Starting phenix.real_space_refine on Sat Jun 7 13:35:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wv9_32850/06_2025/7wv9_32850.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wv9_32850/06_2025/7wv9_32850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wv9_32850/06_2025/7wv9_32850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wv9_32850/06_2025/7wv9_32850.map" model { file = "/net/cci-nas-00/data/ceres_data/7wv9_32850/06_2025/7wv9_32850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wv9_32850/06_2025/7wv9_32850.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 26 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5660 2.51 5 N 1508 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8848 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1732 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2583 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 434 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2306 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1740 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'7IC': 1, '9GF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.08, per 1000 atoms: 0.57 Number of scatterers: 8848 At special positions: 0 Unit cell: (130.05, 113.9, 109.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1614 8.00 N 1508 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 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: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 38.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.756A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.563A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.509A pdb=" N CYS A 215 " --> pdb=" O TRP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.999A pdb=" N ALA A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.993A pdb=" N THR A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 283 through 288 removed outlier: 4.271A pdb=" N CYS A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.144A pdb=" N ALA A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.595A pdb=" N LYS A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.658A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.890A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.889A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.609A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 142 removed outlier: 4.134A pdb=" N ALA R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 149 Processing helix chain 'R' and resid 150 through 179 removed outlier: 3.620A pdb=" N HIS R 154 " --> pdb=" O ARG R 150 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL R 168 " --> pdb=" O LEU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 220 removed outlier: 4.043A pdb=" N GLY R 195 " --> pdb=" O PHE R 191 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL R 196 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR R 197 " --> pdb=" O LEU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 228 removed outlier: 3.507A pdb=" N VAL R 228 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 255 Proline residue: R 251 - end of helix removed outlier: 3.654A pdb=" N GLY R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 312 removed outlier: 3.605A pdb=" N TRP R 279 " --> pdb=" O TYR R 275 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE R 280 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY R 312 " --> pdb=" O MET R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 357 removed outlier: 4.397A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE R 348 " --> pdb=" O THR R 344 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU R 349 " --> pdb=" O LEU R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 369 removed outlier: 4.064A pdb=" N VAL R 364 " --> pdb=" O LEU R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 372 through 398 removed outlier: 4.259A pdb=" N LYS R 376 " --> pdb=" O ASN R 372 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR R 377 " --> pdb=" O LYS R 373 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS R 386 " --> pdb=" O CYS R 382 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER R 390 " --> pdb=" O CYS R 386 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 401 through 411 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.220A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 74 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 6.753A pdb=" N VAL A 34 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N ALA A 221 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.135A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.015A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 4.153A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 150 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.605A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.086A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.569A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 317 removed outlier: 3.997A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7 removed outlier: 4.318A pdb=" N LEU S 79 " --> pdb=" O CYS S 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.150A pdb=" N MET S 93 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR S 59 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AB4, first strand: chain 'S' and resid 173 through 174 387 hydrogen bonds defined for protein. 1092 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: 2.56 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1404 1.30 - 1.43: 2415 1.43 - 1.56: 5114 1.56 - 1.68: 3 1.68 - 1.81: 98 Bond restraints: 9034 Sorted by residual: bond pdb=" N2 7IC R 502 " pdb=" O1 7IC R 502 " ideal model delta sigma weight residual 1.220 1.402 -0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C16 7IC R 502 " pdb=" C7 7IC R 502 " ideal model delta sigma weight residual 1.463 1.384 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" N TRP R 356 " pdb=" CA TRP R 356 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.16e-02 7.43e+03 1.41e+01 bond pdb=" C ALA A 13 " pdb=" O ALA A 13 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.34e-02 5.57e+03 8.80e+00 bond pdb=" C7 7IC R 502 " pdb=" N8 7IC R 502 " ideal model delta sigma weight residual 1.382 1.323 0.059 2.00e-02 2.50e+03 8.77e+00 ... (remaining 9029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 12202 4.36 - 8.72: 41 8.72 - 13.07: 1 13.07 - 17.43: 1 17.43 - 21.79: 1 Bond angle restraints: 12246 Sorted by residual: angle pdb=" CAM 9GF R 501 " pdb=" CAN 9GF R 501 " pdb=" CAO 9GF R 501 " ideal model delta sigma weight residual 110.47 88.68 21.79 3.00e+00 1.11e-01 5.28e+01 angle pdb=" N GLU A 14 " pdb=" CA GLU A 14 " pdb=" C GLU A 14 " ideal model delta sigma weight residual 113.50 105.96 7.54 1.23e+00 6.61e-01 3.75e+01 angle pdb=" N MET A 248 " pdb=" CA MET A 248 " pdb=" C MET A 248 " ideal model delta sigma weight residual 111.07 105.48 5.59 1.07e+00 8.73e-01 2.73e+01 angle pdb=" CAM 9GF R 501 " pdb=" CAN 9GF R 501 " pdb=" CAT 9GF R 501 " ideal model delta sigma weight residual 112.87 127.31 -14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" N ALA A 13 " pdb=" CA ALA A 13 " pdb=" C ALA A 13 " ideal model delta sigma weight residual 112.92 107.02 5.90 1.23e+00 6.61e-01 2.30e+01 ... (remaining 12241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 5218 32.69 - 65.37: 122 65.37 - 98.06: 17 98.06 - 130.75: 0 130.75 - 163.43: 7 Dihedral angle restraints: 5364 sinusoidal: 2053 harmonic: 3311 Sorted by residual: dihedral pdb=" CA THR B 164 " pdb=" C THR B 164 " pdb=" N THR B 165 " pdb=" CA THR B 165 " ideal model delta harmonic sigma weight residual -180.00 -153.66 -26.34 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CAF 9GF R 501 " pdb=" CAG 9GF R 501 " pdb=" CAJ 9GF R 501 " pdb=" CAK 9GF R 501 " ideal model delta sinusoidal sigma weight residual -124.02 39.41 -163.43 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CAF 9GF R 501 " pdb=" CAG 9GF R 501 " pdb=" CAJ 9GF R 501 " pdb=" CBA 9GF R 501 " ideal model delta sinusoidal sigma weight residual 56.56 -140.73 -162.71 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 5361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1218 0.062 - 0.125: 167 0.125 - 0.187: 19 0.187 - 0.249: 3 0.249 - 0.312: 2 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CA ASN A 47 " pdb=" N ASN A 47 " pdb=" C ASN A 47 " pdb=" CB ASN A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA MET A 248 " pdb=" N MET A 248 " pdb=" C MET A 248 " pdb=" CB MET A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASP S 74 " pdb=" N ASP S 74 " pdb=" C ASP S 74 " pdb=" CB ASP S 74 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1406 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 12 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.83e+00 pdb=" CD GLU B 12 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU B 12 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU B 12 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 356 " -0.021 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP R 356 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP R 356 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP R 356 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 356 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP R 356 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 356 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 356 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 356 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 356 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 305 " 0.011 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C GLN A 305 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 305 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 306 " 0.012 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 774 2.74 - 3.28: 8934 3.28 - 3.82: 14226 3.82 - 4.36: 16330 4.36 - 4.90: 28162 Nonbonded interactions: 68426 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR S 95 " pdb=" O GLN S 171 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.259 3.040 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.263 3.120 nonbonded pdb=" OG SER A 6 " pdb=" OH TYR S 161 " model vdw 2.264 3.040 ... (remaining 68421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.690 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 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 : 0.004 0.182 9035 Z= 0.230 Angle : 0.729 21.789 12248 Z= 0.400 Chirality : 0.046 0.312 1409 Planarity : 0.004 0.047 1532 Dihedral : 16.047 163.433 3221 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 0.53 % Allowed : 0.43 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1125 helix: 0.99 (0.28), residues: 358 sheet: -0.61 (0.34), residues: 236 loop : -1.56 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 356 HIS 0.005 0.001 HIS B 91 PHE 0.017 0.001 PHE S 80 TYR 0.015 0.001 TYR S 102 ARG 0.006 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.17093 ( 387) hydrogen bonds : angle 6.20381 ( 1092) SS BOND : bond 0.00070 ( 1) SS BOND : angle 1.17883 ( 2) covalent geometry : bond 0.00410 ( 9034) covalent geometry : angle 0.72879 (12246) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.6911 (ttt) cc_final: 0.6700 (ttm) REVERT: A 248 MET cc_start: 0.7274 (ttm) cc_final: 0.6304 (mmt) REVERT: A 278 LYS cc_start: 0.7320 (pttm) cc_final: 0.7026 (pttt) REVERT: A 288 PHE cc_start: 0.5862 (p90) cc_final: 0.5443 (p90) REVERT: S 18 ARG cc_start: 0.4698 (ttt180) cc_final: 0.4435 (ttm170) REVERT: S 65 LYS cc_start: 0.7451 (mppt) cc_final: 0.7011 (mptt) outliers start: 5 outliers final: 2 residues processed: 178 average time/residue: 0.1806 time to fit residues: 45.9519 Evaluate side-chains 139 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 196 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.218267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.180432 restraints weight = 12570.344| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 3.09 r_work: 0.3954 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9035 Z= 0.128 Angle : 0.569 7.608 12248 Z= 0.302 Chirality : 0.043 0.179 1409 Planarity : 0.004 0.050 1532 Dihedral : 13.611 155.664 1282 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.49 % Allowed : 10.13 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1125 helix: 1.24 (0.27), residues: 363 sheet: -0.72 (0.32), residues: 269 loop : -1.50 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.008 0.001 HIS B 91 PHE 0.018 0.002 PHE S 80 TYR 0.011 0.001 TYR A 303 ARG 0.004 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 387) hydrogen bonds : angle 5.09109 ( 1092) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.39328 ( 2) covalent geometry : bond 0.00272 ( 9034) covalent geometry : angle 0.56856 (12246) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.6418 (mmt) cc_final: 0.5565 (mmt) REVERT: A 248 MET cc_start: 0.7435 (ttm) cc_final: 0.6213 (mmt) REVERT: A 269 LEU cc_start: 0.7099 (mt) cc_final: 0.6889 (mp) REVERT: A 278 LYS cc_start: 0.7249 (pttm) cc_final: 0.6989 (pttt) REVERT: R 251 PRO cc_start: 0.7353 (Cg_exo) cc_final: 0.7107 (Cg_endo) REVERT: R 371 MET cc_start: 0.8024 (mmm) cc_final: 0.7325 (mmm) REVERT: S 3 GLN cc_start: 0.7376 (pp30) cc_final: 0.7104 (pp30) REVERT: S 18 ARG cc_start: 0.5191 (ttt180) cc_final: 0.4880 (ttm170) REVERT: S 65 LYS cc_start: 0.7679 (mppt) cc_final: 0.7080 (mptt) outliers start: 14 outliers final: 11 residues processed: 152 average time/residue: 0.1790 time to fit residues: 39.1564 Evaluate side-chains 142 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 81 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 196 HIS B 17 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.216832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178186 restraints weight = 12694.198| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 3.07 r_work: 0.3934 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9035 Z= 0.126 Angle : 0.547 7.891 12248 Z= 0.293 Chirality : 0.042 0.197 1409 Planarity : 0.004 0.042 1532 Dihedral : 12.997 150.805 1280 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.92 % Allowed : 14.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.26), residues: 1125 helix: 1.34 (0.27), residues: 363 sheet: -0.75 (0.33), residues: 263 loop : -1.48 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.010 0.001 HIS B 91 PHE 0.016 0.001 PHE A 190 TYR 0.012 0.001 TYR S 216 ARG 0.005 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 387) hydrogen bonds : angle 4.92080 ( 1092) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.36440 ( 2) covalent geometry : bond 0.00273 ( 9034) covalent geometry : angle 0.54726 (12246) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: A 244 MET cc_start: 0.6704 (mmt) cc_final: 0.6073 (mmt) REVERT: A 248 MET cc_start: 0.7413 (ttm) cc_final: 0.6272 (mmt) REVERT: A 278 LYS cc_start: 0.7324 (pttm) cc_final: 0.7022 (pttt) REVERT: S 3 GLN cc_start: 0.7397 (pp30) cc_final: 0.7159 (pp30) REVERT: S 18 ARG cc_start: 0.5186 (ttt180) cc_final: 0.4798 (ttm170) outliers start: 18 outliers final: 14 residues processed: 152 average time/residue: 0.2236 time to fit residues: 48.9680 Evaluate side-chains 144 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.0040 chunk 64 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 196 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.216106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.178263 restraints weight = 12577.213| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 3.10 r_work: 0.3921 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9035 Z= 0.124 Angle : 0.547 8.178 12248 Z= 0.291 Chirality : 0.042 0.203 1409 Planarity : 0.003 0.044 1532 Dihedral : 12.336 146.691 1280 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.77 % Allowed : 15.67 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1125 helix: 1.29 (0.27), residues: 362 sheet: -0.82 (0.33), residues: 255 loop : -1.51 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.009 0.001 HIS B 91 PHE 0.015 0.001 PHE A 190 TYR 0.010 0.001 TYR S 103 ARG 0.003 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 387) hydrogen bonds : angle 4.87718 ( 1092) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.36435 ( 2) covalent geometry : bond 0.00273 ( 9034) covalent geometry : angle 0.54703 (12246) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: A 244 MET cc_start: 0.6626 (mmt) cc_final: 0.6064 (mmt) REVERT: A 248 MET cc_start: 0.7413 (ttm) cc_final: 0.6268 (mmt) REVERT: A 278 LYS cc_start: 0.7309 (pttm) cc_final: 0.7029 (pttt) REVERT: A 298 ASP cc_start: 0.7902 (m-30) cc_final: 0.7509 (m-30) REVERT: A 303 TYR cc_start: 0.5905 (t80) cc_final: 0.5603 (t80) REVERT: B 101 MET cc_start: 0.7354 (mtt) cc_final: 0.7115 (mtt) REVERT: B 273 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8644 (mp) REVERT: C 26 ASP cc_start: 0.7617 (t0) cc_final: 0.7190 (t0) REVERT: R 371 MET cc_start: 0.8043 (mmm) cc_final: 0.7335 (mmm) REVERT: S 18 ARG cc_start: 0.5136 (ttt180) cc_final: 0.4768 (ttm170) outliers start: 26 outliers final: 17 residues processed: 157 average time/residue: 0.1831 time to fit residues: 41.2883 Evaluate side-chains 145 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 0.0770 chunk 66 optimal weight: 8.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 196 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.217363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.179342 restraints weight = 12624.443| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 3.23 r_work: 0.3932 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9035 Z= 0.110 Angle : 0.542 8.238 12248 Z= 0.286 Chirality : 0.042 0.205 1409 Planarity : 0.004 0.056 1532 Dihedral : 11.591 141.323 1280 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.35 % Allowed : 18.02 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1125 helix: 1.47 (0.28), residues: 361 sheet: -0.69 (0.33), residues: 259 loop : -1.52 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.007 0.001 HIS B 91 PHE 0.016 0.001 PHE A 190 TYR 0.010 0.001 TYR S 178 ARG 0.012 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 387) hydrogen bonds : angle 4.75089 ( 1092) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.27540 ( 2) covalent geometry : bond 0.00233 ( 9034) covalent geometry : angle 0.54225 (12246) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: A 244 MET cc_start: 0.6677 (mmt) cc_final: 0.6122 (mmt) REVERT: A 248 MET cc_start: 0.7416 (ttm) cc_final: 0.6266 (mmt) REVERT: A 278 LYS cc_start: 0.7305 (pttm) cc_final: 0.7042 (pttt) REVERT: A 298 ASP cc_start: 0.7846 (m-30) cc_final: 0.7632 (m-30) REVERT: A 303 TYR cc_start: 0.5942 (t80) cc_final: 0.5668 (t80) REVERT: B 101 MET cc_start: 0.7391 (mtt) cc_final: 0.7165 (mtt) REVERT: B 273 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8601 (mp) REVERT: C 26 ASP cc_start: 0.7650 (t0) cc_final: 0.7226 (t0) REVERT: R 371 MET cc_start: 0.8095 (mmm) cc_final: 0.7452 (mmm) REVERT: S 18 ARG cc_start: 0.5220 (ttt180) cc_final: 0.4789 (ttm170) REVERT: S 128 MET cc_start: 0.6206 (pmm) cc_final: 0.4338 (ptp) outliers start: 22 outliers final: 16 residues processed: 154 average time/residue: 0.2714 time to fit residues: 61.4475 Evaluate side-chains 150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.0970 chunk 91 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.211898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.172578 restraints weight = 12579.946| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 3.30 r_work: 0.3850 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9035 Z= 0.177 Angle : 0.607 8.178 12248 Z= 0.323 Chirality : 0.045 0.234 1409 Planarity : 0.004 0.041 1532 Dihedral : 11.392 137.131 1279 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.09 % Allowed : 18.76 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1125 helix: 1.16 (0.28), residues: 364 sheet: -0.98 (0.34), residues: 235 loop : -1.61 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 36 HIS 0.014 0.001 HIS B 91 PHE 0.027 0.002 PHE A 308 TYR 0.016 0.002 TYR S 216 ARG 0.008 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 387) hydrogen bonds : angle 5.06865 ( 1092) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.24411 ( 2) covalent geometry : bond 0.00404 ( 9034) covalent geometry : angle 0.60668 (12246) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7517 (mp10) REVERT: A 244 MET cc_start: 0.6896 (mmt) cc_final: 0.6271 (mmt) REVERT: A 248 MET cc_start: 0.7535 (ttm) cc_final: 0.6302 (mmt) REVERT: A 298 ASP cc_start: 0.7938 (m-30) cc_final: 0.7711 (m-30) REVERT: B 273 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8706 (mp) REVERT: C 26 ASP cc_start: 0.7679 (t0) cc_final: 0.7225 (t0) REVERT: R 178 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.6489 (m-70) REVERT: R 371 MET cc_start: 0.8068 (mmm) cc_final: 0.7394 (mmm) REVERT: S 39 GLN cc_start: 0.6415 (tp40) cc_final: 0.6141 (tp40) REVERT: S 70 ILE cc_start: 0.4227 (OUTLIER) cc_final: 0.3877 (mm) REVERT: S 128 MET cc_start: 0.6440 (pmm) cc_final: 0.4747 (ptp) outliers start: 29 outliers final: 20 residues processed: 159 average time/residue: 0.2524 time to fit residues: 57.2806 Evaluate side-chains 154 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 0.0040 chunk 48 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS R 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.215330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.177298 restraints weight = 12612.212| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.15 r_work: 0.3912 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9035 Z= 0.120 Angle : 0.560 9.081 12248 Z= 0.297 Chirality : 0.042 0.213 1409 Planarity : 0.004 0.039 1532 Dihedral : 10.651 133.423 1279 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.77 % Allowed : 19.62 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1125 helix: 1.30 (0.28), residues: 363 sheet: -0.68 (0.33), residues: 246 loop : -1.57 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.009 0.001 HIS B 91 PHE 0.016 0.001 PHE A 190 TYR 0.021 0.001 TYR S 103 ARG 0.006 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 387) hydrogen bonds : angle 4.87818 ( 1092) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.40406 ( 2) covalent geometry : bond 0.00259 ( 9034) covalent geometry : angle 0.56046 (12246) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6747 (mmt) cc_final: 0.6237 (mmt) REVERT: A 248 MET cc_start: 0.7458 (ttm) cc_final: 0.6282 (mmt) REVERT: A 298 ASP cc_start: 0.7855 (m-30) cc_final: 0.7618 (m-30) REVERT: B 273 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8649 (mp) REVERT: C 26 ASP cc_start: 0.7647 (t0) cc_final: 0.7187 (t0) REVERT: R 178 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.6388 (m-70) REVERT: R 371 MET cc_start: 0.7981 (mmm) cc_final: 0.7380 (mmm) REVERT: S 18 ARG cc_start: 0.5004 (ttt180) cc_final: 0.4586 (ttm170) REVERT: S 39 GLN cc_start: 0.6407 (tp40) cc_final: 0.5947 (tp-100) REVERT: S 70 ILE cc_start: 0.4311 (OUTLIER) cc_final: 0.4016 (mm) REVERT: S 128 MET cc_start: 0.6504 (pmm) cc_final: 0.4733 (ptp) outliers start: 26 outliers final: 17 residues processed: 154 average time/residue: 0.1923 time to fit residues: 42.0784 Evaluate side-chains 150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 104 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 196 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.216977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178102 restraints weight = 12840.272| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 3.31 r_work: 0.3915 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9035 Z= 0.111 Angle : 0.564 9.976 12248 Z= 0.295 Chirality : 0.042 0.216 1409 Planarity : 0.003 0.039 1532 Dihedral : 9.995 129.946 1279 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.03 % Allowed : 20.79 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.26), residues: 1125 helix: 1.44 (0.28), residues: 363 sheet: -0.74 (0.33), residues: 253 loop : -1.50 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.007 0.001 HIS B 91 PHE 0.016 0.001 PHE A 190 TYR 0.022 0.001 TYR S 103 ARG 0.006 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 387) hydrogen bonds : angle 4.77334 ( 1092) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.32278 ( 2) covalent geometry : bond 0.00235 ( 9034) covalent geometry : angle 0.56440 (12246) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6711 (mmt) cc_final: 0.6252 (mmt) REVERT: A 248 MET cc_start: 0.7395 (ttm) cc_final: 0.6271 (mmt) REVERT: A 298 ASP cc_start: 0.7817 (m-30) cc_final: 0.7592 (m-30) REVERT: B 101 MET cc_start: 0.7364 (mtt) cc_final: 0.7125 (mtt) REVERT: B 205 ASP cc_start: 0.8441 (m-30) cc_final: 0.8041 (p0) REVERT: B 273 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8614 (mp) REVERT: C 26 ASP cc_start: 0.7638 (t0) cc_final: 0.7208 (t0) REVERT: R 178 HIS cc_start: 0.6654 (OUTLIER) cc_final: 0.6399 (m-70) REVERT: R 371 MET cc_start: 0.7947 (mmm) cc_final: 0.7356 (mmm) REVERT: S 39 GLN cc_start: 0.6485 (tp40) cc_final: 0.6278 (tp40) REVERT: S 128 MET cc_start: 0.6454 (pmm) cc_final: 0.4747 (ptp) REVERT: S 149 SER cc_start: 0.7674 (m) cc_final: 0.7157 (p) outliers start: 19 outliers final: 16 residues processed: 152 average time/residue: 0.1985 time to fit residues: 42.4091 Evaluate side-chains 151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.215960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.178365 restraints weight = 12663.071| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.98 r_work: 0.3925 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9035 Z= 0.120 Angle : 0.585 10.916 12248 Z= 0.306 Chirality : 0.042 0.214 1409 Planarity : 0.004 0.039 1532 Dihedral : 9.713 128.164 1279 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.56 % Allowed : 20.15 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.26), residues: 1125 helix: 1.37 (0.28), residues: 363 sheet: -0.88 (0.33), residues: 249 loop : -1.52 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.008 0.001 HIS B 91 PHE 0.015 0.001 PHE A 190 TYR 0.024 0.001 TYR S 103 ARG 0.005 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 387) hydrogen bonds : angle 4.77092 ( 1092) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.36701 ( 2) covalent geometry : bond 0.00263 ( 9034) covalent geometry : angle 0.58541 (12246) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6746 (mmt) cc_final: 0.6327 (mmt) REVERT: A 248 MET cc_start: 0.7436 (ttm) cc_final: 0.6319 (mmt) REVERT: A 298 ASP cc_start: 0.7831 (m-30) cc_final: 0.7602 (m-30) REVERT: B 101 MET cc_start: 0.7371 (mtt) cc_final: 0.7138 (mtt) REVERT: B 273 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8636 (mp) REVERT: C 26 ASP cc_start: 0.7643 (t0) cc_final: 0.7193 (t0) REVERT: R 178 HIS cc_start: 0.6546 (OUTLIER) cc_final: 0.6275 (m-70) REVERT: R 371 MET cc_start: 0.7989 (mmm) cc_final: 0.7383 (mmm) REVERT: S 70 ILE cc_start: 0.4427 (OUTLIER) cc_final: 0.4017 (mm) REVERT: S 128 MET cc_start: 0.6500 (pmm) cc_final: 0.4788 (ptp) REVERT: S 149 SER cc_start: 0.7665 (m) cc_final: 0.7137 (p) outliers start: 24 outliers final: 21 residues processed: 152 average time/residue: 0.1987 time to fit residues: 42.5552 Evaluate side-chains 156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain S residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 35 optimal weight: 0.0040 chunk 105 optimal weight: 2.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.215211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.176226 restraints weight = 12648.238| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 3.08 r_work: 0.3904 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9035 Z= 0.128 Angle : 0.596 10.038 12248 Z= 0.312 Chirality : 0.043 0.219 1409 Planarity : 0.003 0.039 1532 Dihedral : 9.468 127.316 1279 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.67 % Allowed : 20.26 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 1125 helix: 1.32 (0.28), residues: 363 sheet: -0.89 (0.33), residues: 247 loop : -1.52 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 356 HIS 0.009 0.001 HIS B 91 PHE 0.016 0.001 PHE A 190 TYR 0.023 0.001 TYR S 103 ARG 0.005 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 387) hydrogen bonds : angle 4.83792 ( 1092) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.28068 ( 2) covalent geometry : bond 0.00283 ( 9034) covalent geometry : angle 0.59635 (12246) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6746 (mmt) cc_final: 0.6316 (mmt) REVERT: A 248 MET cc_start: 0.7466 (ttm) cc_final: 0.6317 (mmt) REVERT: A 298 ASP cc_start: 0.7848 (m-30) cc_final: 0.7612 (m-30) REVERT: B 101 MET cc_start: 0.7392 (mtt) cc_final: 0.7160 (mtt) REVERT: B 273 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8680 (mp) REVERT: C 26 ASP cc_start: 0.7650 (t0) cc_final: 0.7189 (t0) REVERT: R 178 HIS cc_start: 0.6656 (OUTLIER) cc_final: 0.6317 (m-70) REVERT: R 371 MET cc_start: 0.7953 (mmm) cc_final: 0.7331 (mmm) REVERT: S 70 ILE cc_start: 0.4458 (OUTLIER) cc_final: 0.4055 (mm) REVERT: S 128 MET cc_start: 0.6538 (pmm) cc_final: 0.4861 (ptp) REVERT: S 149 SER cc_start: 0.7689 (m) cc_final: 0.7155 (p) REVERT: S 151 LYS cc_start: 0.6834 (ptmt) cc_final: 0.6486 (ptpt) outliers start: 25 outliers final: 22 residues processed: 151 average time/residue: 0.1891 time to fit residues: 40.3148 Evaluate side-chains 154 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 96 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 74 optimal weight: 0.0970 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS R 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.213562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.175683 restraints weight = 12737.942| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 3.25 r_work: 0.3879 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9035 Z= 0.150 Angle : 0.604 9.240 12248 Z= 0.318 Chirality : 0.044 0.219 1409 Planarity : 0.004 0.039 1532 Dihedral : 9.454 127.406 1279 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.09 % Allowed : 20.15 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1125 helix: 1.14 (0.28), residues: 364 sheet: -0.91 (0.33), residues: 235 loop : -1.62 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 356 HIS 0.012 0.001 HIS B 91 PHE 0.020 0.002 PHE A 308 TYR 0.022 0.002 TYR S 103 ARG 0.005 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 387) hydrogen bonds : angle 4.92960 ( 1092) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.30211 ( 2) covalent geometry : bond 0.00340 ( 9034) covalent geometry : angle 0.60379 (12246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4894.15 seconds wall clock time: 86 minutes 25.81 seconds (5185.81 seconds total)