0.741 22.504 60936 Z= 0.373 Chirality : 0.046 0.211 6984 Planarity : 0.005 0.067 7968 Dihedral : 5.764 87.613 6216 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.35 % Allowed : 20.60 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.11), residues: 5616 helix: -0.80 (0.11), residues: 1992 sheet: -0.94 (0.16), residues: 888 loop : -1.31 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 198 TYR 0.020 0.002 TYR B 350 PHE 0.048 0.002 PHE L 314 HIS 0.018 0.001 HIS M 207 Details of bonding type rmsd covalent geometry : bond 0.00346 (45216) covalent geometry : angle 0.74147 (60936) hydrogen bonds : bond 0.03647 ( 1752) hydrogen bonds : angle 5.68469 ( 4968) Misc. bond : bond 0.00229 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 582 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7991 (mmp) cc_final: 0.7540 (tmm) REVERT: A 166 ARG cc_start: 0.7988 (tpt170) cc_final: 0.7617 (mmm160) REVERT: A 170 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7308 (pmm-80) REVERT: B 163 MET cc_start: 0.3762 (pp-130) cc_final: 0.3529 (tmt) REVERT: B 278 ARG cc_start: 0.2097 (OUTLIER) cc_final: 0.1776 (mpt-90) REVERT: B 297 MET cc_start: 0.0012 (mtm) cc_final: -0.0646 (mtt) REVERT: B 314 PHE cc_start: 0.1207 (p90) cc_final: 0.0193 (p90) REVERT: B 339 ILE cc_start: 0.7798 (mm) cc_final: 0.7518 (mm) REVERT: B 342 LYS cc_start: 0.7536 (pptt) cc_final: 0.6236 (pptt) REVERT: B 344 GLU cc_start: 0.7575 (pt0) cc_final: 0.7175 (pm20) REVERT: B 349 MET cc_start: 0.2701 (OUTLIER) cc_final: 0.1219 (mpm) REVERT: B 370 ARG cc_start: 0.2943 (OUTLIER) cc_final: 0.2356 (mmp80) REVERT: C 214 MET cc_start: 0.3624 (OUTLIER) cc_final: 0.2750 (pp-130) REVERT: D 160 MET cc_start: 0.2760 (mtt) cc_final: 0.2306 (mtp) REVERT: D 163 MET cc_start: 0.5889 (mmp) cc_final: 0.5040 (mpm) REVERT: D 297 MET cc_start: 0.4118 (tpt) cc_final: 0.3225 (mmt) REVERT: E 160 MET cc_start: 0.1315 (mpp) cc_final: 0.1058 (mtp) REVERT: E 195 MET cc_start: 0.8611 (ttt) cc_final: 0.8215 (ttt) REVERT: E 206 LYS cc_start: 0.3484 (pttt) cc_final: 0.3097 (pttt) REVERT: E 271 MET cc_start: 0.4785 (ppp) cc_final: 0.4269 (mtm) REVERT: E 297 MET cc_start: 0.6113 (tmm) cc_final: 0.4747 (ttt) REVERT: E 361 ASP cc_start: 0.7808 (t70) cc_final: 0.7364 (m-30) REVERT: F 214 MET cc_start: 0.5960 (tpt) cc_final: 0.4945 (mpt) REVERT: F 349 MET cc_start: 0.1200 (ttm) cc_final: 0.0824 (tmt) REVERT: G 163 MET cc_start: 0.5222 (OUTLIER) cc_final: 0.4362 (mmm) REVERT: G 195 MET cc_start: 0.1351 (OUTLIER) cc_final: 0.0796 (mpt) REVERT: G 348 MET cc_start: 0.1513 (tpp) cc_final: -0.0448 (tpp) REVERT: H 158 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7074 (pp20) REVERT: H 172 LYS cc_start: 0.5411 (mmmt) cc_final: 0.4073 (mmtt) REVERT: H 342 LYS cc_start: 0.8890 (ptmt) cc_final: 0.8564 (pptt) REVERT: I 335 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7037 (mtm-85) REVERT: I 344 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: J 166 ARG cc_start: 0.1895 (OUTLIER) cc_final: 0.1619 (mmp-170) REVERT: J 214 MET cc_start: 0.3878 (tpt) cc_final: 0.3294 (pmt) REVERT: J 244 TYR cc_start: 0.0681 (OUTLIER) cc_final: -0.1529 (m-80) REVERT: K 180 MET cc_start: -0.0315 (tmt) cc_final: -0.1302 (tmt) REVERT: K 214 MET cc_start: 0.4758 (mmm) cc_final: 0.3906 (tmm) REVERT: K 260 LEU cc_start: 0.2138 (tt) cc_final: 0.1207 (mt) REVERT: K 297 MET cc_start: 0.0204 (OUTLIER) cc_final: -0.0090 (mmm) REVERT: L 198 ARG cc_start: 0.7162 (tpp80) cc_final: 0.6539 (ttt-90) REVERT: L 266 ARG cc_start: 0.4606 (OUTLIER) cc_final: 0.4060 (mtt-85) REVERT: L 330 HIS cc_start: 0.2307 (OUTLIER) cc_final: -0.0411 (m90) REVERT: L 348 MET cc_start: 0.0068 (mmt) cc_final: -0.0555 (ttp) REVERT: M 201 GLU cc_start: 0.7518 (pm20) cc_final: 0.7257 (pm20) REVERT: M 205 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8304 (ttpt) REVERT: M 214 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7130 (tmm) REVERT: M 271 MET cc_start: 0.6641 (mtp) cc_final: 0.6245 (ttm) REVERT: M 339 ILE cc_start: 0.8685 (mt) cc_final: 0.8409 (mm) REVERT: M 342 LYS cc_start: 0.8914 (ptmt) cc_final: 0.8602 (pptt) REVERT: N 206 LYS cc_start: 0.4271 (ptpt) cc_final: 0.3581 (tptt) REVERT: N 277 GLU cc_start: 0.6036 (mm-30) cc_final: 0.5438 (mt-10) REVERT: N 297 MET cc_start: 0.4944 (tpt) cc_final: 0.4445 (tpt) REVERT: O 214 MET cc_start: 0.3299 (tpt) cc_final: 0.2564 (pmm) REVERT: O 271 MET cc_start: 0.1382 (OUTLIER) cc_final: 0.0757 (ttp) REVERT: O 302 PHE cc_start: 0.1446 (t80) cc_final: -0.1093 (t80) REVERT: P 155 GLU cc_start: 0.2024 (pt0) cc_final: 0.0233 (tm-30) REVERT: P 172 LYS cc_start: 0.1491 (tppt) cc_final: -0.0356 (mmtt) REVERT: P 189 MET cc_start: 0.3776 (mmm) cc_final: 0.2903 (mpp) REVERT: P 195 MET cc_start: -0.0113 (OUTLIER) cc_final: -0.0640 (mmp) REVERT: P 297 MET cc_start: -0.0283 (tpp) cc_final: -0.0553 (mmm) REVERT: Q 160 MET cc_start: 0.1579 (mtt) cc_final: 0.1263 (mtt) REVERT: Q 180 MET cc_start: 0.3194 (OUTLIER) cc_final: 0.1975 (mtm) REVERT: Q 210 LYS cc_start: 0.7093 (tppt) cc_final: 0.6818 (tmmt) REVERT: Q 271 MET cc_start: 0.2833 (OUTLIER) cc_final: 0.1779 (pp-130) REVERT: Q 329 MET cc_start: -0.0335 (OUTLIER) cc_final: -0.1275 (mmp) REVERT: Q 342 LYS cc_start: 0.8865 (pmtt) cc_final: 0.8562 (pptt) REVERT: Q 383 LEU cc_start: -0.0174 (mt) cc_final: -0.0477 (tt) REVERT: R 160 MET cc_start: -0.2220 (pmm) cc_final: -0.2707 (ptp) REVERT: R 163 MET cc_start: 0.4753 (mmm) cc_final: 0.3819 (ttt) REVERT: R 180 MET cc_start: 0.0153 (pmm) cc_final: -0.0897 (mtp) REVERT: S 180 MET cc_start: -0.0342 (tmt) cc_final: -0.0883 (tmt) REVERT: S 297 MET cc_start: 0.3614 (mtt) cc_final: 0.3379 (mmt) REVERT: S 329 MET cc_start: 0.1171 (mmp) cc_final: 0.0111 (tpp) REVERT: S 357 HIS cc_start: 0.2831 (OUTLIER) cc_final: 0.2546 (t-90) REVERT: T 163 MET cc_start: 0.2919 (OUTLIER) cc_final: 0.2627 (mmm) REVERT: T 172 LYS cc_start: 0.1849 (tppt) cc_final: -0.0424 (mmtt) REVERT: T 189 MET cc_start: 0.3580 (mmm) cc_final: 0.2301 (mpp) REVERT: T 245 ARG cc_start: 0.2655 (mpt180) cc_final: 0.1094 (ptp-170) REVERT: T 297 MET cc_start: -0.0765 (mmm) cc_final: -0.3389 (ttp) REVERT: T 329 MET cc_start: 0.0115 (OUTLIER) cc_final: -0.0741 (pmm) REVERT: T 348 MET cc_start: 0.2679 (mtt) cc_final: 0.1346 (ttm) REVERT: U 163 MET cc_start: 0.5073 (mmm) cc_final: 0.3917 (ttt) REVERT: U 173 GLU cc_start: 0.7282 (pp20) cc_final: 0.7005 (pp20) REVERT: V 166 ARG cc_start: 0.7996 (tpp-160) cc_final: 0.7768 (tpp80) REVERT: V 297 MET cc_start: 0.7225 (mmm) cc_final: 0.6951 (mmm) REVERT: V 349 MET cc_start: 0.9198 (ttm) cc_final: 0.8969 (ttm) REVERT: W 160 MET cc_start: 0.1089 (mpp) cc_final: 0.0862 (mtp) REVERT: W 175 GLN cc_start: 0.4092 (OUTLIER) cc_final: 0.1255 (pm20) REVERT: W 215 SER cc_start: 0.7999 (p) cc_final: 0.7631 (p) REVERT: W 217 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6968 (t80) REVERT: W 219 LYS cc_start: 0.6062 (ttmm) cc_final: 0.5304 (mttp) REVERT: W 329 MET cc_start: 0.8430 (mpp) cc_final: 0.8170 (mpp) REVERT: X 163 MET cc_start: 0.1235 (tpt) cc_final: 0.0711 (tmt) REVERT: X 180 MET cc_start: 0.1791 (ttp) cc_final: 0.1511 (tmm) REVERT: X 186 GLU cc_start: -0.1101 (OUTLIER) cc_final: -0.2411 (mm-30) REVERT: X 297 MET cc_start: 0.0804 (OUTLIER) cc_final: -0.0297 (mpt) outliers start: 160 outliers final: 58 residues processed: 682 average time/residue: 0.8066 time to fit residues: 670.5744 Evaluate side-chains 615 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 529 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 172 LYS Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 335 ARG Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain J residue 166 ARG Chi-restraints excluded: chain J residue 188 ASP Chi-restraints excluded: chain J residue 203 PHE Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain K residue 297 MET Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain L residue 200 LYS Chi-restraints excluded: chain L residue 266 ARG Chi-restraints excluded: chain L residue 314 PHE Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 343 VAL Chi-restraints excluded: chain M residue 160 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain N residue 326 ILE Chi-restraints excluded: chain O residue 271 MET Chi-restraints excluded: chain P residue 195 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 283 LEU Chi-restraints excluded: chain Q residue 180 MET Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 225 LEU Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain Q residue 314 PHE Chi-restraints excluded: chain Q residue 329 MET Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain S residue 357 HIS Chi-restraints excluded: chain T residue 163 MET Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 329 MET Chi-restraints excluded: chain T residue 378 ASP Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain U residue 189 MET Chi-restraints excluded: chain V residue 303 THR Chi-restraints excluded: chain W residue 175 GLN Chi-restraints excluded: chain W residue 217 PHE Chi-restraints excluded: chain W residue 316 THR Chi-restraints excluded: chain W residue 349 MET Chi-restraints excluded: chain W residue 359 LEU Chi-restraints excluded: chain X residue 186 GLU Chi-restraints excluded: chain X residue 297 MET Chi-restraints excluded: chain X residue 326 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 250 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 393 optimal weight: 8.9990 chunk 327 optimal weight: 8.9990 chunk 163 optimal weight: 0.3980 chunk 427 optimal weight: 20.0000 chunk 416 optimal weight: 9.9990 chunk 43 optimal weight: 0.0470 chunk 62 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 440 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 ASN I 226 GLN ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 272 ASN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 GLN N 330 HIS P 185 ASN ** P 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 165 GLN V 226 GLN V 228 GLN ** V 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5389 r_free = 0.5389 target = 0.299428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5179 r_free = 0.5179 target = 0.272378 restraints weight = 70330.363| |-----------------------------------------------------------------------------| r_work (start): 0.5146 rms_B_bonded: 3.32 r_work: 0.5043 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.5043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4256 moved from start: 1.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 45240 Z= 0.131 Angle : 0.713 16.269 60936 Z= 0.356 Chirality : 0.045 0.383 6984 Planarity : 0.005 0.067 7968 Dihedral : 5.538 87.769 6216 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.58 % Allowed : 22.53 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.11), residues: 5616 helix: -0.55 (0.12), residues: 1992 sheet: -0.79 (0.16), residues: 888 loop : -1.21 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG V 170 TYR 0.020 0.001 TYR F 247 PHE 0.037 0.002 PHE L 314 HIS 0.024 0.001 HIS V 357 Details of bonding type rmsd covalent geometry : bond 0.00296 (45216) covalent geometry : angle 0.71314 (60936) hydrogen bonds : bond 0.03256 ( 1752) hydrogen bonds : angle 5.43287 ( 4968) Misc. bond : bond 0.00361 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 540 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8081 (mmp) cc_final: 0.7634 (tmm) REVERT: A 166 ARG cc_start: 0.7950 (tpt170) cc_final: 0.7674 (mmm160) REVERT: B 163 MET cc_start: 0.3772 (pp-130) cc_final: 0.3530 (tmt) REVERT: B 214 MET cc_start: 0.3957 (mmm) cc_final: 0.3384 (ttt) REVERT: B 314 PHE cc_start: 0.1517 (p90) cc_final: 0.0199 (p90) REVERT: B 339 ILE cc_start: 0.7805 (mm) cc_final: 0.7424 (mm) REVERT: B 342 LYS cc_start: 0.7448 (pptt) cc_final: 0.6704 (pptt) REVERT: B 344 GLU cc_start: 0.7750 (pt0) cc_final: 0.7341 (pm20) REVERT: B 349 MET cc_start: 0.2567 (OUTLIER) cc_final: 0.0729 (mpm) REVERT: C 214 MET cc_start: 0.3730 (OUTLIER) cc_final: 0.2986 (pp-130) REVERT: C 297 MET cc_start: 0.3299 (pmm) cc_final: 0.2091 (pmm) REVERT: C 329 MET cc_start: 0.3201 (mpt) cc_final: 0.2569 (mmt) REVERT: C 335 ARG cc_start: 0.3651 (OUTLIER) cc_final: 0.2138 (mpp80) REVERT: D 160 MET cc_start: 0.2471 (mtt) cc_final: 0.2050 (mtp) REVERT: D 297 MET cc_start: 0.3970 (tpt) cc_final: 0.3145 (mmt) REVERT: E 160 MET cc_start: 0.1214 (mpp) cc_final: 0.1010 (mtp) REVERT: E 206 LYS cc_start: 0.3662 (pttt) cc_final: 0.3372 (pttt) REVERT: E 271 MET cc_start: 0.4867 (ppp) cc_final: 0.4013 (mtm) REVERT: E 297 MET cc_start: 0.6121 (tmm) cc_final: 0.4900 (ttt) REVERT: E 361 ASP cc_start: 0.7565 (t70) cc_final: 0.7135 (m-30) REVERT: F 214 MET cc_start: 0.5897 (tpt) cc_final: 0.4591 (tmt) REVERT: F 297 MET cc_start: 0.0622 (pmm) cc_final: 0.0365 (pmm) REVERT: G 163 MET cc_start: 0.5008 (OUTLIER) cc_final: 0.4195 (mmm) REVERT: G 189 MET cc_start: 0.2087 (mpt) cc_final: -0.1033 (tpp) REVERT: G 195 MET cc_start: 0.0869 (OUTLIER) cc_final: 0.0278 (mpt) REVERT: G 297 MET cc_start: 0.2390 (mtt) cc_final: 0.2094 (mmt) REVERT: G 348 MET cc_start: 0.1453 (tpp) cc_final: 0.0524 (tpp) REVERT: H 158 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7158 (pp20) REVERT: H 172 LYS cc_start: 0.5320 (mmmt) cc_final: 0.4158 (mptt) REVERT: H 342 LYS cc_start: 0.8912 (ptmt) cc_final: 0.8612 (pptt) REVERT: I 335 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6998 (mtm-85) REVERT: J 188 ASP cc_start: 0.3425 (OUTLIER) cc_final: 0.3110 (p0) REVERT: J 214 MET cc_start: 0.4035 (tpt) cc_final: 0.3442 (pmt) REVERT: J 244 TYR cc_start: 0.0560 (OUTLIER) cc_final: -0.1590 (m-80) REVERT: J 272 ASN cc_start: 0.5501 (OUTLIER) cc_final: 0.5255 (t0) REVERT: J 297 MET cc_start: 0.2526 (pmm) cc_final: 0.2306 (mpt) REVERT: K 180 MET cc_start: -0.0218 (tmt) cc_final: -0.0799 (tmt) REVERT: K 189 MET cc_start: 0.3478 (mpp) cc_final: 0.2882 (mmm) REVERT: K 214 MET cc_start: 0.4811 (mmm) cc_final: 0.3967 (tmm) REVERT: K 297 MET cc_start: -0.0036 (OUTLIER) cc_final: -0.0309 (mmm) REVERT: L 266 ARG cc_start: 0.4616 (OUTLIER) cc_final: 0.4032 (mtt-85) REVERT: L 330 HIS cc_start: 0.1486 (OUTLIER) cc_final: -0.0773 (m90) REVERT: L 348 MET cc_start: -0.0558 (mmt) cc_final: -0.1184 (mmt) REVERT: M 205 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8145 (mtmp) REVERT: M 271 MET cc_start: 0.6709 (mtp) cc_final: 0.6418 (ttm) REVERT: M 339 ILE cc_start: 0.8646 (mt) cc_final: 0.8398 (mm) REVERT: M 342 LYS cc_start: 0.8939 (ptmt) cc_final: 0.8624 (pptt) REVERT: N 163 MET cc_start: 0.4728 (mtt) cc_final: 0.4101 (tmt) REVERT: N 191 ASN cc_start: 0.8394 (t0) cc_final: 0.8065 (t0) REVERT: N 206 LYS cc_start: 0.4283 (ptpt) cc_final: 0.3628 (tptm) REVERT: N 277 GLU cc_start: 0.6153 (mm-30) cc_final: 0.5622 (mt-10) REVERT: N 297 MET cc_start: 0.4982 (tpt) cc_final: 0.4480 (mmm) REVERT: O 214 MET cc_start: 0.3235 (tpt) cc_final: 0.2523 (pmm) REVERT: O 271 MET cc_start: 0.0717 (OUTLIER) cc_final: 0.0174 (ttp) REVERT: O 302 PHE cc_start: 0.0629 (t80) cc_final: -0.1731 (t80) REVERT: O 348 MET cc_start: 0.2134 (pmm) cc_final: 0.1037 (pmm) REVERT: P 189 MET cc_start: 0.3795 (mmm) cc_final: 0.2945 (mpp) REVERT: P 195 MET cc_start: 0.0328 (OUTLIER) cc_final: -0.0282 (mmp) REVERT: P 214 MET cc_start: 0.4344 (tmm) cc_final: 0.4112 (mpt) REVERT: P 277 GLU cc_start: 0.5137 (pt0) cc_final: 0.3955 (pp20) REVERT: P 297 MET cc_start: -0.0356 (tpp) cc_final: -0.0582 (mmm) REVERT: P 348 MET cc_start: 0.2115 (mtt) cc_final: 0.0916 (ttm) REVERT: Q 160 MET cc_start: 0.1369 (mtt) cc_final: 0.1047 (mtt) REVERT: Q 186 GLU cc_start: 0.3097 (pp20) cc_final: 0.2753 (pp20) REVERT: Q 210 LYS cc_start: 0.7314 (tppt) cc_final: 0.7001 (tmmt) REVERT: Q 329 MET cc_start: -0.0239 (mmp) cc_final: -0.1202 (tpp) REVERT: Q 342 LYS cc_start: 0.8881 (pmtt) cc_final: 0.8592 (pptt) REVERT: R 160 MET cc_start: -0.2257 (pmm) cc_final: -0.2870 (ptp) REVERT: R 163 MET cc_start: 0.4535 (mmm) cc_final: 0.3770 (ttt) REVERT: R 180 MET cc_start: 0.0220 (pmm) cc_final: -0.0552 (mtp) REVERT: R 205 LYS cc_start: 0.7730 (mtmp) cc_final: 0.7183 (mmmt) REVERT: R 329 MET cc_start: 0.3433 (pmt) cc_final: 0.1900 (mpp) REVERT: S 180 MET cc_start: -0.0436 (tmt) cc_final: -0.1006 (tmt) REVERT: S 297 MET cc_start: 0.3530 (mtt) cc_final: 0.3245 (mmt) REVERT: S 329 MET cc_start: 0.1198 (mmp) cc_final: 0.0280 (mpp) REVERT: S 357 HIS cc_start: 0.2644 (OUTLIER) cc_final: 0.2413 (t-90) REVERT: T 163 MET cc_start: 0.3224 (mmp) cc_final: 0.2965 (mmm) REVERT: T 172 LYS cc_start: 0.1895 (tppt) cc_final: -0.0261 (mmtt) REVERT: T 245 ARG cc_start: 0.1976 (mpt180) cc_final: 0.0823 (ptp-170) REVERT: T 277 GLU cc_start: 0.4431 (mt-10) cc_final: 0.4080 (mt-10) REVERT: T 297 MET cc_start: -0.0813 (mmm) cc_final: -0.3396 (ttp) REVERT: T 348 MET cc_start: 0.2847 (mtt) cc_final: 0.1348 (ttm) REVERT: U 163 MET cc_start: 0.4936 (mmm) cc_final: 0.3767 (ttt) REVERT: U 173 GLU cc_start: 0.7249 (pp20) cc_final: 0.7022 (pp20) REVERT: V 303 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8584 (m) REVERT: V 349 MET cc_start: 0.9120 (ttm) cc_final: 0.8907 (ttm) REVERT: W 175 GLN cc_start: 0.3819 (OUTLIER) cc_final: 0.1590 (pm20) REVERT: W 185 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8300 (t0) REVERT: W 258 ARG cc_start: 0.3099 (pmt170) cc_final: 0.2846 (tmm-80) REVERT: W 277 GLU cc_start: 0.4688 (mm-30) cc_final: 0.3386 (mm-30) REVERT: W 360 ILE cc_start: 0.6210 (mm) cc_final: 0.5823 (mp) REVERT: X 160 MET cc_start: -0.3718 (OUTLIER) cc_final: -0.3963 (ptt) REVERT: X 163 MET cc_start: 0.1455 (tpt) cc_final: 0.0813 (tmt) REVERT: X 180 MET cc_start: 0.1789 (ttp) cc_final: 0.1529 (tmm) REVERT: X 186 GLU cc_start: -0.1331 (OUTLIER) cc_final: -0.2170 (mm-30) REVERT: X 297 MET cc_start: 0.0743 (OUTLIER) cc_final: -0.0335 (mpt) REVERT: X 370 ARG cc_start: 0.3193 (OUTLIER) cc_final: 0.2255 (ppt-90) REVERT: X 373 LYS cc_start: 0.3191 (OUTLIER) cc_final: 0.2695 (pttt) outliers start: 123 outliers final: 45 residues processed: 622 average time/residue: 0.6985 time to fit residues: 530.8523 Evaluate side-chains 567 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 498 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 335 ARG Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 188 ASP Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain J residue 272 ASN Chi-restraints excluded: chain K residue 297 MET Chi-restraints excluded: chain L residue 200 LYS Chi-restraints excluded: chain L residue 266 ARG Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 343 VAL Chi-restraints excluded: chain L residue 349 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 244 TYR Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 182 THR Chi-restraints excluded: chain O residue 271 MET Chi-restraints excluded: chain P residue 195 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 283 LEU Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain R residue 360 ILE Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain S residue 357 HIS Chi-restraints excluded: chain T residue 160 MET Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain V residue 303 THR Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain W residue 175 GLN Chi-restraints excluded: chain W residue 185 ASN Chi-restraints excluded: chain W residue 349 MET Chi-restraints excluded: chain X residue 160 MET Chi-restraints excluded: chain X residue 186 GLU Chi-restraints excluded: chain X residue 297 MET Chi-restraints excluded: chain X residue 326 ILE Chi-restraints excluded: chain X residue 370 ARG Chi-restraints excluded: chain X residue 373 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 281 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 465 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 491 optimal weight: 7.9990 chunk 284 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 274 optimal weight: 2.9990 chunk 444 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN E 208 ASN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 ASN H 228 GLN ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 GLN L 175 GLN ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 GLN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 HIS ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 207 HIS R 228 GLN V 175 GLN V 226 GLN V 228 GLN W 228 GLN ** X 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5364 r_free = 0.5364 target = 0.295930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.266855 restraints weight = 69390.240| |-----------------------------------------------------------------------------| r_work (start): 0.5091 rms_B_bonded: 3.42 r_work: 0.4992 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4432 moved from start: 1.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 45240 Z= 0.156 Angle : 0.787 39.443 60936 Z= 0.387 Chirality : 0.047 0.507 6984 Planarity : 0.005 0.085 7968 Dihedral : 5.666 89.449 6216 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 2.62 % Allowed : 22.80 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.11), residues: 5616 helix: -0.58 (0.11), residues: 1987 sheet: -0.88 (0.16), residues: 887 loop : -1.17 (0.11), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG V 166 TYR 0.025 0.001 TYR B 350 PHE 0.038 0.002 PHE J 368 HIS 0.007 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00358 (45216) covalent geometry : angle 0.78669 (60936) hydrogen bonds : bond 0.03565 ( 1752) hydrogen bonds : angle 5.58990 ( 4968) Misc. bond : bond 0.00466 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 547 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8084 (mmp) cc_final: 0.7703 (tmm) REVERT: B 186 GLU cc_start: 0.4626 (OUTLIER) cc_final: 0.4375 (pm20) REVERT: B 214 MET cc_start: 0.3973 (mmm) cc_final: 0.3118 (ttt) REVERT: B 297 MET cc_start: -0.0030 (mtm) cc_final: -0.0777 (mtt) REVERT: B 314 PHE cc_start: 0.1492 (p90) cc_final: 0.0311 (p90) REVERT: B 339 ILE cc_start: 0.8103 (mm) cc_final: 0.7824 (mm) REVERT: B 342 LYS cc_start: 0.7779 (pptt) cc_final: 0.7392 (mtpp) REVERT: B 349 MET cc_start: 0.3390 (OUTLIER) cc_final: 0.0994 (mpm) REVERT: C 214 MET cc_start: 0.3905 (OUTLIER) cc_final: 0.2929 (pp-130) REVERT: C 271 MET cc_start: 0.1570 (ptt) cc_final: 0.1364 (ptt) REVERT: C 297 MET cc_start: 0.3105 (pmm) cc_final: 0.1865 (pmm) REVERT: C 335 ARG cc_start: 0.3797 (OUTLIER) cc_final: 0.2225 (mpp80) REVERT: C 354 THR cc_start: 0.2084 (OUTLIER) cc_final: 0.1870 (m) REVERT: D 160 MET cc_start: 0.2478 (mtt) cc_final: 0.2044 (mtp) REVERT: D 297 MET cc_start: 0.3893 (tpt) cc_final: 0.3241 (mmt) REVERT: D 371 LYS cc_start: 0.6853 (mttt) cc_final: 0.5339 (pttt) REVERT: E 206 LYS cc_start: 0.3791 (pttt) cc_final: 0.3524 (pttt) REVERT: E 271 MET cc_start: 0.4789 (ppp) cc_final: 0.4278 (mtm) REVERT: E 275 ASP cc_start: 0.7373 (p0) cc_final: 0.6813 (t0) REVERT: E 297 MET cc_start: 0.5888 (tmm) cc_final: 0.5174 (ttt) REVERT: E 329 MET cc_start: 0.8834 (mpp) cc_final: 0.8464 (mpp) REVERT: E 361 ASP cc_start: 0.7656 (t70) cc_final: 0.7257 (m-30) REVERT: F 214 MET cc_start: 0.6021 (tpt) cc_final: 0.4883 (tmt) REVERT: F 297 MET cc_start: 0.0571 (pmm) cc_final: 0.0302 (pmm) REVERT: F 349 MET cc_start: 0.0848 (ttm) cc_final: 0.0443 (tmt) REVERT: G 163 MET cc_start: 0.5161 (OUTLIER) cc_final: 0.4374 (mmm) REVERT: G 189 MET cc_start: 0.2025 (mpt) cc_final: -0.1113 (tpp) REVERT: G 195 MET cc_start: 0.1555 (OUTLIER) cc_final: 0.0982 (mpt) REVERT: G 214 MET cc_start: 0.4318 (tpt) cc_final: 0.4052 (tpt) REVERT: G 228 GLN cc_start: 0.3097 (mt0) cc_final: 0.2574 (mt0) REVERT: G 348 MET cc_start: 0.2024 (tpp) cc_final: 0.0452 (tpp) REVERT: G 349 MET cc_start: 0.4354 (tmm) cc_final: 0.3612 (tmt) REVERT: H 172 LYS cc_start: 0.5694 (mmmt) cc_final: 0.4784 (mptt) REVERT: H 280 ILE cc_start: 0.8155 (mt) cc_final: 0.7944 (mm) REVERT: H 342 LYS cc_start: 0.8891 (ptmt) cc_final: 0.8606 (pptt) REVERT: I 335 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.6929 (mtm-85) REVERT: J 214 MET cc_start: 0.3980 (tpt) cc_final: 0.3448 (pmt) REVERT: J 217 PHE cc_start: 0.3819 (m-10) cc_final: 0.3022 (m-10) REVERT: J 244 TYR cc_start: 0.0529 (OUTLIER) cc_final: -0.1682 (m-80) REVERT: J 329 MET cc_start: 0.4010 (mpt) cc_final: 0.3122 (mmp) REVERT: K 180 MET cc_start: -0.0024 (tmt) cc_final: -0.0642 (tmt) REVERT: K 189 MET cc_start: 0.3403 (mpp) cc_final: 0.2787 (mmm) REVERT: K 297 MET cc_start: 0.0210 (OUTLIER) cc_final: -0.0029 (mmm) REVERT: L 266 ARG cc_start: 0.4869 (OUTLIER) cc_final: 0.4168 (mtt-85) REVERT: M 180 MET cc_start: -0.2427 (OUTLIER) cc_final: -0.2632 (ptp) REVERT: M 205 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8204 (mtmp) REVERT: M 271 MET cc_start: 0.6888 (mtp) cc_final: 0.6633 (ttm) REVERT: M 339 ILE cc_start: 0.8691 (mt) cc_final: 0.8426 (mm) REVERT: M 342 LYS cc_start: 0.8953 (ptmt) cc_final: 0.8632 (pptt) REVERT: N 163 MET cc_start: 0.4604 (mtt) cc_final: 0.4062 (tmt) REVERT: N 206 LYS cc_start: 0.4397 (ptpt) cc_final: 0.3492 (tptm) REVERT: N 210 LYS cc_start: 0.8030 (ptmm) cc_final: 0.7788 (ttmm) REVERT: N 277 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6064 (mt-10) REVERT: N 297 MET cc_start: 0.5210 (tpt) cc_final: 0.4579 (tpt) REVERT: O 214 MET cc_start: 0.3217 (tpt) cc_final: 0.2450 (pmm) REVERT: O 271 MET cc_start: 0.0936 (OUTLIER) cc_final: 0.0386 (ttp) REVERT: O 302 PHE cc_start: 0.1390 (t80) cc_final: -0.1037 (t80) REVERT: P 163 MET cc_start: 0.2599 (tpt) cc_final: 0.1902 (mmm) REVERT: P 172 LYS cc_start: 0.1461 (tppt) cc_final: -0.0568 (mmtt) REVERT: P 189 MET cc_start: 0.3980 (mmm) cc_final: 0.3190 (mpp) REVERT: P 195 MET cc_start: -0.0161 (OUTLIER) cc_final: -0.0520 (mmp) REVERT: P 297 MET cc_start: -0.0332 (OUTLIER) cc_final: -0.0591 (mmm) REVERT: P 348 MET cc_start: 0.2518 (mtt) cc_final: 0.1334 (ttm) REVERT: Q 160 MET cc_start: 0.2064 (mtt) cc_final: 0.1653 (mtt) REVERT: Q 210 LYS cc_start: 0.7729 (tppt) cc_final: 0.7378 (tmmt) REVERT: Q 297 MET cc_start: 0.3497 (mmt) cc_final: 0.3226 (mpp) REVERT: Q 342 LYS cc_start: 0.8934 (pmtt) cc_final: 0.8518 (pptt) REVERT: R 160 MET cc_start: -0.2592 (pmm) cc_final: -0.3115 (ptp) REVERT: R 163 MET cc_start: 0.4588 (mmm) cc_final: 0.3870 (ttt) REVERT: R 180 MET cc_start: -0.0029 (pmm) cc_final: -0.1103 (mtp) REVERT: R 342 LYS cc_start: 0.8835 (ptmt) cc_final: 0.8532 (pptt) REVERT: S 180 MET cc_start: -0.0292 (tmt) cc_final: -0.1188 (tmt) REVERT: S 297 MET cc_start: 0.3701 (mtt) cc_final: 0.3472 (mmt) REVERT: S 329 MET cc_start: 0.0859 (mmp) cc_final: 0.0246 (mpp) REVERT: S 357 HIS cc_start: 0.2945 (OUTLIER) cc_final: 0.2722 (t-90) REVERT: T 172 LYS cc_start: 0.1929 (tppt) cc_final: -0.0390 (mmtt) REVERT: T 277 GLU cc_start: 0.4793 (mt-10) cc_final: 0.4518 (mt-10) REVERT: T 297 MET cc_start: -0.0336 (mmm) cc_final: -0.2771 (ttp) REVERT: T 329 MET cc_start: -0.0061 (OUTLIER) cc_final: -0.0915 (pmm) REVERT: U 163 MET cc_start: 0.4939 (mmm) cc_final: 0.3801 (ttt) REVERT: U 173 GLU cc_start: 0.7225 (pp20) cc_final: 0.6950 (pp20) REVERT: U 214 MET cc_start: 0.3426 (mmm) cc_final: 0.3155 (tpt) REVERT: U 232 ASN cc_start: 0.2510 (t0) cc_final: 0.2246 (t0) REVERT: U 318 ILE cc_start: 0.2455 (OUTLIER) cc_final: 0.2149 (pt) REVERT: U 348 MET cc_start: 0.3160 (tmm) cc_final: 0.1401 (ttt) REVERT: V 166 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.7330 (tpm170) REVERT: V 170 ARG cc_start: 0.7028 (ptp-110) cc_final: 0.6800 (ptp-110) REVERT: V 194 GLU cc_start: 0.7761 (pp20) cc_final: 0.7526 (pp20) REVERT: V 297 MET cc_start: 0.7100 (mmm) cc_final: 0.6875 (mmm) REVERT: V 349 MET cc_start: 0.9153 (ttm) cc_final: 0.8899 (ttm) REVERT: W 175 GLN cc_start: 0.4006 (OUTLIER) cc_final: 0.1830 (pm20) REVERT: W 194 GLU cc_start: 0.7098 (pp20) cc_final: 0.6828 (pp20) REVERT: W 217 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7002 (t80) REVERT: W 258 ARG cc_start: 0.3354 (pmt170) cc_final: 0.3140 (tmm-80) REVERT: W 277 GLU cc_start: 0.4732 (mm-30) cc_final: 0.3677 (mt-10) REVERT: W 329 MET cc_start: 0.8462 (mpp) cc_final: 0.8085 (mpp) REVERT: X 163 MET cc_start: 0.1130 (tpt) cc_final: 0.0605 (tmt) REVERT: X 180 MET cc_start: 0.1334 (ttp) cc_final: 0.1010 (tmm) REVERT: X 297 MET cc_start: 0.0894 (OUTLIER) cc_final: -0.0233 (mpt) REVERT: X 370 ARG cc_start: 0.3173 (OUTLIER) cc_final: 0.2218 (ppt-90) REVERT: X 373 LYS cc_start: 0.3304 (OUTLIER) cc_final: 0.2648 (pttt) outliers start: 125 outliers final: 53 residues processed: 630 average time/residue: 0.6600 time to fit residues: 508.8479 Evaluate side-chains 583 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 507 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 335 ARG Chi-restraints excluded: chain J residue 188 ASP Chi-restraints excluded: chain J residue 203 PHE Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain K residue 297 MET Chi-restraints excluded: chain L residue 200 LYS Chi-restraints excluded: chain L residue 266 ARG Chi-restraints excluded: chain L residue 314 PHE Chi-restraints excluded: chain L residue 343 VAL Chi-restraints excluded: chain L residue 349 MET Chi-restraints excluded: chain M residue 180 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 182 THR Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 271 MET Chi-restraints excluded: chain P residue 195 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 283 LEU Chi-restraints excluded: chain P residue 297 MET Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 314 PHE Chi-restraints excluded: chain R residue 360 ILE Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain S residue 357 HIS Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 329 MET Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain U residue 180 MET Chi-restraints excluded: chain U residue 318 ILE Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain V residue 303 THR Chi-restraints excluded: chain W residue 175 GLN Chi-restraints excluded: chain W residue 217 PHE Chi-restraints excluded: chain W residue 316 THR Chi-restraints excluded: chain W residue 349 MET Chi-restraints excluded: chain X residue 297 MET Chi-restraints excluded: chain X residue 326 ILE Chi-restraints excluded: chain X residue 370 ARG Chi-restraints excluded: chain X residue 373 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 422 optimal weight: 0.8980 chunk 496 optimal weight: 5.9990 chunk 457 optimal weight: 4.9990 chunk 381 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 360 optimal weight: 0.5980 chunk 362 optimal weight: 5.9990 chunk 326 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 476 optimal weight: 1.9990 chunk 498 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 ASN H 228 GLN ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 GLN ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 GLN Q 175 GLN R 267 ASN ** S 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 193 GLN V 226 GLN V 228 GLN ** X 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 357 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5338 r_free = 0.5338 target = 0.292294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.262054 restraints weight = 70023.738| |-----------------------------------------------------------------------------| r_work (start): 0.5051 rms_B_bonded: 3.61 r_work: 0.4934 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4594 moved from start: 1.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 45240 Z= 0.172 Angle : 0.801 22.746 60936 Z= 0.402 Chirality : 0.048 0.602 6984 Planarity : 0.006 0.085 7968 Dihedral : 5.907 88.643 6216 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.14 % Allowed : 24.06 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.11), residues: 5616 helix: -0.58 (0.11), residues: 2004 sheet: -0.97 (0.16), residues: 872 loop : -1.21 (0.11), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG V 288 TYR 0.023 0.002 TYR U 355 PHE 0.029 0.002 PHE J 368 HIS 0.015 0.001 HIS X 330 Details of bonding type rmsd covalent geometry : bond 0.00392 (45216) covalent geometry : angle 0.80138 (60936) hydrogen bonds : bond 0.03792 ( 1752) hydrogen bonds : angle 5.76195 ( 4968) Misc. bond : bond 0.00362 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 591 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8087 (mmp) cc_final: 0.7657 (tmm) REVERT: B 214 MET cc_start: 0.3757 (mmm) cc_final: 0.2784 (ttt) REVERT: B 297 MET cc_start: -0.0079 (mtm) cc_final: -0.0814 (mtt) REVERT: B 314 PHE cc_start: 0.1182 (p90) cc_final: 0.0142 (p90) REVERT: B 346 ARG cc_start: 0.6749 (ttp-170) cc_final: 0.6474 (ttp-170) REVERT: B 378 ASP cc_start: 0.6950 (p0) cc_final: 0.6671 (p0) REVERT: C 195 MET cc_start: 0.2394 (tpp) cc_final: 0.1842 (mmm) REVERT: C 214 MET cc_start: 0.4221 (OUTLIER) cc_final: 0.3152 (pp-130) REVERT: C 297 MET cc_start: 0.3137 (pmm) cc_final: 0.2106 (pmm) REVERT: C 335 ARG cc_start: 0.4617 (OUTLIER) cc_final: 0.2596 (mpt90) REVERT: D 160 MET cc_start: 0.1979 (mtt) cc_final: 0.1560 (mtp) REVERT: D 297 MET cc_start: 0.3770 (tpt) cc_final: 0.3521 (mmt) REVERT: D 337 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8459 (m) REVERT: D 371 LYS cc_start: 0.8142 (mttt) cc_final: 0.6917 (pttt) REVERT: E 206 LYS cc_start: 0.4206 (pttt) cc_final: 0.3827 (pttt) REVERT: E 241 GLU cc_start: 0.4617 (OUTLIER) cc_final: 0.3973 (mm-30) REVERT: E 275 ASP cc_start: 0.7301 (p0) cc_final: 0.6880 (t0) REVERT: E 297 MET cc_start: 0.6285 (tmm) cc_final: 0.6048 (ttt) REVERT: E 361 ASP cc_start: 0.7658 (t70) cc_final: 0.7332 (m-30) REVERT: F 214 MET cc_start: 0.6295 (tpt) cc_final: 0.5088 (ptp) REVERT: F 297 MET cc_start: 0.0735 (pmm) cc_final: 0.0445 (pmm) REVERT: G 163 MET cc_start: 0.5043 (OUTLIER) cc_final: 0.4283 (mmm) REVERT: G 180 MET cc_start: 0.0400 (pmm) cc_final: -0.1616 (mtp) REVERT: G 189 MET cc_start: 0.2227 (mpt) cc_final: -0.1118 (tpp) REVERT: G 214 MET cc_start: 0.4264 (tpt) cc_final: 0.4053 (tpt) REVERT: G 228 GLN cc_start: 0.2988 (mt0) cc_final: 0.2402 (mt0) REVERT: G 348 MET cc_start: 0.2245 (tpp) cc_final: 0.1257 (tpp) REVERT: G 349 MET cc_start: 0.4350 (tmm) cc_final: 0.3794 (tmt) REVERT: H 165 GLN cc_start: 0.6236 (pt0) cc_final: 0.5998 (pt0) REVERT: H 172 LYS cc_start: 0.5706 (mmmt) cc_final: 0.4842 (mptt) REVERT: H 342 LYS cc_start: 0.8934 (ptmt) cc_final: 0.8647 (pptt) REVERT: I 335 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7147 (mtm-85) REVERT: J 214 MET cc_start: 0.4055 (tpt) cc_final: 0.3592 (pmt) REVERT: J 217 PHE cc_start: 0.3712 (m-10) cc_final: 0.3141 (m-10) REVERT: J 244 TYR cc_start: 0.0776 (OUTLIER) cc_final: -0.1599 (m-80) REVERT: J 297 MET cc_start: 0.2836 (mpt) cc_final: 0.2606 (mpp) REVERT: J 329 MET cc_start: 0.4151 (mpt) cc_final: 0.3243 (mmt) REVERT: K 189 MET cc_start: 0.3094 (mpp) cc_final: 0.2611 (mmm) REVERT: K 214 MET cc_start: 0.5206 (tmm) cc_final: 0.4863 (mmm) REVERT: K 297 MET cc_start: 0.0088 (mmm) cc_final: -0.0117 (mmm) REVERT: K 348 MET cc_start: 0.3461 (mtt) cc_final: 0.1754 (ttm) REVERT: L 198 ARG cc_start: 0.7750 (tpp80) cc_final: 0.7548 (ttm-80) REVERT: L 266 ARG cc_start: 0.4873 (OUTLIER) cc_final: 0.4268 (mtt-85) REVERT: L 342 LYS cc_start: 0.8926 (pmtt) cc_final: 0.8486 (pptt) REVERT: M 205 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8350 (mtmp) REVERT: M 271 MET cc_start: 0.7217 (mtp) cc_final: 0.6753 (ttm) REVERT: M 342 LYS cc_start: 0.8943 (ptmt) cc_final: 0.8330 (pptt) REVERT: N 163 MET cc_start: 0.4678 (mtt) cc_final: 0.4264 (tmt) REVERT: N 194 GLU cc_start: 0.7640 (pp20) cc_final: 0.7329 (pp20) REVERT: N 206 LYS cc_start: 0.4727 (ptpt) cc_final: 0.4286 (ttpt) REVERT: N 277 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6656 (mt-10) REVERT: N 297 MET cc_start: 0.5760 (tpt) cc_final: 0.5203 (tpt) REVERT: O 175 GLN cc_start: 0.5465 (pt0) cc_final: 0.4855 (tt0) REVERT: O 214 MET cc_start: 0.2925 (tpt) cc_final: 0.2119 (pmm) REVERT: O 271 MET cc_start: 0.1023 (OUTLIER) cc_final: 0.0456 (ttp) REVERT: O 302 PHE cc_start: 0.1255 (t80) cc_final: -0.1041 (t80) REVERT: P 163 MET cc_start: 0.2863 (tpt) cc_final: 0.2142 (mmm) REVERT: P 172 LYS cc_start: 0.1319 (tppt) cc_final: -0.0781 (mmtt) REVERT: P 189 MET cc_start: 0.4069 (mmm) cc_final: 0.3336 (mpp) REVERT: P 297 MET cc_start: -0.0010 (OUTLIER) cc_final: -0.0398 (mmm) REVERT: P 339 ILE cc_start: 0.7769 (mt) cc_final: 0.7457 (pp) REVERT: P 348 MET cc_start: 0.2325 (mtt) cc_final: 0.1731 (ptp) REVERT: P 385 ASP cc_start: -0.1188 (OUTLIER) cc_final: -0.1658 (m-30) REVERT: Q 160 MET cc_start: 0.2417 (mtt) cc_final: 0.1983 (mtt) REVERT: Q 271 MET cc_start: 0.4195 (mtt) cc_final: 0.3973 (mtt) REVERT: Q 329 MET cc_start: 0.0617 (OUTLIER) cc_final: -0.0979 (mmp) REVERT: Q 342 LYS cc_start: 0.8982 (pmtt) cc_final: 0.8582 (pptt) REVERT: R 160 MET cc_start: -0.2692 (pmm) cc_final: -0.3150 (ptp) REVERT: R 163 MET cc_start: 0.4564 (mmm) cc_final: 0.3761 (ttt) REVERT: R 180 MET cc_start: -0.0151 (pmm) cc_final: -0.1156 (ttm) REVERT: R 292 LEU cc_start: 0.4151 (tp) cc_final: 0.3837 (pt) REVERT: R 342 LYS cc_start: 0.8927 (ptmt) cc_final: 0.8589 (pptt) REVERT: S 180 MET cc_start: -0.0483 (tmt) cc_final: -0.1441 (tmt) REVERT: S 189 MET cc_start: 0.4131 (mpp) cc_final: 0.3084 (mmm) REVERT: S 223 PHE cc_start: 0.2917 (OUTLIER) cc_final: 0.2699 (p90) REVERT: S 336 PRO cc_start: 0.3906 (Cg_endo) cc_final: 0.3479 (Cg_exo) REVERT: T 172 LYS cc_start: 0.1974 (tppt) cc_final: -0.0240 (mptm) REVERT: T 271 MET cc_start: 0.0857 (OUTLIER) cc_final: 0.0232 (tmt) REVERT: T 277 GLU cc_start: 0.4916 (mt-10) cc_final: 0.4628 (mt-10) REVERT: T 329 MET cc_start: 0.0156 (OUTLIER) cc_final: -0.0741 (pmm) REVERT: U 163 MET cc_start: 0.4962 (mmm) cc_final: 0.3856 (ttt) REVERT: U 180 MET cc_start: 0.0503 (OUTLIER) cc_final: -0.1682 (ptp) REVERT: U 184 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.4857 (m-80) REVERT: U 214 MET cc_start: 0.3405 (mmm) cc_final: 0.3191 (tpt) REVERT: U 302 PHE cc_start: 0.0918 (t80) cc_final: -0.1072 (t80) REVERT: U 312 SER cc_start: 0.5913 (OUTLIER) cc_final: 0.5534 (p) REVERT: V 166 ARG cc_start: 0.8018 (tpp-160) cc_final: 0.7774 (tpp80) REVERT: V 244 TYR cc_start: 0.8544 (m-80) cc_final: 0.8245 (m-80) REVERT: V 297 MET cc_start: 0.7301 (mmm) cc_final: 0.7050 (mmm) REVERT: V 303 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8568 (m) REVERT: W 175 GLN cc_start: 0.3834 (OUTLIER) cc_final: 0.1898 (pm20) REVERT: W 194 GLU cc_start: 0.7186 (pp20) cc_final: 0.6968 (pp20) REVERT: W 217 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7607 (t80) REVERT: W 277 GLU cc_start: 0.5277 (mm-30) cc_final: 0.4635 (mt-10) REVERT: X 180 MET cc_start: 0.1063 (ttp) cc_final: 0.0773 (tmm) REVERT: X 297 MET cc_start: 0.0916 (OUTLIER) cc_final: 0.0083 (mpp) REVERT: X 373 LYS cc_start: 0.3674 (OUTLIER) cc_final: 0.2990 (pttt) outliers start: 102 outliers final: 52 residues processed: 656 average time/residue: 0.5946 time to fit residues: 479.2125 Evaluate side-chains 598 residues out of total 4776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 523 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain H residue 228 GLN Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 335 ARG Chi-restraints excluded: chain J residue 188 ASP Chi-restraints excluded: chain J residue 203 PHE Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 266 ARG Chi-restraints excluded: chain L residue 314 PHE Chi-restraints excluded: chain L residue 349 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 182 THR Chi-restraints excluded: chain N residue 326 ILE Chi-restraints excluded: chain O residue 271 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 283 LEU Chi-restraints excluded: chain P residue 297 MET Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain P residue 385 ASP Chi-restraints excluded: chain P residue 386 LEU Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 329 MET Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 360 ILE Chi-restraints excluded: chain S residue 223 PHE Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 271 MET Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 329 MET Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain U residue 180 MET Chi-restraints excluded: chain U residue 184 PHE Chi-restraints excluded: chain U residue 232 ASN Chi-restraints excluded: chain U residue 304 ILE Chi-restraints excluded: chain U residue 312 SER Chi-restraints excluded: chain U residue 318 ILE Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain V residue 303 THR Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain W residue 175 GLN Chi-restraints excluded: chain W residue 217 PHE Chi-restraints excluded: chain W residue 316 THR Chi-restraints excluded: chain W residue 349 MET Chi-restraints excluded: chain X residue 297 MET Chi-restraints excluded: chain X residue 326 ILE Chi-restraints excluded: chain X residue 373 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 277 optimal weight: 5.9990 chunk 512 optimal weight: 0.9990 chunk 348 optimal weight: 0.6980 chunk 340 optimal weight: 0.0980 chunk 207 optimal weight: 40.0000 chunk 439 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 406 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN E 175 GLN E 208 ASN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 ASN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 ASN I 228 GLN ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 357 HIS ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 ASN N 226 GLN ** N 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 GLN R 208 ASN R 267 ASN ** R 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 165 GLN V 228 GLN ** V 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5343 r_free = 0.5343 target = 0.292623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.262639 restraints weight = 68829.558| |-----------------------------------------------------------------------------| r_work (start): 0.5058 rms_B_bonded: 3.37 r_work: 0.4949 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4588 moved from start: 1.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 45240 Z= 0.154 Angle : 0.777 17.734 60936 Z= 0.389 Chirality : 0.046 0.429 6984 Planarity : 0.006 0.083 7968 Dihedral : 5.762 88.604 6216 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.18 % Allowed : 24.96 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.11), residues: 5616 helix: -0.49 (0.11), residues: 2017 sheet: -0.98 (0.16), residues: 881 loop : -1.18 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG V 170 TYR 0.026 0.001 TYR U 350 PHE 0.035 0.002 PHE J 368 HIS 0.012 0.001 HIS N 357 Details of bonding type rmsd covalent geometry : bond 0.00356 (45216) covalent geometry : angle 0.77742 (60936) hydrogen bonds : bond 0.03578 ( 1752) hydrogen bonds : angle 5.60100 ( 4968) Misc. bond : bond 0.00351 ( 24) =============================================================================== Job complete usr+sys time: 17351.66 seconds wall clock time: 295 minutes 37.85 seconds (17737.85 seconds total)