Starting phenix.real_space_refine on Thu Mar 13 07:22:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvj_32141/03_2025/7vvj_32141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvj_32141/03_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_32141/03_2025/7vvj_32141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvj_32141/03_2025/7vvj_32141.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvj_32141/03_2025/7vvj_32141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvj_32141/03_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-5624/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: 4.97, per 1000 atoms: 0.56 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 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: 0.98 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: 2.38 Time building geometry restraints manager: 2.72 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- 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 9059 Z= 0.999 Angle : 1.783 7.673 12289 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 *********************** 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 : 0.879 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: 0.2845 time to fit residues: 63.0440 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 : 0.998 ------------------------------------------------------------------------------- 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 9059 Z= 0.231 Angle : 0.572 8.477 12289 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 *********************** 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 : 1.006 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: 0.2895 time to fit residues: 59.3539 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 : 0.910 ------------------------------------------------------------------------------- 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 9059 Z= 0.272 Angle : 0.553 7.625 12289 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 *********************** 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 : 0.983 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: 0.2891 time to fit residues: 56.6754 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 : 0.969 ------------------------------------------------------------------------------- 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: 0.9990 chunk 82 optimal weight: 50.0000 chunk 104 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 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: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.150782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117162 restraints weight = 10710.144| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.73 r_work: 0.3219 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9059 Z= 0.169 Angle : 0.490 7.417 12289 Z= 0.266 Chirality : 0.041 0.141 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.715 58.794 1253 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.21 % Allowed : 14.93 % Favored : 82.85 % 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: 0.56 (0.25), residues: 1134 helix: 1.64 (0.26), residues: 434 sheet: -0.37 (0.32), residues: 223 loop : -0.36 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.007 0.000 ARG R 396 *********************** 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 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.014 Fit side-chains REVERT: A 24 LYS cc_start: 0.7858 (tptt) cc_final: 0.7399 (tptt) REVERT: A 28 LYS cc_start: 0.8630 (pptt) cc_final: 0.7834 (tptt) REVERT: A 333 ASP cc_start: 0.8353 (t70) cc_final: 0.8097 (t0) REVERT: B 175 GLN cc_start: 0.8481 (pm20) cc_final: 0.7877 (pm20) REVERT: B 217 MET cc_start: 0.8180 (ppp) cc_final: 0.7808 (ppp) REVERT: G 21 MET cc_start: 0.6756 (ttm) cc_final: 0.6369 (mtt) REVERT: N 53 GLN cc_start: 0.8588 (mp10) cc_final: 0.8217 (mp10) REVERT: R 35 GLU cc_start: 0.7672 (mp0) cc_final: 0.7456 (mp0) REVERT: R 321 LEU cc_start: 0.7761 (tp) cc_final: 0.7549 (tt) REVERT: R 364 GLN cc_start: 0.8289 (pt0) cc_final: 0.8060 (pt0) REVERT: R 409 SER cc_start: 0.8270 (p) cc_final: 0.7941 (m) outliers start: 20 outliers final: 12 residues processed: 154 average time/residue: 0.2702 time to fit residues: 54.4092 Evaluate side-chains 146 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 N residue 20 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET 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: 0.9980 chunk 102 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.151619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118076 restraints weight = 10808.266| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.70 r_work: 0.3216 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9059 Z= 0.208 Angle : 0.514 7.460 12289 Z= 0.276 Chirality : 0.042 0.145 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.445 39.838 1251 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.77 % Allowed : 15.93 % Favored : 81.31 % 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 (0.25), residues: 1134 helix: 1.77 (0.26), residues: 428 sheet: -0.27 (0.32), residues: 226 loop : -0.33 (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 0.006 0.000 ARG R 396 *********************** 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 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.151 Fit side-chains REVERT: A 24 LYS cc_start: 0.7872 (tptt) cc_final: 0.7410 (tptt) REVERT: A 333 ASP cc_start: 0.8355 (t70) cc_final: 0.8090 (t0) REVERT: B 175 GLN cc_start: 0.8494 (pm20) cc_final: 0.7897 (pm20) REVERT: B 217 MET cc_start: 0.8198 (ppp) cc_final: 0.7831 (ppp) REVERT: G 21 MET cc_start: 0.6735 (ttm) cc_final: 0.6393 (mtt) REVERT: G 47 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.5780 (mp0) REVERT: N 6 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7306 (mm-30) REVERT: N 83 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8340 (mtp) REVERT: R 321 LEU cc_start: 0.7809 (tp) cc_final: 0.7585 (tt) REVERT: R 364 GLN cc_start: 0.8312 (pt0) cc_final: 0.8065 (pt0) REVERT: R 409 SER cc_start: 0.8240 (p) cc_final: 0.7920 (m) outliers start: 25 outliers final: 21 residues processed: 151 average time/residue: 0.2821 time to fit residues: 56.4771 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 : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 110 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 0.0000 chunk 50 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.152544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119007 restraints weight = 10727.309| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.74 r_work: 0.3243 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9059 Z= 0.162 Angle : 0.500 9.008 12289 Z= 0.269 Chirality : 0.041 0.142 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.439 40.640 1251 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.21 % Allowed : 16.59 % Favored : 81.19 % 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: 2.01 (0.26), residues: 428 sheet: -0.19 (0.33), residues: 220 loop : -0.32 (0.29), residues: 486 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 *********************** 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 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.911 Fit side-chains REVERT: A 24 LYS cc_start: 0.7904 (tptt) cc_final: 0.7431 (tptt) REVERT: A 333 ASP cc_start: 0.8360 (t70) cc_final: 0.8100 (t0) REVERT: B 175 GLN cc_start: 0.8440 (pm20) cc_final: 0.7840 (pm20) REVERT: B 217 MET cc_start: 0.8147 (ppp) cc_final: 0.7787 (ppp) REVERT: G 21 MET cc_start: 0.6728 (ttm) cc_final: 0.6377 (mtt) REVERT: N 6 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7394 (mm-30) REVERT: N 53 GLN cc_start: 0.8550 (mp10) cc_final: 0.8207 (mp10) REVERT: R 35 GLU cc_start: 0.7657 (mp0) cc_final: 0.7407 (mp0) REVERT: R 189 MET cc_start: 0.7526 (tmm) cc_final: 0.7225 (tmm) REVERT: R 321 LEU cc_start: 0.7805 (tp) cc_final: 0.7568 (tt) REVERT: R 409 SER cc_start: 0.8190 (p) cc_final: 0.7869 (m) REVERT: R 431 GLU cc_start: 0.6981 (tt0) cc_final: 0.6752 (tt0) outliers start: 20 outliers final: 18 residues processed: 153 average time/residue: 0.2697 time to fit residues: 53.8637 Evaluate side-chains 149 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 8.9990 chunk 83 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.150110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116646 restraints weight = 10945.545| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.71 r_work: 0.3201 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.004 0.058 9059 Z= 0.270 Angle : 0.550 8.748 12289 Z= 0.296 Chirality : 0.043 0.163 1383 Planarity : 0.003 0.039 1576 Dihedral : 4.592 43.416 1250 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.88 % Allowed : 16.70 % Favored : 80.42 % 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: 0.68 (0.25), residues: 1134 helix: 1.83 (0.25), residues: 428 sheet: -0.31 (0.32), residues: 229 loop : -0.36 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 298 HIS 0.005 0.001 HIS A 347 PHE 0.020 0.002 PHE R 311 TYR 0.029 0.002 TYR R 191 ARG 0.007 0.000 ARG R 396 *********************** 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 158 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.923 Fit side-chains REVERT: A 15 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6742 (tp30) REVERT: A 24 LYS cc_start: 0.7927 (tptt) cc_final: 0.7441 (tptt) REVERT: A 333 ASP cc_start: 0.8368 (t70) cc_final: 0.8100 (t0) REVERT: B 156 GLN cc_start: 0.8562 (mt0) cc_final: 0.8282 (mt0) REVERT: B 175 GLN cc_start: 0.8538 (pm20) cc_final: 0.7956 (pm20) REVERT: B 217 MET cc_start: 0.8160 (ppp) cc_final: 0.7821 (ppp) REVERT: G 21 MET cc_start: 0.6747 (ttm) cc_final: 0.6446 (mtt) REVERT: G 47 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.5720 (mp0) REVERT: N 83 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8348 (mtp) REVERT: R 189 MET cc_start: 0.7441 (tmm) cc_final: 0.7179 (tmm) REVERT: R 321 LEU cc_start: 0.7859 (tp) cc_final: 0.7618 (tt) REVERT: R 326 VAL cc_start: 0.8064 (m) cc_final: 0.7827 (p) REVERT: R 391 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7197 (pt0) REVERT: R 409 SER cc_start: 0.8306 (p) cc_final: 0.7994 (m) outliers start: 26 outliers final: 23 residues processed: 147 average time/residue: 0.2744 time to fit residues: 52.2726 Evaluate side-chains 148 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 221 THR Chi-restraints excluded: chain B residue 270 ILE 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 B residue 340 ASN 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: 1.9990 chunk 55 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.150929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117406 restraints weight = 10938.840| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.74 r_work: 0.3220 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9059 Z= 0.181 Angle : 0.507 7.514 12289 Z= 0.274 Chirality : 0.041 0.153 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.478 41.203 1250 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.54 % Allowed : 17.26 % 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: 0.86 (0.25), residues: 1134 helix: 2.01 (0.25), residues: 430 sheet: -0.21 (0.31), residues: 224 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 0.028 0.001 TYR R 191 ARG 0.007 0.000 ARG R 396 *********************** 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 151 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.966 Fit side-chains REVERT: A 15 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6761 (tp30) REVERT: A 24 LYS cc_start: 0.7934 (tptt) cc_final: 0.7457 (tptt) REVERT: A 28 LYS cc_start: 0.8674 (pptt) cc_final: 0.8239 (tttt) REVERT: A 333 ASP cc_start: 0.8381 (t70) cc_final: 0.8109 (t0) REVERT: B 175 GLN cc_start: 0.8528 (pm20) cc_final: 0.7946 (pm20) REVERT: B 217 MET cc_start: 0.8145 (ppp) cc_final: 0.7806 (ppp) REVERT: G 21 MET cc_start: 0.6677 (ttm) cc_final: 0.6363 (mtt) REVERT: G 47 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.5793 (mp0) REVERT: N 6 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7273 (mm-30) REVERT: N 53 GLN cc_start: 0.8510 (mp10) cc_final: 0.8201 (mp10) REVERT: N 83 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8390 (mtp) REVERT: R 35 GLU cc_start: 0.7566 (mp0) cc_final: 0.7340 (mp0) REVERT: R 189 MET cc_start: 0.7450 (tmm) cc_final: 0.7230 (tmm) REVERT: R 321 LEU cc_start: 0.7828 (tp) cc_final: 0.7583 (tt) REVERT: R 391 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7200 (pt0) REVERT: R 409 SER cc_start: 0.8233 (p) cc_final: 0.7891 (m) outliers start: 23 outliers final: 19 residues processed: 141 average time/residue: 0.2671 time to fit residues: 49.5538 Evaluate side-chains 145 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 80 optimal weight: 0.0370 chunk 4 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.9262 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.150748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117421 restraints weight = 10987.774| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.69 r_work: 0.3209 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9059 Z= 0.236 Angle : 0.536 7.720 12289 Z= 0.287 Chirality : 0.042 0.160 1383 Planarity : 0.003 0.039 1576 Dihedral : 4.513 41.831 1250 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.65 % Allowed : 17.81 % Favored : 79.54 % 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: 0.81 (0.25), residues: 1134 helix: 2.03 (0.25), residues: 425 sheet: -0.25 (0.32), residues: 221 loop : -0.37 (0.29), residues: 488 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 0.007 0.000 ARG R 396 *********************** 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 144 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.879 Fit side-chains REVERT: A 15 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6718 (tp30) REVERT: A 24 LYS cc_start: 0.7955 (tptt) cc_final: 0.7473 (tptt) REVERT: A 28 LYS cc_start: 0.8669 (pptt) cc_final: 0.8241 (tttt) REVERT: A 333 ASP cc_start: 0.8376 (t70) cc_final: 0.8095 (t0) REVERT: B 175 GLN cc_start: 0.8553 (pm20) cc_final: 0.7972 (pm20) REVERT: B 217 MET cc_start: 0.8155 (ppp) cc_final: 0.7804 (ppp) REVERT: G 21 MET cc_start: 0.6686 (ttm) cc_final: 0.6395 (mtt) REVERT: G 47 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.5702 (mp0) REVERT: N 6 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7306 (mm-30) REVERT: N 53 GLN cc_start: 0.8563 (mp10) cc_final: 0.8229 (mp10) REVERT: N 83 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8394 (mtp) REVERT: R 35 GLU cc_start: 0.7556 (mp0) cc_final: 0.7338 (mp0) REVERT: R 189 MET cc_start: 0.7490 (tmm) cc_final: 0.7261 (tmm) REVERT: R 321 LEU cc_start: 0.7847 (tp) cc_final: 0.7594 (tt) REVERT: R 391 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7203 (pt0) REVERT: R 409 SER cc_start: 0.8243 (p) cc_final: 0.7917 (m) outliers start: 24 outliers final: 20 residues processed: 133 average time/residue: 0.2660 time to fit residues: 46.7911 Evaluate side-chains 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 161 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.150060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116563 restraints weight = 10886.689| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.73 r_work: 0.3212 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9059 Z= 0.204 Angle : 0.514 7.407 12289 Z= 0.277 Chirality : 0.041 0.155 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.426 40.780 1250 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.99 % Allowed : 17.81 % Favored : 79.20 % 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: 0.87 (0.25), residues: 1134 helix: 2.10 (0.25), residues: 425 sheet: -0.24 (0.32), residues: 221 loop : -0.33 (0.29), residues: 488 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 0.027 0.001 TYR R 191 ARG 0.007 0.000 ARG R 396 ********************** 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 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.934 Fit side-chains REVERT: A 15 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6720 (tp30) REVERT: A 24 LYS cc_start: 0.7950 (tptt) cc_final: 0.7468 (tptt) REVERT: A 28 LYS cc_start: 0.8655 (pptt) cc_final: 0.8216 (tttt) REVERT: A 333 ASP cc_start: 0.8392 (t70) cc_final: 0.8115 (t0) REVERT: B 175 GLN cc_start: 0.8546 (pm20) cc_final: 0.7974 (pm20) REVERT: B 217 MET cc_start: 0.8164 (ppp) cc_final: 0.7822 (ppp) REVERT: G 21 MET cc_start: 0.6694 (ttm) cc_final: 0.6390 (mtt) REVERT: G 47 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.5763 (mp0) REVERT: N 6 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7347 (mm-30) REVERT: N 53 GLN cc_start: 0.8556 (mp10) cc_final: 0.8222 (mp10) REVERT: N 83 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8401 (mtp) REVERT: R 35 GLU cc_start: 0.7548 (mp0) cc_final: 0.7333 (mp0) REVERT: R 321 LEU cc_start: 0.7843 (tp) cc_final: 0.7583 (tt) REVERT: R 391 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7224 (pt0) REVERT: R 409 SER cc_start: 0.8240 (p) cc_final: 0.7889 (m) outliers start: 27 outliers final: 21 residues processed: 139 average time/residue: 0.2873 time to fit residues: 52.3273 Evaluate side-chains 143 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 161 SER 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 B residue 340 ASN 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: 5.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 52 optimal weight: 0.0000 chunk 28 optimal weight: 0.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.151804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118635 restraints weight = 10946.791| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.67 r_work: 0.3227 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9059 Z= 0.193 Angle : 0.513 7.406 12289 Z= 0.276 Chirality : 0.041 0.153 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.425 40.477 1250 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.65 % Allowed : 18.47 % Favored : 78.87 % 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: 0.93 (0.25), residues: 1134 helix: 2.16 (0.25), residues: 425 sheet: -0.23 (0.32), residues: 219 loop : -0.31 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 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 0.008 0.000 ARG R 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5569.40 seconds wall clock time: 98 minutes 35.34 seconds (5915.34 seconds total)