Starting phenix.real_space_refine on Tue Nov 18 22:29:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yu8_6844/11_2025/5yu8_6844.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yu8_6844/11_2025/5yu8_6844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5yu8_6844/11_2025/5yu8_6844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yu8_6844/11_2025/5yu8_6844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5yu8_6844/11_2025/5yu8_6844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yu8_6844/11_2025/5yu8_6844.map" } resolution = 3.8 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.001 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 107 5.16 5 C 11496 2.51 5 N 3031 2.21 5 O 3498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18147 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "B" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "D" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "E" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "H" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1299 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "I" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1299 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "J" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1299 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.37, per 1000 atoms: 0.24 Number of scatterers: 18147 At special positions: 0 Unit cell: (119.88, 106.92, 183.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 107 16.00 P 10 15.00 Mg 5 11.99 O 3498 8.00 N 3031 7.00 C 11496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 785.4 milliseconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4280 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 31 sheets defined 44.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.584A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.696A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.554A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.690A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.654A pdb=" N LEU A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.609A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.803A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.690A pdb=" N ARG A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.555A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.557A pdb=" N MET A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 321 removed outlier: 3.533A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.544A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.007A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.584A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.696A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.554A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.689A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.654A pdb=" N LEU B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 217 removed outlier: 3.608A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.803A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.689A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 257' Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.555A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.557A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 321 removed outlier: 3.532A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.543A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.007A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.584A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.696A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.553A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.690A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.654A pdb=" N LEU C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 217 removed outlier: 3.609A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.803A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.690A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.555A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.557A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.533A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.543A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.007A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.583A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.696A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.554A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.689A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.654A pdb=" N LEU D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 217 removed outlier: 3.610A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.803A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.690A pdb=" N ARG D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 257' Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 290 through 295 removed outlier: 3.555A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.557A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 321 removed outlier: 3.533A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.543A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.007A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 91 removed outlier: 3.584A pdb=" N GLU E 83 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.695A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.554A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 removed outlier: 3.690A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 197 removed outlier: 3.654A pdb=" N LEU E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 217 removed outlier: 3.609A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 removed outlier: 3.803A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.690A pdb=" N ARG E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 257' Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.555A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.557A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 321 removed outlier: 3.532A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 removed outlier: 3.544A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 365 through 367 No H-bonds generated for 'chain 'E' and resid 365 through 367' Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.006A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 20 removed outlier: 3.779A pdb=" N ILE H 12 " --> pdb=" O ASN H 8 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL H 20 " --> pdb=" O ASN H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 31 Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 68 through 73 removed outlier: 3.824A pdb=" N LYS H 73 " --> pdb=" O THR H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 119 removed outlier: 4.106A pdb=" N ILE H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 126 Processing helix chain 'H' and resid 139 through 145 removed outlier: 3.965A pdb=" N ILE H 143 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP H 145 " --> pdb=" O ASP H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 154 removed outlier: 3.710A pdb=" N GLY H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS H 152 " --> pdb=" O THR H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 20 removed outlier: 3.779A pdb=" N ILE I 12 " --> pdb=" O ASN I 8 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL I 20 " --> pdb=" O ASN I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 31 Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 68 through 73 removed outlier: 3.824A pdb=" N LYS I 73 " --> pdb=" O THR I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 119 removed outlier: 4.107A pdb=" N ILE I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 126 Processing helix chain 'I' and resid 139 through 145 removed outlier: 3.964A pdb=" N ILE I 143 " --> pdb=" O GLY I 139 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP I 145 " --> pdb=" O ASP I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 154 removed outlier: 3.710A pdb=" N GLY I 150 " --> pdb=" O ARG I 146 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS I 152 " --> pdb=" O THR I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 20 removed outlier: 3.779A pdb=" N ILE J 12 " --> pdb=" O ASN J 8 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 31 Processing helix chain 'J' and resid 58 through 60 No H-bonds generated for 'chain 'J' and resid 58 through 60' Processing helix chain 'J' and resid 68 through 73 removed outlier: 3.824A pdb=" N LYS J 73 " --> pdb=" O THR J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 119 removed outlier: 4.107A pdb=" N ILE J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 126 Processing helix chain 'J' and resid 139 through 145 removed outlier: 3.965A pdb=" N ILE J 143 " --> pdb=" O GLY J 139 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP J 145 " --> pdb=" O ASP J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 154 removed outlier: 3.710A pdb=" N GLY J 150 " --> pdb=" O ARG J 146 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS J 152 " --> pdb=" O THR J 148 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.345A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.088A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.346A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.088A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.346A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.088A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.345A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.088A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.345A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.088A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'H' and resid 6 through 7 removed outlier: 7.400A pdb=" N THR H 6 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N VAL H 49 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL H 49 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU H 40 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N GLU H 51 " --> pdb=" O PHE H 38 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N PHE H 38 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LYS H 53 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL H 36 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE H 55 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS H 34 " --> pdb=" O ASP H 86 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR H 89 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N HIS H 133 " --> pdb=" O GLU H 97 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU H 99 " --> pdb=" O HIS H 133 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N TRP H 135 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE H 101 " --> pdb=" O TRP H 135 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL H 137 " --> pdb=" O PHE H 101 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE H 103 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 6 through 7 removed outlier: 7.400A pdb=" N THR H 6 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N VAL H 49 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL H 49 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU H 40 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N GLU H 51 " --> pdb=" O PHE H 38 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N PHE H 38 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LYS H 53 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL H 36 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE H 55 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS H 34 " --> pdb=" O ASP H 86 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR H 88 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU H 161 " --> pdb=" O THR H 88 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU H 90 " --> pdb=" O VAL H 159 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 6 through 7 removed outlier: 7.400A pdb=" N THR I 6 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N VAL I 49 " --> pdb=" O THR I 6 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL I 49 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU I 40 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N GLU I 51 " --> pdb=" O PHE I 38 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N PHE I 38 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LYS I 53 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL I 36 " --> pdb=" O LYS I 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE I 55 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS I 34 " --> pdb=" O ASP I 86 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR I 89 " --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N HIS I 133 " --> pdb=" O GLU I 97 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU I 99 " --> pdb=" O HIS I 133 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N TRP I 135 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE I 101 " --> pdb=" O TRP I 135 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL I 137 " --> pdb=" O PHE I 101 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE I 103 " --> pdb=" O VAL I 137 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 6 through 7 removed outlier: 7.400A pdb=" N THR I 6 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N VAL I 49 " --> pdb=" O THR I 6 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL I 49 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU I 40 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N GLU I 51 " --> pdb=" O PHE I 38 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N PHE I 38 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LYS I 53 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL I 36 " --> pdb=" O LYS I 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE I 55 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS I 34 " --> pdb=" O ASP I 86 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR I 88 " --> pdb=" O LEU I 161 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU I 161 " --> pdb=" O THR I 88 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU I 90 " --> pdb=" O VAL I 159 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 6 through 7 removed outlier: 7.401A pdb=" N THR J 6 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N VAL J 49 " --> pdb=" O THR J 6 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL J 49 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU J 40 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N GLU J 51 " --> pdb=" O PHE J 38 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N PHE J 38 " --> pdb=" O GLU J 51 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LYS J 53 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL J 36 " --> pdb=" O LYS J 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE J 55 " --> pdb=" O LYS J 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS J 34 " --> pdb=" O ASP J 86 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR J 89 " --> pdb=" O LYS J 96 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N HIS J 133 " --> pdb=" O GLU J 97 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU J 99 " --> pdb=" O HIS J 133 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N TRP J 135 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE J 101 " --> pdb=" O TRP J 135 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL J 137 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE J 103 " --> pdb=" O VAL J 137 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 6 through 7 removed outlier: 7.401A pdb=" N THR J 6 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N VAL J 49 " --> pdb=" O THR J 6 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL J 49 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU J 40 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N GLU J 51 " --> pdb=" O PHE J 38 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N PHE J 38 " --> pdb=" O GLU J 51 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LYS J 53 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL J 36 " --> pdb=" O LYS J 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE J 55 " --> pdb=" O LYS J 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS J 34 " --> pdb=" O ASP J 86 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR J 88 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU J 161 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU J 90 " --> pdb=" O VAL J 159 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1704 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: 3.34 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4541 1.35 - 1.47: 5585 1.47 - 1.59: 8196 1.59 - 1.71: 10 1.71 - 1.83: 183 Bond restraints: 18515 Sorted by residual: bond pdb=" C4 ADP C 402 " pdb=" C5 ADP C 402 " ideal model delta sigma weight residual 1.490 1.371 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C4 ADP B 402 " pdb=" C5 ADP B 402 " ideal model delta sigma weight residual 1.490 1.371 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C4 ADP A 402 " pdb=" C5 ADP A 402 " ideal model delta sigma weight residual 1.490 1.371 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C4 ADP D 402 " pdb=" C5 ADP D 402 " ideal model delta sigma weight residual 1.490 1.371 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C4 ADP E 402 " pdb=" C5 ADP E 402 " ideal model delta sigma weight residual 1.490 1.372 0.118 2.00e-02 2.50e+03 3.49e+01 ... (remaining 18510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 22746 3.07 - 6.14: 2232 6.14 - 9.21: 75 9.21 - 12.28: 15 12.28 - 15.35: 5 Bond angle restraints: 25073 Sorted by residual: angle pdb=" C ASN D 12 " pdb=" N GLY D 13 " pdb=" CA GLY D 13 " ideal model delta sigma weight residual 120.10 125.24 -5.14 9.50e-01 1.11e+00 2.93e+01 angle pdb=" C ASN B 12 " pdb=" N GLY B 13 " pdb=" CA GLY B 13 " ideal model delta sigma weight residual 120.10 125.23 -5.13 9.50e-01 1.11e+00 2.91e+01 angle pdb=" C ASN A 12 " pdb=" N GLY A 13 " pdb=" CA GLY A 13 " ideal model delta sigma weight residual 120.10 125.21 -5.11 9.50e-01 1.11e+00 2.89e+01 angle pdb=" C GLY H 4 " pdb=" N VAL H 5 " pdb=" CA VAL H 5 " ideal model delta sigma weight residual 120.49 127.89 -7.40 1.38e+00 5.25e-01 2.88e+01 angle pdb=" C ASN E 12 " pdb=" N GLY E 13 " pdb=" CA GLY E 13 " ideal model delta sigma weight residual 120.10 125.20 -5.10 9.50e-01 1.11e+00 2.88e+01 ... (remaining 25068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.76: 10812 22.76 - 45.52: 321 45.52 - 68.28: 66 68.28 - 91.04: 23 91.04 - 113.80: 5 Dihedral angle restraints: 11227 sinusoidal: 4578 harmonic: 6649 Sorted by residual: dihedral pdb=" C5' ADP D 402 " pdb=" O5' ADP D 402 " pdb=" PA ADP D 402 " pdb=" O2A ADP D 402 " ideal model delta sinusoidal sigma weight residual -60.00 53.80 -113.80 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" C5' ADP E 402 " pdb=" O5' ADP E 402 " pdb=" PA ADP E 402 " pdb=" O2A ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 53.77 -113.77 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" C5' ADP A 402 " pdb=" O5' ADP A 402 " pdb=" PA ADP A 402 " pdb=" O2A ADP A 402 " ideal model delta sinusoidal sigma weight residual -60.00 53.77 -113.77 1 2.00e+01 2.50e-03 3.37e+01 ... (remaining 11224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1898 0.088 - 0.177: 793 0.177 - 0.265: 89 0.265 - 0.354: 16 0.354 - 0.442: 13 Chirality restraints: 2809 Sorted by residual: chirality pdb=" C3' ADP D 402 " pdb=" C2' ADP D 402 " pdb=" C4' ADP D 402 " pdb=" O3' ADP D 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.95 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" C3' ADP C 402 " pdb=" C2' ADP C 402 " pdb=" C4' ADP C 402 " pdb=" O3' ADP C 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.95 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C3' ADP A 402 " pdb=" C2' ADP A 402 " pdb=" C4' ADP A 402 " pdb=" O3' ADP A 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.95 0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 2806 not shown) Planarity restraints: 3184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 340 " -0.145 2.00e-02 2.50e+03 6.78e-02 1.15e+02 pdb=" CG TRP C 340 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP C 340 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C 340 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP C 340 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP C 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 340 " 0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 340 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 340 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP C 340 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " -0.145 2.00e-02 2.50e+03 6.78e-02 1.15e+02 pdb=" CG TRP B 340 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " 0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 340 " -0.145 2.00e-02 2.50e+03 6.78e-02 1.15e+02 pdb=" CG TRP A 340 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 340 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 340 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP A 340 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 340 " 0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 340 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 340 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP A 340 " -0.056 2.00e-02 2.50e+03 ... (remaining 3181 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 15 2.45 - 3.06: 9524 3.06 - 3.67: 25741 3.67 - 4.29: 40456 4.29 - 4.90: 66729 Nonbonded interactions: 142465 Sorted by model distance: nonbonded pdb=" OG SER B 14 " pdb=" O3B ADP B 402 " model vdw 1.834 3.040 nonbonded pdb=" OG SER A 14 " pdb=" O3B ADP A 402 " model vdw 1.834 3.040 nonbonded pdb=" OG SER E 14 " pdb=" O3B ADP E 402 " model vdw 1.834 3.040 nonbonded pdb=" OG SER D 14 " pdb=" O3B ADP D 402 " model vdw 1.835 3.040 nonbonded pdb=" OG SER C 14 " pdb=" O3B ADP C 402 " model vdw 1.835 3.040 ... (remaining 142460 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.690 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.014 0.119 18515 Z= 0.813 Angle : 1.858 15.348 25073 Z= 1.234 Chirality : 0.092 0.442 2809 Planarity : 0.024 0.228 3184 Dihedral : 12.632 113.798 6947 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.53 % Favored : 97.25 % Rotamer: Outliers : 0.25 % Allowed : 1.32 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.15), residues: 2256 helix: -3.97 (0.09), residues: 832 sheet: -1.82 (0.22), residues: 435 loop : -0.46 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG H 146 TYR 0.093 0.015 TYR I 117 PHE 0.059 0.009 PHE I 71 TRP 0.145 0.025 TRP B 340 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.01435 (18515) covalent geometry : angle 1.85830 (25073) hydrogen bonds : bond 0.30138 ( 637) hydrogen bonds : angle 9.68139 ( 1704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 566 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 71 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 82 MET cc_start: 0.9465 (tpt) cc_final: 0.8628 (tpt) REVERT: B 136 ILE cc_start: 0.9432 (mm) cc_final: 0.9229 (mm) REVERT: C 82 MET cc_start: 0.9501 (tpt) cc_final: 0.8832 (tpt) REVERT: C 111 ASN cc_start: 0.8908 (t0) cc_final: 0.8627 (t0) REVERT: D 111 ASN cc_start: 0.8939 (t0) cc_final: 0.8359 (t0) REVERT: E 78 ASN cc_start: 0.8045 (t0) cc_final: 0.7832 (t0) REVERT: E 111 ASN cc_start: 0.8712 (t0) cc_final: 0.7832 (t0) REVERT: E 159 VAL cc_start: 0.9130 (p) cc_final: 0.8896 (m) REVERT: H 81 ARG cc_start: 0.8856 (mmt-90) cc_final: 0.8538 (mmt-90) REVERT: H 143 ILE cc_start: 0.9065 (tt) cc_final: 0.8853 (tt) REVERT: I 54 GLN cc_start: 0.7630 (pt0) cc_final: 0.7385 (pt0) REVERT: I 81 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.7831 (mmt-90) REVERT: J 81 ARG cc_start: 0.8778 (mmt-90) cc_final: 0.8150 (mpt180) REVERT: J 143 ILE cc_start: 0.9011 (tt) cc_final: 0.8746 (tt) outliers start: 5 outliers final: 0 residues processed: 566 average time/residue: 0.1370 time to fit residues: 119.1355 Evaluate side-chains 336 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 115 ASN A 162 ASN A 353 GLN B 12 ASN B 87 HIS B 115 ASN B 162 ASN B 353 GLN B 360 GLN C 12 ASN C 87 HIS C 162 ASN C 371 HIS D 12 ASN D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 353 GLN E 12 ASN E 87 HIS E 162 ASN E 353 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.108616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.097189 restraints weight = 23841.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.098687 restraints weight = 16964.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.099799 restraints weight = 13137.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.100555 restraints weight = 10808.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.101222 restraints weight = 9441.471| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18515 Z= 0.133 Angle : 0.631 9.471 25073 Z= 0.319 Chirality : 0.046 0.164 2809 Planarity : 0.005 0.037 3184 Dihedral : 6.391 69.685 2536 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.88 % Allowed : 8.69 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.16), residues: 2256 helix: -2.96 (0.13), residues: 876 sheet: -1.05 (0.24), residues: 453 loop : 0.23 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 210 TYR 0.011 0.001 TYR H 85 PHE 0.009 0.001 PHE I 38 TRP 0.022 0.002 TRP D 340 HIS 0.003 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00301 (18515) covalent geometry : angle 0.63140 (25073) hydrogen bonds : bond 0.03999 ( 637) hydrogen bonds : angle 5.64735 ( 1704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 347 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.9508 (mm) cc_final: 0.9166 (mm) REVERT: A 296 ASN cc_start: 0.8937 (m-40) cc_final: 0.8721 (m-40) REVERT: B 136 ILE cc_start: 0.9547 (mm) cc_final: 0.9231 (mt) REVERT: B 313 MET cc_start: 0.8460 (tpp) cc_final: 0.8213 (mmm) REVERT: B 344 SER cc_start: 0.9243 (t) cc_final: 0.9039 (t) REVERT: C 206 ARG cc_start: 0.7717 (ttt-90) cc_final: 0.7317 (tpp80) REVERT: C 283 MET cc_start: 0.8700 (mmt) cc_final: 0.8420 (mmt) REVERT: D 335 ARG cc_start: 0.9220 (ptt-90) cc_final: 0.8958 (ptt-90) REVERT: E 68 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7785 (mttp) REVERT: E 136 ILE cc_start: 0.9329 (mm) cc_final: 0.8982 (mt) REVERT: E 159 VAL cc_start: 0.9161 (p) cc_final: 0.8952 (m) REVERT: H 23 SER cc_start: 0.8934 (p) cc_final: 0.8560 (p) REVERT: H 143 ILE cc_start: 0.9020 (tt) cc_final: 0.8751 (tt) REVERT: I 115 MET cc_start: 0.8527 (tpp) cc_final: 0.8244 (tpp) REVERT: I 162 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7079 (mm-30) REVERT: J 81 ARG cc_start: 0.8773 (mmt-90) cc_final: 0.8559 (mmt90) REVERT: J 143 ILE cc_start: 0.9009 (tt) cc_final: 0.8614 (tt) REVERT: J 149 LEU cc_start: 0.8710 (tt) cc_final: 0.8460 (tp) REVERT: J 162 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6981 (mm-30) outliers start: 37 outliers final: 18 residues processed: 362 average time/residue: 0.1312 time to fit residues: 74.6776 Evaluate side-chains 305 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 287 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain J residue 23 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 217 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 353 GLN B 115 ASN C 275 HIS D 275 HIS E 59 GLN H 78 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.100402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.088549 restraints weight = 25352.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.089870 restraints weight = 20785.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.090823 restraints weight = 15083.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.091389 restraints weight = 12038.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.092434 restraints weight = 10591.795| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 18515 Z= 0.237 Angle : 0.694 8.012 25073 Z= 0.349 Chirality : 0.050 0.177 2809 Planarity : 0.005 0.040 3184 Dihedral : 6.019 51.711 2534 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.59 % Allowed : 11.28 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.17), residues: 2256 helix: -2.63 (0.14), residues: 919 sheet: -0.90 (0.24), residues: 486 loop : 0.14 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 81 TYR 0.015 0.002 TYR D 218 PHE 0.015 0.002 PHE H 38 TRP 0.019 0.002 TRP B 340 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00572 (18515) covalent geometry : angle 0.69420 (25073) hydrogen bonds : bond 0.04542 ( 637) hydrogen bonds : angle 5.41661 ( 1704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8338 (t0) cc_final: 0.8097 (t0) REVERT: A 136 ILE cc_start: 0.9606 (mm) cc_final: 0.9330 (mm) REVERT: B 24 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: B 115 ASN cc_start: 0.8234 (t0) cc_final: 0.7925 (t0) REVERT: B 132 MET cc_start: 0.7812 (tmm) cc_final: 0.7575 (tmm) REVERT: C 132 MET cc_start: 0.7993 (tmm) cc_final: 0.7770 (tmm) REVERT: D 132 MET cc_start: 0.7926 (tmm) cc_final: 0.7560 (tmm) REVERT: D 305 MET cc_start: 0.8334 (mmm) cc_final: 0.8072 (mmm) REVERT: E 68 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7963 (mttp) REVERT: E 136 ILE cc_start: 0.9577 (mm) cc_final: 0.9216 (mt) REVERT: H 17 ASP cc_start: 0.7926 (t0) cc_final: 0.7695 (t0) REVERT: H 81 ARG cc_start: 0.8781 (mmt-90) cc_final: 0.8444 (mmt90) REVERT: H 143 ILE cc_start: 0.9143 (tt) cc_final: 0.8803 (tt) REVERT: J 17 ASP cc_start: 0.7791 (t0) cc_final: 0.7501 (t0) REVERT: J 28 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7757 (tm-30) REVERT: J 79 ASP cc_start: 0.8314 (t0) cc_final: 0.7606 (m-30) REVERT: J 143 ILE cc_start: 0.9031 (tt) cc_final: 0.8819 (tt) outliers start: 51 outliers final: 34 residues processed: 364 average time/residue: 0.1276 time to fit residues: 73.4351 Evaluate side-chains 310 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 275 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS B 101 HIS B 161 HIS C 101 HIS C 275 HIS D 101 HIS D 115 ASN E 101 HIS I 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.098938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.086649 restraints weight = 25491.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.088211 restraints weight = 17927.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.089454 restraints weight = 13746.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.090236 restraints weight = 11307.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.090875 restraints weight = 9807.554| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 18515 Z= 0.253 Angle : 0.684 8.982 25073 Z= 0.342 Chirality : 0.050 0.195 2809 Planarity : 0.004 0.043 3184 Dihedral : 5.905 43.299 2534 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.00 % Allowed : 13.36 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.17), residues: 2256 helix: -2.37 (0.14), residues: 899 sheet: -0.43 (0.25), residues: 416 loop : 0.26 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 210 TYR 0.016 0.002 TYR B 218 PHE 0.012 0.002 PHE J 38 TRP 0.017 0.002 TRP B 340 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00613 (18515) covalent geometry : angle 0.68438 (25073) hydrogen bonds : bond 0.04204 ( 637) hydrogen bonds : angle 5.32526 ( 1704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9235 (tpt) cc_final: 0.8799 (mmm) REVERT: A 136 ILE cc_start: 0.9598 (mm) cc_final: 0.9329 (mm) REVERT: B 24 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: B 115 ASN cc_start: 0.8168 (t0) cc_final: 0.7809 (t0) REVERT: B 132 MET cc_start: 0.7812 (tmm) cc_final: 0.7434 (tmm) REVERT: B 205 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: B 210 ARG cc_start: 0.8634 (tmm-80) cc_final: 0.8209 (ttp80) REVERT: C 34 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8809 (tt) REVERT: C 132 MET cc_start: 0.7957 (tmm) cc_final: 0.7712 (tmm) REVERT: C 283 MET cc_start: 0.8812 (mmt) cc_final: 0.8594 (mmt) REVERT: C 334 GLU cc_start: 0.8339 (pm20) cc_final: 0.8084 (pp20) REVERT: D 54 VAL cc_start: 0.9360 (t) cc_final: 0.9144 (m) REVERT: D 68 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8245 (mttm) REVERT: D 132 MET cc_start: 0.7940 (tmm) cc_final: 0.7599 (tmm) REVERT: D 205 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7346 (mt-10) REVERT: E 54 VAL cc_start: 0.9263 (t) cc_final: 0.9058 (m) REVERT: E 136 ILE cc_start: 0.9626 (mm) cc_final: 0.9264 (mt) REVERT: E 334 GLU cc_start: 0.8283 (pm20) cc_final: 0.8021 (pp20) REVERT: H 31 LYS cc_start: 0.8282 (mptt) cc_final: 0.7630 (mttm) REVERT: H 122 ASP cc_start: 0.8287 (t0) cc_final: 0.8041 (t0) REVERT: H 143 ILE cc_start: 0.9213 (tt) cc_final: 0.8875 (tt) REVERT: J 143 ILE cc_start: 0.9030 (tt) cc_final: 0.8809 (tt) REVERT: J 149 LEU cc_start: 0.9145 (tt) cc_final: 0.8906 (tp) outliers start: 59 outliers final: 39 residues processed: 324 average time/residue: 0.1293 time to fit residues: 66.6336 Evaluate side-chains 314 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 0 optimal weight: 5.9990 chunk 193 optimal weight: 0.0980 chunk 160 optimal weight: 5.9990 chunk 74 optimal weight: 0.0170 chunk 59 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.0370 chunk 43 optimal weight: 4.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 115 ASN B 275 HIS C 275 HIS I 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.106478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.094550 restraints weight = 24074.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.096203 restraints weight = 16609.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.097442 restraints weight = 12639.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.098307 restraints weight = 10319.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.098973 restraints weight = 8853.133| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18515 Z= 0.085 Angle : 0.541 8.060 25073 Z= 0.265 Chirality : 0.043 0.199 2809 Planarity : 0.003 0.034 3184 Dihedral : 5.086 37.561 2534 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.07 % Allowed : 15.24 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2256 helix: -1.79 (0.16), residues: 899 sheet: -0.33 (0.25), residues: 434 loop : 0.72 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 210 TYR 0.008 0.001 TYR D 279 PHE 0.008 0.001 PHE C 352 TRP 0.009 0.001 TRP E 356 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00183 (18515) covalent geometry : angle 0.54067 (25073) hydrogen bonds : bond 0.02696 ( 637) hydrogen bonds : angle 4.73072 ( 1704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 326 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.9472 (mm) cc_final: 0.9149 (mm) REVERT: B 93 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7519 (mm-30) REVERT: B 132 MET cc_start: 0.7712 (tmm) cc_final: 0.7288 (tmm) REVERT: B 253 GLU cc_start: 0.8226 (mp0) cc_final: 0.7926 (mt-10) REVERT: C 82 MET cc_start: 0.9374 (tpt) cc_final: 0.8997 (tpt) REVERT: C 113 LYS cc_start: 0.8769 (mttt) cc_final: 0.8315 (mttm) REVERT: C 132 MET cc_start: 0.7796 (tmm) cc_final: 0.7530 (tmm) REVERT: D 68 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8368 (mttm) REVERT: D 132 MET cc_start: 0.7897 (tmm) cc_final: 0.7480 (tmm) REVERT: E 68 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8127 (mttp) REVERT: E 136 ILE cc_start: 0.9527 (mm) cc_final: 0.9109 (mt) REVERT: E 334 GLU cc_start: 0.8008 (pm20) cc_final: 0.7736 (pp20) REVERT: H 31 LYS cc_start: 0.8182 (mptt) cc_final: 0.7512 (mttm) REVERT: H 143 ILE cc_start: 0.9105 (tt) cc_final: 0.8628 (tt) REVERT: I 45 LYS cc_start: 0.8815 (mttt) cc_final: 0.8569 (ttmt) REVERT: I 78 ASN cc_start: 0.8423 (m110) cc_final: 0.7700 (m-40) REVERT: I 79 ASP cc_start: 0.8306 (t0) cc_final: 0.7564 (m-30) REVERT: J 28 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7771 (tm-30) REVERT: J 30 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7893 (mmmt) REVERT: J 31 LYS cc_start: 0.8199 (mptt) cc_final: 0.7662 (mttm) REVERT: J 86 ASP cc_start: 0.8285 (t0) cc_final: 0.8063 (t0) REVERT: J 98 ASP cc_start: 0.8038 (t0) cc_final: 0.7757 (t0) REVERT: J 149 LEU cc_start: 0.9009 (tt) cc_final: 0.8731 (tp) outliers start: 21 outliers final: 9 residues processed: 338 average time/residue: 0.1290 time to fit residues: 68.8750 Evaluate side-chains 282 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 273 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain J residue 18 MET Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 88 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 108 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.102655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.090850 restraints weight = 24626.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.092412 restraints weight = 17280.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.093635 restraints weight = 13204.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.094538 restraints weight = 10828.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.095168 restraints weight = 9247.832| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18515 Z= 0.161 Angle : 0.600 10.501 25073 Z= 0.293 Chirality : 0.046 0.203 2809 Planarity : 0.004 0.034 3184 Dihedral : 5.181 37.186 2534 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.93 % Allowed : 16.11 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.18), residues: 2256 helix: -1.68 (0.16), residues: 894 sheet: -0.23 (0.26), residues: 416 loop : 0.62 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 81 TYR 0.010 0.001 TYR B 218 PHE 0.009 0.001 PHE J 101 TRP 0.016 0.002 TRP B 340 HIS 0.008 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00388 (18515) covalent geometry : angle 0.59982 (25073) hydrogen bonds : bond 0.03424 ( 637) hydrogen bonds : angle 4.84248 ( 1704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.9571 (mm) cc_final: 0.9300 (mm) REVERT: B 24 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: B 93 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7535 (mm-30) REVERT: B 115 ASN cc_start: 0.8030 (t0) cc_final: 0.7688 (t0) REVERT: B 132 MET cc_start: 0.7746 (tmm) cc_final: 0.7441 (tmm) REVERT: B 206 ARG cc_start: 0.8169 (ttt-90) cc_final: 0.7661 (tpp80) REVERT: C 113 LYS cc_start: 0.8732 (mttt) cc_final: 0.8336 (mttm) REVERT: D 68 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8326 (mttm) REVERT: D 132 MET cc_start: 0.7914 (tmm) cc_final: 0.7481 (tmm) REVERT: E 136 ILE cc_start: 0.9610 (mm) cc_final: 0.9224 (mt) REVERT: H 31 LYS cc_start: 0.8246 (mptt) cc_final: 0.7547 (mttm) REVERT: H 143 ILE cc_start: 0.9245 (tt) cc_final: 0.8881 (tt) REVERT: J 31 LYS cc_start: 0.8176 (mptt) cc_final: 0.7667 (mttm) REVERT: J 98 ASP cc_start: 0.8087 (t0) cc_final: 0.7875 (t0) REVERT: J 143 ILE cc_start: 0.9060 (tt) cc_final: 0.8837 (tt) REVERT: J 149 LEU cc_start: 0.9110 (tt) cc_final: 0.8793 (tp) outliers start: 38 outliers final: 23 residues processed: 296 average time/residue: 0.1251 time to fit residues: 59.3073 Evaluate side-chains 288 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 88 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 195 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 175 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 133 HIS I 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.103129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.091498 restraints weight = 24651.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.093037 restraints weight = 17436.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.094233 restraints weight = 13387.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.094986 restraints weight = 11019.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.095621 restraints weight = 9553.623| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18515 Z= 0.144 Angle : 0.587 9.712 25073 Z= 0.286 Chirality : 0.045 0.218 2809 Planarity : 0.003 0.033 3184 Dihedral : 5.084 34.882 2534 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.68 % Allowed : 16.36 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.18), residues: 2256 helix: -1.55 (0.16), residues: 894 sheet: -0.20 (0.26), residues: 416 loop : 0.58 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 81 TYR 0.009 0.001 TYR C 306 PHE 0.007 0.001 PHE H 101 TRP 0.013 0.001 TRP B 340 HIS 0.007 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00347 (18515) covalent geometry : angle 0.58651 (25073) hydrogen bonds : bond 0.03219 ( 637) hydrogen bonds : angle 4.80437 ( 1704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 136 ILE cc_start: 0.9568 (mm) cc_final: 0.9297 (mm) REVERT: B 24 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: B 93 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7606 (mm-30) REVERT: B 115 ASN cc_start: 0.7989 (t0) cc_final: 0.7664 (t0) REVERT: B 132 MET cc_start: 0.7730 (tmm) cc_final: 0.7511 (tmm) REVERT: B 205 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: B 206 ARG cc_start: 0.8143 (ttt-90) cc_final: 0.7682 (tpp80) REVERT: B 292 ASP cc_start: 0.8388 (t0) cc_final: 0.7910 (t0) REVERT: C 113 LYS cc_start: 0.8782 (mttt) cc_final: 0.8380 (mttm) REVERT: D 68 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8321 (mttm) REVERT: D 132 MET cc_start: 0.7904 (tmm) cc_final: 0.7591 (tmm) REVERT: D 167 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7726 (mm-30) REVERT: E 136 ILE cc_start: 0.9607 (mm) cc_final: 0.9239 (mt) REVERT: H 28 GLU cc_start: 0.8562 (tm-30) cc_final: 0.7804 (tm-30) REVERT: H 31 LYS cc_start: 0.8231 (mptt) cc_final: 0.7572 (mttm) REVERT: H 143 ILE cc_start: 0.9206 (tt) cc_final: 0.8786 (tt) REVERT: J 31 LYS cc_start: 0.8110 (mptt) cc_final: 0.7648 (mttm) REVERT: J 45 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8424 (ttmm) REVERT: J 98 ASP cc_start: 0.8082 (t0) cc_final: 0.7877 (t0) REVERT: J 143 ILE cc_start: 0.9082 (tt) cc_final: 0.8854 (tt) REVERT: J 149 LEU cc_start: 0.9099 (tt) cc_final: 0.8793 (tp) outliers start: 33 outliers final: 26 residues processed: 290 average time/residue: 0.1248 time to fit residues: 57.5452 Evaluate side-chains 290 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 88 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 112 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 184 optimal weight: 0.0270 chunk 180 optimal weight: 1.9990 overall best weight: 1.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.104244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.092256 restraints weight = 24499.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.093837 restraints weight = 17108.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.095142 restraints weight = 13127.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.096079 restraints weight = 10683.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.096591 restraints weight = 9152.341| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18515 Z= 0.132 Angle : 0.582 9.133 25073 Z= 0.282 Chirality : 0.045 0.225 2809 Planarity : 0.003 0.033 3184 Dihedral : 5.002 33.950 2534 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.83 % Allowed : 16.82 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 2256 helix: -1.41 (0.16), residues: 894 sheet: -0.16 (0.26), residues: 416 loop : 0.56 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.010 0.001 TYR E 169 PHE 0.007 0.001 PHE H 101 TRP 0.013 0.001 TRP B 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00319 (18515) covalent geometry : angle 0.58169 (25073) hydrogen bonds : bond 0.03121 ( 637) hydrogen bonds : angle 4.75970 ( 1704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 136 ILE cc_start: 0.9550 (mm) cc_final: 0.9285 (mm) REVERT: B 24 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: B 93 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7524 (mm-30) REVERT: B 115 ASN cc_start: 0.7988 (t0) cc_final: 0.7672 (t0) REVERT: B 132 MET cc_start: 0.7831 (tmm) cc_final: 0.7491 (tmm) REVERT: B 206 ARG cc_start: 0.8141 (ttt-90) cc_final: 0.7713 (tpp80) REVERT: B 253 GLU cc_start: 0.8231 (mp0) cc_final: 0.7989 (mt-10) REVERT: B 292 ASP cc_start: 0.8393 (t0) cc_final: 0.8155 (t0) REVERT: C 113 LYS cc_start: 0.8787 (mttt) cc_final: 0.8351 (mttm) REVERT: D 68 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8408 (mttm) REVERT: D 132 MET cc_start: 0.7945 (tmm) cc_final: 0.7587 (tmm) REVERT: D 167 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7714 (mm-30) REVERT: E 136 ILE cc_start: 0.9605 (mm) cc_final: 0.9248 (mt) REVERT: E 334 GLU cc_start: 0.8048 (pp20) cc_final: 0.7818 (pp20) REVERT: E 364 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: H 28 GLU cc_start: 0.8521 (tm-30) cc_final: 0.7840 (tm-30) REVERT: H 31 LYS cc_start: 0.8208 (mptt) cc_final: 0.7525 (mttm) REVERT: H 143 ILE cc_start: 0.9153 (tt) cc_final: 0.8773 (tt) REVERT: J 30 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7675 (tttt) REVERT: J 31 LYS cc_start: 0.8117 (mptt) cc_final: 0.7665 (mttm) REVERT: J 45 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8370 (ttmm) REVERT: J 98 ASP cc_start: 0.8061 (t0) cc_final: 0.7764 (t0) REVERT: J 143 ILE cc_start: 0.9082 (tt) cc_final: 0.8844 (tt) REVERT: J 149 LEU cc_start: 0.9053 (tt) cc_final: 0.8774 (tp) outliers start: 36 outliers final: 28 residues processed: 292 average time/residue: 0.1255 time to fit residues: 57.7005 Evaluate side-chains 288 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 88 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 88 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 HIS I 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.101923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.089976 restraints weight = 24672.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.091611 restraints weight = 17164.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.092829 restraints weight = 13062.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.093750 restraints weight = 10605.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.094365 restraints weight = 9117.567| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18515 Z= 0.190 Angle : 0.639 10.096 25073 Z= 0.311 Chirality : 0.047 0.238 2809 Planarity : 0.004 0.034 3184 Dihedral : 5.246 33.356 2534 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.83 % Allowed : 17.33 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 2256 helix: -1.50 (0.16), residues: 894 sheet: -0.18 (0.26), residues: 416 loop : 0.41 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 210 TYR 0.012 0.001 TYR E 133 PHE 0.009 0.001 PHE J 101 TRP 0.013 0.001 TRP B 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00463 (18515) covalent geometry : angle 0.63884 (25073) hydrogen bonds : bond 0.03564 ( 637) hydrogen bonds : angle 4.92856 ( 1704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 136 ILE cc_start: 0.9575 (mm) cc_final: 0.9320 (mm) REVERT: B 24 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: B 93 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7605 (mm-30) REVERT: B 115 ASN cc_start: 0.8144 (t0) cc_final: 0.7791 (t0) REVERT: B 132 MET cc_start: 0.7807 (tmm) cc_final: 0.7539 (tmm) REVERT: B 205 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: B 292 ASP cc_start: 0.8506 (t0) cc_final: 0.8213 (t0) REVERT: B 313 MET cc_start: 0.8764 (tpp) cc_final: 0.8514 (tpp) REVERT: C 34 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8787 (tt) REVERT: C 113 LYS cc_start: 0.8780 (mttt) cc_final: 0.8371 (mttm) REVERT: D 132 MET cc_start: 0.8013 (tmm) cc_final: 0.7812 (tmm) REVERT: D 167 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7790 (mm-30) REVERT: E 136 ILE cc_start: 0.9633 (mm) cc_final: 0.9317 (mt) REVERT: H 28 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8057 (tm-30) REVERT: H 31 LYS cc_start: 0.8190 (mptt) cc_final: 0.7526 (mttm) REVERT: H 143 ILE cc_start: 0.9158 (tt) cc_final: 0.8776 (tt) REVERT: I 45 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8539 (ttmt) REVERT: J 31 LYS cc_start: 0.8148 (mptt) cc_final: 0.7716 (mttm) REVERT: J 45 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8423 (ttmm) outliers start: 36 outliers final: 29 residues processed: 294 average time/residue: 0.1281 time to fit residues: 59.2915 Evaluate side-chains 293 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 18 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.104503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.092594 restraints weight = 24457.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.094293 restraints weight = 17009.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.095568 restraints weight = 12871.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.096467 restraints weight = 10456.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.097089 restraints weight = 8978.586| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18515 Z= 0.123 Angle : 0.590 11.228 25073 Z= 0.285 Chirality : 0.045 0.228 2809 Planarity : 0.003 0.041 3184 Dihedral : 4.964 32.282 2534 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.37 % Allowed : 18.09 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2256 helix: -1.32 (0.17), residues: 894 sheet: -0.13 (0.26), residues: 416 loop : 0.48 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 81 TYR 0.009 0.001 TYR E 133 PHE 0.007 0.001 PHE A 90 TRP 0.011 0.001 TRP B 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00294 (18515) covalent geometry : angle 0.59040 (25073) hydrogen bonds : bond 0.03046 ( 637) hydrogen bonds : angle 4.75770 ( 1704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8260 (mttt) REVERT: A 136 ILE cc_start: 0.9536 (mm) cc_final: 0.9266 (mm) REVERT: B 24 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: B 93 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 115 ASN cc_start: 0.8053 (t0) cc_final: 0.7733 (t0) REVERT: B 132 MET cc_start: 0.7776 (tmm) cc_final: 0.7433 (tmm) REVERT: B 253 GLU cc_start: 0.8172 (mp0) cc_final: 0.7940 (mt-10) REVERT: B 292 ASP cc_start: 0.8433 (t0) cc_final: 0.8212 (t0) REVERT: B 313 MET cc_start: 0.8711 (tpp) cc_final: 0.8473 (tpp) REVERT: C 113 LYS cc_start: 0.8786 (mttt) cc_final: 0.8388 (mttm) REVERT: D 68 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8328 (mttm) REVERT: D 132 MET cc_start: 0.7967 (tmm) cc_final: 0.7645 (tmm) REVERT: D 167 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7709 (mm-30) REVERT: E 136 ILE cc_start: 0.9602 (mm) cc_final: 0.9272 (mt) REVERT: H 31 LYS cc_start: 0.8192 (mptt) cc_final: 0.7526 (mttm) REVERT: H 143 ILE cc_start: 0.9121 (tt) cc_final: 0.8753 (tt) REVERT: I 45 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8504 (ttmt) REVERT: J 28 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7988 (tm-30) REVERT: J 30 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7674 (tttt) REVERT: J 31 LYS cc_start: 0.8140 (mptt) cc_final: 0.7680 (mttm) REVERT: J 45 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8332 (ttmm) outliers start: 27 outliers final: 21 residues processed: 280 average time/residue: 0.1332 time to fit residues: 58.2625 Evaluate side-chains 282 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 196 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.105611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.093897 restraints weight = 24303.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.095574 restraints weight = 17078.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.096861 restraints weight = 12924.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.097668 restraints weight = 10505.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.098383 restraints weight = 9029.076| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18515 Z= 0.110 Angle : 0.577 12.177 25073 Z= 0.277 Chirality : 0.044 0.225 2809 Planarity : 0.003 0.031 3184 Dihedral : 4.805 32.244 2534 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.42 % Allowed : 18.29 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.18), residues: 2256 helix: -1.11 (0.17), residues: 879 sheet: -0.07 (0.26), residues: 416 loop : 0.57 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 81 TYR 0.009 0.001 TYR E 133 PHE 0.007 0.001 PHE A 90 TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00263 (18515) covalent geometry : angle 0.57664 (25073) hydrogen bonds : bond 0.02918 ( 637) hydrogen bonds : angle 4.65769 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2766.45 seconds wall clock time: 48 minutes 47.00 seconds (2927.00 seconds total)