Starting phenix.real_space_refine on Sat Jul 26 16:36:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvj_32141/07_2025/7vvj_32141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvj_32141/07_2025/7vvj_32141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vvj_32141/07_2025/7vvj_32141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvj_32141/07_2025/7vvj_32141.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvj_32141/07_2025/7vvj_32141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvj_32141/07_2025/7vvj_32141.cif" } resolution = 3.2 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5630 2.51 5 N 1559 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1932 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2560 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 424 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 249 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2734 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 11, 'TRANS': 354} Chain breaks: 3 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 200 Time building chain proxies: 5.27, per 1000 atoms: 0.59 Number of scatterers: 8872 At special positions: 0 Unit cell: (130.725, 104.58, 127.82, 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 51 16.00 O 1632 8.00 N 1559 7.00 C 5630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.09 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.02 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 41.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.582A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.927A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.627A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.991A pdb=" N ARG A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.585A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.180A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.603A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.578A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.791A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.371A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.798A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.864A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.793A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 52 Processing helix chain 'R' and resid 182 through 212 removed outlier: 3.637A pdb=" N GLY R 194 " --> pdb=" O ILE R 190 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU R 202 " --> pdb=" O SER R 198 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 219 through 245 Processing helix chain 'R' and resid 277 through 312 removed outlier: 4.406A pdb=" N CYS R 281 " --> pdb=" O GLY R 277 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET R 312 " --> pdb=" O SER R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 329 Processing helix chain 'R' and resid 329 through 346 removed outlier: 3.979A pdb=" N ALA R 333 " --> pdb=" O TRP R 329 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.555A pdb=" N THR R 387 " --> pdb=" O ARG R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 402 through 417 removed outlier: 3.585A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU R 413 " --> pdb=" O SER R 409 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.108A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 480 removed outlier: 3.575A pdb=" N GLU R 469 " --> pdb=" O GLU R 465 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER R 475 " --> pdb=" O LYS R 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 4.007A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.817A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.220A 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: 3.587A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.213A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.787A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.215A 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: 3.617A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.876A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.785A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 439 hydrogen bonds defined for protein. 1257 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: 2.61 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1449 1.30 - 1.43: 2504 1.43 - 1.57: 5032 1.57 - 1.70: 0 1.70 - 1.84: 74 Bond restraints: 9059 Sorted by residual: bond pdb=" C VAL B 327 " pdb=" O VAL B 327 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.00e-02 1.00e+04 3.79e+01 bond pdb=" C PRO A 351 " pdb=" O PRO A 351 " ideal model delta sigma weight residual 1.233 1.167 0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" C ARG B 137 " pdb=" O ARG B 137 " ideal model delta sigma weight residual 1.234 1.161 0.073 1.22e-02 6.72e+03 3.59e+01 bond pdb=" C ASP N 109 " pdb=" O ASP N 109 " ideal model delta sigma weight residual 1.232 1.170 0.062 1.12e-02 7.97e+03 3.03e+01 bond pdb=" C LEU R 187 " pdb=" O LEU R 187 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.17e-02 7.31e+03 2.75e+01 ... (remaining 9054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 7484 1.53 - 3.07: 3816 3.07 - 4.60: 864 4.60 - 6.14: 104 6.14 - 7.67: 21 Bond angle restraints: 12289 Sorted by residual: angle pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" O CYS N 107 " ideal model delta sigma weight residual 120.36 113.06 7.30 1.08e+00 8.57e-01 4.56e+01 angle pdb=" CA ILE B 80 " pdb=" C ILE B 80 " pdb=" O ILE B 80 " ideal model delta sigma weight residual 120.39 113.60 6.79 1.05e+00 9.07e-01 4.19e+01 angle pdb=" CA GLY N 121 " pdb=" C GLY N 121 " pdb=" O GLY N 121 " ideal model delta sigma weight residual 122.22 118.35 3.87 6.50e-01 2.37e+00 3.55e+01 angle pdb=" CA VAL R 384 " pdb=" C VAL R 384 " pdb=" O VAL R 384 " ideal model delta sigma weight residual 119.29 114.79 4.50 8.40e-01 1.42e+00 2.86e+01 angle pdb=" N VAL R 419 " pdb=" CA VAL R 419 " pdb=" C VAL R 419 " ideal model delta sigma weight residual 111.90 107.69 4.21 8.10e-01 1.52e+00 2.70e+01 ... (remaining 12284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 4796 17.21 - 34.42: 446 34.42 - 51.63: 78 51.63 - 68.84: 22 68.84 - 86.05: 10 Dihedral angle restraints: 5352 sinusoidal: 2002 harmonic: 3350 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -165.05 79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 29.98 63.02 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 150.03 -57.03 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 5349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 863 0.081 - 0.162: 442 0.162 - 0.243: 69 0.243 - 0.325: 8 0.325 - 0.406: 1 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CA LEU A 378 " pdb=" N LEU A 378 " pdb=" C LEU A 378 " pdb=" CB LEU A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA PHE N 108 " pdb=" N PHE N 108 " pdb=" C PHE N 108 " pdb=" CB PHE N 108 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA LEU B 318 " pdb=" N LEU B 318 " pdb=" C LEU B 318 " pdb=" CB LEU B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1380 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 271 " 0.058 2.00e-02 2.50e+03 3.14e-02 2.47e+01 pdb=" CG TRP A 271 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 271 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 271 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 271 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP A 271 " 0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP A 271 " -0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 271 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 271 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 271 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 335 " 0.059 2.00e-02 2.50e+03 3.64e-02 2.31e+01 pdb=" CG PHE B 335 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 335 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE B 335 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE B 335 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE B 335 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE B 335 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.037 2.00e-02 2.50e+03 2.95e-02 1.74e+01 pdb=" CG TYR B 59 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.009 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 618 2.74 - 3.28: 8973 3.28 - 3.82: 13778 3.82 - 4.36: 18956 4.36 - 4.90: 30834 Nonbonded interactions: 73159 Sorted by model distance: nonbonded pdb=" OG1 THR N 28 " pdb=" OD1 ASN N 31 " model vdw 2.205 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.231 3.040 nonbonded pdb=" O MET R 445 " pdb=" OG SER R 449 " model vdw 2.254 3.040 nonbonded pdb=" NE2 HIS B 311 " pdb=" OG1 THR B 329 " model vdw 2.279 3.120 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.291 3.040 ... (remaining 73154 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: 0.260 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.820 Find NCS groups from input model: 0.100 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 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 : 0.015 0.080 9062 Z= 1.080 Angle : 1.784 7.673 12295 Z= 1.297 Chirality : 0.088 0.406 1383 Planarity : 0.009 0.037 1576 Dihedral : 14.241 86.051 3177 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 1.77 % Allowed : 5.53 % Favored : 92.70 % Cbeta Deviations : 0.09 % 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: -1.52 (0.23), residues: 1134 helix: -0.87 (0.23), residues: 427 sheet: -0.90 (0.35), residues: 214 loop : -1.01 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.013 TRP A 271 HIS 0.019 0.006 HIS A 352 PHE 0.059 0.010 PHE B 335 TYR 0.058 0.011 TYR B 59 ARG 0.021 0.003 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.23662 ( 439) hydrogen bonds : angle 8.56813 ( 1257) SS BOND : bond 0.03350 ( 3) SS BOND : angle 2.88827 ( 6) covalent geometry : bond 0.01507 ( 9059) covalent geometry : angle 1.78291 (12289) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.923 Fit side-chains REVERT: A 50 ASN cc_start: 0.6210 (m110) cc_final: 0.6007 (p0) REVERT: A 221 MET cc_start: 0.8718 (ttp) cc_final: 0.8488 (ttp) REVERT: A 295 LYS cc_start: 0.7681 (mmpt) cc_final: 0.7309 (mmtp) REVERT: A 376 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7745 (tmm) REVERT: B 161 SER cc_start: 0.9017 (m) cc_final: 0.8771 (m) REVERT: B 175 GLN cc_start: 0.7910 (pm20) cc_final: 0.7364 (pm20) REVERT: B 189 SER cc_start: 0.8980 (m) cc_final: 0.8658 (p) REVERT: N 53 GLN cc_start: 0.8005 (mp10) cc_final: 0.7740 (mp10) REVERT: R 218 THR cc_start: 0.8349 (t) cc_final: 0.8127 (t) REVERT: R 219 ARG cc_start: 0.7075 (ptt90) cc_final: 0.6591 (ptp90) REVERT: R 441 MET cc_start: 0.8456 (mmt) cc_final: 0.7986 (mmt) REVERT: R 443 TYR cc_start: 0.7926 (t80) cc_final: 0.7508 (t80) REVERT: R 445 MET cc_start: 0.8168 (mmm) cc_final: 0.7771 (mmm) REVERT: R 465 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7564 (mt-10) outliers start: 16 outliers final: 6 residues processed: 173 average time/residue: 0.2852 time to fit residues: 63.2379 Evaluate side-chains 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 25 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 31 ASN R 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117489 restraints weight = 10674.256| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.67 r_work: 0.3226 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9062 Z= 0.155 Angle : 0.573 8.477 12295 Z= 0.311 Chirality : 0.043 0.159 1383 Planarity : 0.004 0.035 1576 Dihedral : 5.582 56.300 1262 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.10 % Allowed : 11.39 % Favored : 86.50 % 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: -0.06 (0.25), residues: 1134 helix: 0.89 (0.25), residues: 432 sheet: -0.72 (0.33), residues: 227 loop : -0.42 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 298 HIS 0.006 0.001 HIS B 91 PHE 0.015 0.002 PHE R 335 TYR 0.029 0.002 TYR R 191 ARG 0.006 0.001 ARG R 396 Details of bonding type rmsd hydrogen bonds : bond 0.04780 ( 439) hydrogen bonds : angle 4.99043 ( 1257) SS BOND : bond 0.00254 ( 3) SS BOND : angle 1.44884 ( 6) covalent geometry : bond 0.00352 ( 9059) covalent geometry : angle 0.57221 (12289) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.899 Fit side-chains REVERT: A 28 LYS cc_start: 0.8554 (pptt) cc_final: 0.7863 (tptt) REVERT: A 333 ASP cc_start: 0.8371 (t70) cc_final: 0.8035 (t0) REVERT: B 175 GLN cc_start: 0.8400 (pm20) cc_final: 0.7780 (pm20) REVERT: B 217 MET cc_start: 0.8177 (ppp) cc_final: 0.7885 (ppp) REVERT: B 262 MET cc_start: 0.8548 (ttm) cc_final: 0.8331 (ttm) REVERT: G 21 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6443 (mtt) REVERT: N 53 GLN cc_start: 0.8572 (mp10) cc_final: 0.8364 (mp10) REVERT: N 106 ASP cc_start: 0.8759 (p0) cc_final: 0.8559 (p0) REVERT: R 39 PHE cc_start: 0.6971 (t80) cc_final: 0.6417 (t80) REVERT: R 228 LEU cc_start: 0.7992 (tp) cc_final: 0.7751 (mt) REVERT: R 383 ARG cc_start: 0.6559 (mmp-170) cc_final: 0.6310 (mmp-170) REVERT: R 446 LEU cc_start: 0.8528 (tp) cc_final: 0.8311 (tp) outliers start: 19 outliers final: 12 residues processed: 160 average time/residue: 0.2922 time to fit residues: 60.3882 Evaluate side-chains 146 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 217 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 213 GLN A 254 ASN B 32 GLN B 340 ASN N 31 ASN R 358 ASN R 374 ASN R 448 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.148023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114044 restraints weight = 10805.159| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.77 r_work: 0.3196 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9062 Z= 0.178 Angle : 0.554 7.625 12295 Z= 0.300 Chirality : 0.044 0.159 1383 Planarity : 0.004 0.038 1576 Dihedral : 5.049 58.302 1253 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.77 % Allowed : 12.50 % Favored : 84.73 % 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: 0.21 (0.25), residues: 1134 helix: 1.28 (0.25), residues: 434 sheet: -0.61 (0.32), residues: 228 loop : -0.44 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 298 HIS 0.005 0.001 HIS A 347 PHE 0.018 0.002 PHE R 335 TYR 0.025 0.002 TYR R 191 ARG 0.006 0.000 ARG R 396 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 439) hydrogen bonds : angle 4.64269 ( 1257) SS BOND : bond 0.00282 ( 3) SS BOND : angle 1.11403 ( 6) covalent geometry : bond 0.00414 ( 9059) covalent geometry : angle 0.55331 (12289) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.994 Fit side-chains REVERT: A 24 LYS cc_start: 0.7918 (tptt) cc_final: 0.7458 (tptt) REVERT: A 333 ASP cc_start: 0.8372 (t70) cc_final: 0.8108 (t0) REVERT: B 175 GLN cc_start: 0.8508 (pm20) cc_final: 0.7872 (pm20) REVERT: B 217 MET cc_start: 0.8245 (ppp) cc_final: 0.7883 (ppp) REVERT: G 21 MET cc_start: 0.6802 (ttm) cc_final: 0.6447 (mtt) REVERT: N 53 GLN cc_start: 0.8665 (mp10) cc_final: 0.8301 (mp10) REVERT: N 106 ASP cc_start: 0.8696 (p0) cc_final: 0.8492 (p0) REVERT: R 35 GLU cc_start: 0.7671 (mp0) cc_final: 0.7416 (mp0) REVERT: R 39 PHE cc_start: 0.6871 (t80) cc_final: 0.6391 (t80) REVERT: R 228 LEU cc_start: 0.8059 (tp) cc_final: 0.7818 (mt) REVERT: R 431 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6665 (tt0) outliers start: 25 outliers final: 21 residues processed: 152 average time/residue: 0.2880 time to fit residues: 56.3738 Evaluate side-chains 147 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 431 GLU Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 5.9990 chunk 82 optimal weight: 50.0000 chunk 104 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 50.0000 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.115506 restraints weight = 10752.347| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.73 r_work: 0.3195 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9062 Z= 0.143 Angle : 0.513 7.476 12295 Z= 0.278 Chirality : 0.042 0.148 1383 Planarity : 0.003 0.039 1576 Dihedral : 4.859 59.839 1253 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.77 % Allowed : 14.71 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.25), residues: 1134 helix: 1.52 (0.26), residues: 434 sheet: -0.44 (0.32), residues: 225 loop : -0.39 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 298 HIS 0.004 0.001 HIS A 347 PHE 0.017 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.006 0.000 ARG R 396 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 439) hydrogen bonds : angle 4.38168 ( 1257) SS BOND : bond 0.00256 ( 3) SS BOND : angle 0.96693 ( 6) covalent geometry : bond 0.00329 ( 9059) covalent geometry : angle 0.51299 (12289) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.921 Fit side-chains REVERT: A 24 LYS cc_start: 0.7903 (tptt) cc_final: 0.7444 (tptt) REVERT: A 28 LYS cc_start: 0.8617 (pptt) cc_final: 0.7797 (tptt) REVERT: A 333 ASP cc_start: 0.8356 (t70) cc_final: 0.8093 (t0) REVERT: B 175 GLN cc_start: 0.8532 (pm20) cc_final: 0.7936 (pm20) REVERT: B 217 MET cc_start: 0.8212 (ppp) cc_final: 0.7845 (ppp) REVERT: G 21 MET cc_start: 0.6770 (ttm) cc_final: 0.6382 (mtt) REVERT: N 53 GLN cc_start: 0.8609 (mp10) cc_final: 0.8217 (mp10) REVERT: R 228 LEU cc_start: 0.8068 (tp) cc_final: 0.7822 (mt) REVERT: R 321 LEU cc_start: 0.7806 (tp) cc_final: 0.7598 (tt) REVERT: R 409 SER cc_start: 0.8346 (p) cc_final: 0.8008 (m) outliers start: 25 outliers final: 18 residues processed: 153 average time/residue: 0.2655 time to fit residues: 52.8015 Evaluate side-chains 151 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119306 restraints weight = 10773.584| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.67 r_work: 0.3235 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9062 Z= 0.113 Angle : 0.501 7.415 12295 Z= 0.269 Chirality : 0.041 0.137 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.383 40.629 1251 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.54 % Allowed : 15.93 % Favored : 81.53 % 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: 0.71 (0.25), residues: 1134 helix: 1.83 (0.26), residues: 428 sheet: -0.32 (0.32), residues: 226 loop : -0.30 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 347 PHE 0.018 0.001 PHE R 335 TYR 0.029 0.001 TYR R 191 ARG 0.007 0.000 ARG R 396 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 439) hydrogen bonds : angle 4.14894 ( 1257) SS BOND : bond 0.00194 ( 3) SS BOND : angle 3.11424 ( 6) covalent geometry : bond 0.00252 ( 9059) covalent geometry : angle 0.49616 (12289) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.029 Fit side-chains REVERT: A 24 LYS cc_start: 0.7880 (tptt) cc_final: 0.7432 (tptt) REVERT: A 333 ASP cc_start: 0.8336 (t70) cc_final: 0.8081 (t0) REVERT: B 175 GLN cc_start: 0.8477 (pm20) cc_final: 0.7888 (pm20) REVERT: B 217 MET cc_start: 0.8129 (ppp) cc_final: 0.7765 (ppp) REVERT: G 21 MET cc_start: 0.6742 (ttm) cc_final: 0.6405 (mtt) REVERT: G 47 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.5794 (mp0) REVERT: N 6 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7482 (mm-30) REVERT: R 35 GLU cc_start: 0.7773 (mp0) cc_final: 0.7500 (mp0) REVERT: R 321 LEU cc_start: 0.7785 (tp) cc_final: 0.7565 (tt) REVERT: R 409 SER cc_start: 0.8250 (p) cc_final: 0.7898 (m) REVERT: R 431 GLU cc_start: 0.6938 (tt0) cc_final: 0.6696 (tt0) outliers start: 23 outliers final: 19 residues processed: 157 average time/residue: 0.2780 time to fit residues: 58.4209 Evaluate side-chains 151 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.151863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118571 restraints weight = 10844.347| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.68 r_work: 0.3225 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9062 Z= 0.135 Angle : 0.535 9.560 12295 Z= 0.285 Chirality : 0.042 0.167 1383 Planarity : 0.003 0.039 1576 Dihedral : 4.521 43.504 1250 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.88 % Allowed : 16.26 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.73 (0.25), residues: 1134 helix: 1.88 (0.26), residues: 428 sheet: -0.25 (0.32), residues: 226 loop : -0.36 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.004 0.001 HIS A 347 PHE 0.018 0.001 PHE R 335 TYR 0.029 0.001 TYR R 191 ARG 0.007 0.000 ARG R 396 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 439) hydrogen bonds : angle 4.13032 ( 1257) SS BOND : bond 0.00651 ( 3) SS BOND : angle 4.27081 ( 6) covalent geometry : bond 0.00317 ( 9059) covalent geometry : angle 0.52626 (12289) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.031 Fit side-chains REVERT: A 24 LYS cc_start: 0.7902 (tptt) cc_final: 0.7446 (tptt) REVERT: A 333 ASP cc_start: 0.8353 (t70) cc_final: 0.8088 (t0) REVERT: B 175 GLN cc_start: 0.8499 (pm20) cc_final: 0.7913 (pm20) REVERT: B 217 MET cc_start: 0.8150 (ppp) cc_final: 0.7805 (ppp) REVERT: G 21 MET cc_start: 0.6731 (ttm) cc_final: 0.6376 (mtt) REVERT: G 47 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.5825 (mp0) REVERT: N 53 GLN cc_start: 0.8560 (mp10) cc_final: 0.8206 (mp10) REVERT: R 321 LEU cc_start: 0.7819 (tp) cc_final: 0.7579 (tt) REVERT: R 409 SER cc_start: 0.8242 (p) cc_final: 0.7909 (m) REVERT: R 431 GLU cc_start: 0.7015 (tt0) cc_final: 0.6798 (tt0) outliers start: 26 outliers final: 22 residues processed: 148 average time/residue: 0.2708 time to fit residues: 51.9352 Evaluate side-chains 153 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 31 ASN R 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116749 restraints weight = 10935.614| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.69 r_work: 0.3203 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9062 Z= 0.163 Angle : 0.550 8.687 12295 Z= 0.294 Chirality : 0.043 0.162 1383 Planarity : 0.003 0.039 1576 Dihedral : 4.604 43.139 1250 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.88 % Allowed : 16.92 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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 (0.25), residues: 1134 helix: 1.83 (0.25), residues: 428 sheet: -0.33 (0.32), residues: 228 loop : -0.40 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 298 HIS 0.004 0.001 HIS A 347 PHE 0.018 0.001 PHE R 335 TYR 0.029 0.001 TYR R 191 ARG 0.006 0.000 ARG R 396 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 439) hydrogen bonds : angle 4.20693 ( 1257) SS BOND : bond 0.00410 ( 3) SS BOND : angle 3.82707 ( 6) covalent geometry : bond 0.00386 ( 9059) covalent geometry : angle 0.54398 (12289) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.877 Fit side-chains REVERT: A 15 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6741 (tp30) REVERT: A 24 LYS cc_start: 0.7942 (tptt) cc_final: 0.7451 (tptt) REVERT: A 333 ASP cc_start: 0.8357 (t70) cc_final: 0.8093 (t0) REVERT: B 175 GLN cc_start: 0.8544 (pm20) cc_final: 0.7967 (pm20) REVERT: B 217 MET cc_start: 0.8174 (ppp) cc_final: 0.7823 (ppp) REVERT: G 21 MET cc_start: 0.6698 (ttm) cc_final: 0.6395 (mtt) REVERT: G 47 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.5716 (mp0) REVERT: N 6 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7290 (mm-30) REVERT: N 83 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8312 (mtp) REVERT: R 189 MET cc_start: 0.7454 (tmm) cc_final: 0.7190 (tmm) REVERT: R 321 LEU cc_start: 0.7825 (tp) cc_final: 0.7576 (tt) REVERT: R 326 VAL cc_start: 0.8063 (m) cc_final: 0.7817 (p) REVERT: R 409 SER cc_start: 0.8281 (p) cc_final: 0.7976 (m) outliers start: 26 outliers final: 22 residues processed: 149 average time/residue: 0.2656 time to fit residues: 51.5403 Evaluate side-chains 151 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 50.0000 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118825 restraints weight = 10894.401| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.75 r_work: 0.3240 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9062 Z= 0.106 Angle : 0.497 7.368 12295 Z= 0.267 Chirality : 0.040 0.148 1383 Planarity : 0.003 0.037 1576 Dihedral : 4.346 39.383 1250 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.43 % Allowed : 17.92 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.89 (0.25), residues: 1134 helix: 2.12 (0.26), residues: 425 sheet: -0.30 (0.32), residues: 226 loop : -0.28 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 347 PHE 0.018 0.001 PHE R 335 TYR 0.027 0.001 TYR R 191 ARG 0.007 0.000 ARG R 396 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 439) hydrogen bonds : angle 3.98062 ( 1257) SS BOND : bond 0.00265 ( 3) SS BOND : angle 2.92414 ( 6) covalent geometry : bond 0.00241 ( 9059) covalent geometry : angle 0.49251 (12289) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.933 Fit side-chains REVERT: A 15 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6730 (tp30) REVERT: A 24 LYS cc_start: 0.7904 (tptt) cc_final: 0.7439 (tptt) REVERT: A 28 LYS cc_start: 0.8700 (pptt) cc_final: 0.8261 (tttt) REVERT: A 333 ASP cc_start: 0.8357 (t70) cc_final: 0.8096 (t0) REVERT: B 175 GLN cc_start: 0.8541 (pm20) cc_final: 0.7949 (pm20) REVERT: B 217 MET cc_start: 0.8137 (ppp) cc_final: 0.7788 (ppp) REVERT: G 21 MET cc_start: 0.6730 (ttm) cc_final: 0.6346 (mtt) REVERT: G 47 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.5850 (mp0) REVERT: N 6 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7353 (mm-30) REVERT: N 53 GLN cc_start: 0.8506 (mp10) cc_final: 0.8220 (mp10) REVERT: R 35 GLU cc_start: 0.7559 (mp0) cc_final: 0.7333 (mp0) REVERT: R 321 LEU cc_start: 0.7800 (tp) cc_final: 0.7549 (tt) REVERT: R 391 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7136 (pt0) REVERT: R 409 SER cc_start: 0.8153 (p) cc_final: 0.7828 (m) outliers start: 22 outliers final: 20 residues processed: 147 average time/residue: 0.3002 time to fit residues: 57.0500 Evaluate side-chains 144 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117101 restraints weight = 10893.622| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.76 r_work: 0.3221 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9062 Z= 0.132 Angle : 0.530 7.617 12295 Z= 0.282 Chirality : 0.042 0.281 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.404 40.390 1250 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.65 % Allowed : 18.36 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.85 (0.25), residues: 1134 helix: 2.03 (0.25), residues: 431 sheet: -0.24 (0.32), residues: 221 loop : -0.32 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.004 0.001 HIS A 347 PHE 0.018 0.001 PHE R 335 TYR 0.028 0.001 TYR R 191 ARG 0.007 0.000 ARG R 396 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 439) hydrogen bonds : angle 4.00483 ( 1257) SS BOND : bond 0.00296 ( 3) SS BOND : angle 3.14576 ( 6) covalent geometry : bond 0.00309 ( 9059) covalent geometry : angle 0.52603 (12289) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.915 Fit side-chains REVERT: A 15 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6736 (tp30) REVERT: A 24 LYS cc_start: 0.7912 (tptt) cc_final: 0.7446 (tptt) REVERT: A 28 LYS cc_start: 0.8694 (pptt) cc_final: 0.8253 (tttt) REVERT: A 333 ASP cc_start: 0.8367 (t70) cc_final: 0.8098 (t0) REVERT: B 175 GLN cc_start: 0.8549 (pm20) cc_final: 0.7988 (pm20) REVERT: B 217 MET cc_start: 0.8163 (ppp) cc_final: 0.7812 (ppp) REVERT: G 21 MET cc_start: 0.6743 (ttm) cc_final: 0.6425 (mtt) REVERT: G 47 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.5952 (mp0) REVERT: N 6 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7372 (mm-30) REVERT: N 53 GLN cc_start: 0.8536 (mp10) cc_final: 0.8212 (mp10) REVERT: R 35 GLU cc_start: 0.7573 (mp0) cc_final: 0.7343 (mp0) REVERT: R 321 LEU cc_start: 0.7848 (tp) cc_final: 0.7599 (tt) REVERT: R 391 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7210 (pt0) REVERT: R 409 SER cc_start: 0.8153 (p) cc_final: 0.7825 (m) outliers start: 24 outliers final: 21 residues processed: 142 average time/residue: 0.3067 time to fit residues: 57.8499 Evaluate side-chains 145 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 31 ASN R 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117344 restraints weight = 10964.969| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.70 r_work: 0.3211 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9062 Z= 0.158 Angle : 0.544 7.820 12295 Z= 0.291 Chirality : 0.042 0.160 1383 Planarity : 0.003 0.039 1576 Dihedral : 4.487 41.309 1250 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.88 % Allowed : 18.36 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.83 (0.25), residues: 1134 helix: 2.10 (0.25), residues: 423 sheet: -0.37 (0.32), residues: 225 loop : -0.32 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 298 HIS 0.004 0.001 HIS A 347 PHE 0.018 0.001 PHE R 335 TYR 0.028 0.001 TYR R 191 ARG 0.008 0.000 ARG R 396 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 439) hydrogen bonds : angle 4.10109 ( 1257) SS BOND : bond 0.00304 ( 3) SS BOND : angle 3.27060 ( 6) covalent geometry : bond 0.00376 ( 9059) covalent geometry : angle 0.53920 (12289) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.018 Fit side-chains REVERT: A 15 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6705 (tp30) REVERT: A 24 LYS cc_start: 0.7943 (tptt) cc_final: 0.7459 (tptt) REVERT: A 333 ASP cc_start: 0.8371 (t70) cc_final: 0.8093 (t0) REVERT: B 175 GLN cc_start: 0.8541 (pm20) cc_final: 0.7982 (pm20) REVERT: B 217 MET cc_start: 0.8152 (ppp) cc_final: 0.7629 (ppp) REVERT: G 47 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6059 (mp0) REVERT: N 6 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7385 (mm-30) REVERT: N 53 GLN cc_start: 0.8555 (mp10) cc_final: 0.8230 (mp10) REVERT: N 83 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8370 (mtp) REVERT: R 35 GLU cc_start: 0.7547 (mp0) cc_final: 0.7329 (mp0) REVERT: R 321 LEU cc_start: 0.7851 (tp) cc_final: 0.7596 (tt) REVERT: R 391 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7161 (pt0) outliers start: 26 outliers final: 21 residues processed: 133 average time/residue: 0.2718 time to fit residues: 47.4607 Evaluate side-chains 139 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 340 ASN N 31 ASN R 380 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.115990 restraints weight = 11000.204| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.71 r_work: 0.3192 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9062 Z= 0.180 Angle : 0.566 8.009 12295 Z= 0.303 Chirality : 0.043 0.166 1383 Planarity : 0.004 0.060 1576 Dihedral : 4.603 42.192 1250 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.21 % Allowed : 18.14 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.74 (0.25), residues: 1134 helix: 1.98 (0.25), residues: 423 sheet: -0.44 (0.31), residues: 228 loop : -0.31 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 298 HIS 0.006 0.001 HIS A 347 PHE 0.019 0.002 PHE R 335 TYR 0.029 0.002 TYR R 191 ARG 0.007 0.000 ARG R 396 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 439) hydrogen bonds : angle 4.22440 ( 1257) SS BOND : bond 0.00307 ( 3) SS BOND : angle 3.38285 ( 6) covalent geometry : bond 0.00430 ( 9059) covalent geometry : angle 0.56094 (12289) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5529.09 seconds wall clock time: 95 minutes 32.49 seconds (5732.49 seconds total)