Starting phenix.real_space_refine on Fri Sep 11 12:28:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nbi_0412/09_2026/6nbi_0412.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbi_0412/09_2026/6nbi_0412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nbi_0412/09_2026/6nbi_0412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbi_0412/09_2026/6nbi_0412.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nbi_0412/09_2026/6nbi_0412.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nbi_0412/09_2026/6nbi_0412.cif" model { file = "/net/cci-nas-00/data/ceres_data/6nbi_0412/09_2026/6nbi_0412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbi_0412/09_2026/6nbi_0412.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 57 5.16 5 C 5875 2.51 5 N 1599 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9195 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3020 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 10, 'TRANS': 358} Chain breaks: 4 Chain: "P" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 253 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "A" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1840 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.06, per 1000 atoms: 0.22 Number of scatterers: 9195 At special positions: 0 Unit cell: (127.764, 99.372, 148.044, 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 57 16.00 O 1664 8.00 N 1599 7.00 C 5875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.04 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.04 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 327.0 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 41.1% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 32 through 53 removed outlier: 4.162A pdb=" N GLU R 36 " --> pdb=" O MET R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 201 removed outlier: 3.878A pdb=" N GLU R 182 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU R 187 " --> pdb=" O VAL R 183 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU R 199 " --> pdb=" O TYR R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 218 through 250 removed outlier: 3.793A pdb=" N MET R 224 " --> pdb=" O ASN R 220 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS R 240 " --> pdb=" O SER R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 313 removed outlier: 4.227A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE R 311 " --> pdb=" O HIS R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 4.153A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.629A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 369 removed outlier: 3.546A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 371 through 395 removed outlier: 3.708A pdb=" N VAL R 384 " --> pdb=" O ASN R 380 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR R 392 " --> pdb=" O LYS R 388 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA R 394 " --> pdb=" O ARG R 390 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY R 395 " --> pdb=" O GLU R 391 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 412 Processing helix chain 'R' and resid 419 through 424 Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.747A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR R 459 " --> pdb=" O VAL R 455 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing helix chain 'P' and resid 2 through 16 Processing helix chain 'P' and resid 17 through 25 removed outlier: 3.932A pdb=" N ARG P 21 " --> pdb=" O ASP P 17 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS P 25 " --> pdb=" O ARG P 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.667A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.725A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.502A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.797A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.099A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.636A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.515A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.025A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 126 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.591A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS A 220 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.133A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.133A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.866A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.534A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.660A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.595A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.626A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.819A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1206 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: 1.38 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2960 1.35 - 1.47: 2312 1.47 - 1.59: 4051 1.59 - 1.71: 0 1.71 - 1.83: 80 Bond restraints: 9403 Sorted by residual: bond pdb=" C THR A 320 " pdb=" N PRO A 321 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.19e-02 7.06e+03 6.81e+00 bond pdb=" C MET R 414 " pdb=" N PRO R 415 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.23e-02 6.61e+03 4.91e+00 bond pdb=" C PHE A 312 " pdb=" O PHE A 312 " ideal model delta sigma weight residual 1.249 1.232 0.017 8.50e-03 1.38e+04 4.05e+00 bond pdb=" C ALA R 122 " pdb=" N PRO R 123 " ideal model delta sigma weight residual 1.331 1.354 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 1.518 1.539 -0.021 1.13e-02 7.83e+03 3.36e+00 ... (remaining 9398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 11283 1.33 - 2.66: 1286 2.66 - 3.99: 150 3.99 - 5.32: 25 5.32 - 6.65: 2 Bond angle restraints: 12746 Sorted by residual: angle pdb=" C ASP A 354 " pdb=" N GLY A 355 " pdb=" CA GLY A 355 " ideal model delta sigma weight residual 119.98 124.68 -4.70 1.11e+00 8.12e-01 1.79e+01 angle pdb=" N VAL R 171 " pdb=" CA VAL R 171 " pdb=" C VAL R 171 " ideal model delta sigma weight residual 106.21 109.86 -3.65 1.07e+00 8.73e-01 1.17e+01 angle pdb=" C THR N 61 " pdb=" N GLY N 62 " pdb=" CA GLY N 62 " ideal model delta sigma weight residual 120.03 123.78 -3.75 1.12e+00 7.97e-01 1.12e+01 angle pdb=" C GLU A 370 " pdb=" N ASN A 371 " pdb=" CA ASN A 371 " ideal model delta sigma weight residual 120.38 124.88 -4.50 1.37e+00 5.33e-01 1.08e+01 angle pdb=" C GLN R 451 " pdb=" N GLY R 452 " pdb=" CA GLY R 452 " ideal model delta sigma weight residual 119.99 123.65 -3.66 1.13e+00 7.83e-01 1.05e+01 ... (remaining 12741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.33: 5182 13.33 - 26.67: 292 26.67 - 40.00: 49 40.00 - 53.33: 11 53.33 - 66.66: 6 Dihedral angle restraints: 5540 sinusoidal: 2223 harmonic: 3317 Sorted by residual: 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 93.00 134.92 -41.92 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU R 289 " pdb=" C LEU R 289 " pdb=" N TYR R 290 " pdb=" CA TYR R 290 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 5537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 871 0.046 - 0.091: 428 0.091 - 0.137: 97 0.137 - 0.183: 19 0.183 - 0.228: 1 Chirality restraints: 1416 Sorted by residual: chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C10 CLR R 603 " pdb=" C1 CLR R 603 " pdb=" C5 CLR R 603 " pdb=" C9 CLR R 603 " both_signs ideal model delta sigma weight residual False -2.85 -2.67 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" C10 CLR R 602 " pdb=" C1 CLR R 602 " pdb=" C5 CLR R 602 " pdb=" C9 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.85 -2.67 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 1413 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS R 34 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C LYS R 34 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS R 34 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU R 35 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO G 49 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 32 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.91e+00 pdb=" C LYS A 32 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS A 32 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 33 " -0.010 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2845 2.85 - 3.36: 7823 3.36 - 3.87: 14237 3.87 - 4.39: 16041 4.39 - 4.90: 28235 Nonbonded interactions: 69181 Sorted by model distance: nonbonded pdb=" OH TYR R 421 " pdb=" OE1 GLN R 451 " model vdw 2.337 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.373 3.040 nonbonded pdb=" O MET R 425 " pdb=" N ALA P 1 " model vdw 2.373 3.120 nonbonded pdb=" O SER R 341 " pdb=" OG1 THR R 345 " model vdw 2.390 3.040 ... (remaining 69176 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.490 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 0.005 0.031 9409 Z= 0.363 Angle : 0.880 7.200 12758 Z= 0.594 Chirality : 0.053 0.228 1416 Planarity : 0.004 0.068 1604 Dihedral : 8.852 66.664 3376 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.31 % Allowed : 0.72 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.22), residues: 1115 helix: -0.65 (0.22), residues: 447 sheet: -0.86 (0.33), residues: 217 loop : -1.61 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.025 0.002 TYR R 191 PHE 0.014 0.002 PHE R 447 TRP 0.024 0.002 TRP R 154 HIS 0.006 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.36 ( 9403) covalent geometry : angle 0.87594 / 0.59 (12746) SS BOND : bond 0.00647 / 0.34 ( 6) SS BOND : angle 2.78457 / 1.21 ( 12) hydrogen bonds : bond 0.17252 / 11.47 ( 421) hydrogen bonds : angle 7.22663 / 5.17 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 528 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 307 HIS cc_start: 0.8222 (t-90) cc_final: 0.7725 (t-90) REVERT: R 445 MET cc_start: 0.8003 (mmp) cc_final: 0.7617 (mmp) REVERT: P 9 HIS cc_start: 0.8751 (m90) cc_final: 0.8517 (m90) REVERT: A 13 ARG cc_start: 0.8455 (mtt180) cc_final: 0.7538 (mpt180) REVERT: A 16 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8824 (pt0) REVERT: A 278 ASN cc_start: 0.8348 (m110) cc_final: 0.7768 (m-40) REVERT: A 286 SER cc_start: 0.9489 (t) cc_final: 0.9266 (p) REVERT: B 20 ASP cc_start: 0.9095 (m-30) cc_final: 0.8650 (m-30) REVERT: B 51 LEU cc_start: 0.7980 (mt) cc_final: 0.7776 (mp) REVERT: B 184 THR cc_start: 0.8195 (p) cc_final: 0.7924 (t) REVERT: B 301 LYS cc_start: 0.8297 (mmmm) cc_final: 0.7864 (mmtp) REVERT: B 316 SER cc_start: 0.8935 (p) cc_final: 0.8725 (t) REVERT: G 38 MET cc_start: 0.9299 (mtm) cc_final: 0.9085 (mtt) REVERT: N 77 ASN cc_start: 0.9057 (m-40) cc_final: 0.8783 (t0) REVERT: N 122 THR cc_start: 0.7405 (t) cc_final: 0.6807 (p) outliers start: 3 outliers final: 2 residues processed: 530 average time/residue: 0.1148 time to fit residues: 79.5217 Evaluate side-chains 302 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 300 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 295 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 438 GLN P 10 GLN ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS B 156 GLN B 268 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.111652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088222 restraints weight = 30423.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.090646 restraints weight = 19384.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.092335 restraints weight = 14090.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093483 restraints weight = 11122.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.094244 restraints weight = 9382.226| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9409 Z= 0.169 Angle : 0.688 10.059 12758 Z= 0.361 Chirality : 0.044 0.337 1416 Planarity : 0.005 0.047 1604 Dihedral : 4.798 43.458 1281 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 5.25 % Allowed : 15.53 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1115 helix: 1.10 (0.25), residues: 437 sheet: -0.31 (0.31), residues: 237 loop : -1.22 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 38 TYR 0.014 0.002 TYR N 32 PHE 0.022 0.002 PHE B 222 TRP 0.014 0.002 TRP R 118 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 9403) covalent geometry : angle 0.68511 / 0.36 (12746) SS BOND : bond 0.01095 / 0.51 ( 6) SS BOND : angle 2.26577 / 1.16 ( 12) hydrogen bonds : bond 0.04762 / 3.24 ( 421) hydrogen bonds : angle 5.28464 / 3.79 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 307 HIS cc_start: 0.8330 (t-90) cc_final: 0.8093 (t-90) REVERT: R 364 GLN cc_start: 0.9354 (tp40) cc_final: 0.9154 (tp40) REVERT: R 440 GLN cc_start: 0.9063 (pp30) cc_final: 0.8535 (pp30) REVERT: R 442 HIS cc_start: 0.8789 (m90) cc_final: 0.8575 (m90) REVERT: P 6 GLN cc_start: 0.8687 (mt0) cc_final: 0.8452 (tp40) REVERT: P 9 HIS cc_start: 0.8471 (m90) cc_final: 0.8123 (m-70) REVERT: A 17 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8867 (mmtt) REVERT: A 218 ASN cc_start: 0.8241 (p0) cc_final: 0.7989 (p0) REVERT: A 240 ASP cc_start: 0.8627 (p0) cc_final: 0.8181 (p0) REVERT: A 264 ASN cc_start: 0.8513 (t0) cc_final: 0.7741 (t0) REVERT: B 12 GLU cc_start: 0.8963 (tp30) cc_final: 0.8761 (tp30) REVERT: B 16 ASN cc_start: 0.9310 (m-40) cc_final: 0.8867 (m-40) REVERT: B 51 LEU cc_start: 0.9568 (mt) cc_final: 0.9215 (mp) REVERT: B 184 THR cc_start: 0.8626 (p) cc_final: 0.8094 (t) REVERT: B 275 SER cc_start: 0.9482 (t) cc_final: 0.9278 (m) REVERT: B 308 LEU cc_start: 0.9099 (mp) cc_final: 0.8774 (tp) REVERT: B 339 TRP cc_start: 0.7933 (m100) cc_final: 0.7124 (m100) REVERT: G 11 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8619 (pp30) REVERT: N 20 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.6558 (mt) outliers start: 51 outliers final: 30 residues processed: 348 average time/residue: 0.1015 time to fit residues: 48.4507 Evaluate side-chains 295 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 216 HIS R 295 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 19 GLN A 29 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 271 ASN A 377 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.111167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.088186 restraints weight = 31559.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.090221 restraints weight = 21494.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.091492 restraints weight = 16447.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.092452 restraints weight = 13680.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.093130 restraints weight = 11974.624| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9409 Z= 0.208 Angle : 0.688 10.413 12758 Z= 0.358 Chirality : 0.044 0.334 1416 Planarity : 0.005 0.060 1604 Dihedral : 4.931 46.942 1281 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 6.17 % Allowed : 17.39 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.24), residues: 1115 helix: 1.09 (0.24), residues: 437 sheet: -0.05 (0.31), residues: 235 loop : -0.99 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 19 TYR 0.019 0.002 TYR R 191 PHE 0.019 0.002 PHE R 327 TRP 0.015 0.002 TRP R 352 HIS 0.005 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 ( 9403) covalent geometry : angle 0.68638 / 0.36 (12746) SS BOND : bond 0.00368 / 0.16 ( 6) SS BOND : angle 1.84190 / 0.93 ( 12) hydrogen bonds : bond 0.04537 / 3.08 ( 421) hydrogen bonds : angle 5.30982 / 3.80 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 220 ASN cc_start: 0.8956 (m-40) cc_final: 0.8601 (m-40) REVERT: R 237 ILE cc_start: 0.9353 (mm) cc_final: 0.9130 (mm) REVERT: R 324 PHE cc_start: 0.8355 (m-10) cc_final: 0.8118 (m-80) REVERT: R 442 HIS cc_start: 0.8326 (m90) cc_final: 0.8113 (m90) REVERT: R 445 MET cc_start: 0.7675 (mmp) cc_final: 0.7400 (mmp) REVERT: P 9 HIS cc_start: 0.8246 (m90) cc_final: 0.7480 (m-70) REVERT: A 33 ASP cc_start: 0.8014 (p0) cc_final: 0.7712 (t0) REVERT: A 365 CYS cc_start: 0.7952 (t) cc_final: 0.7566 (m) REVERT: B 6 GLN cc_start: 0.9450 (pp30) cc_final: 0.9111 (pm20) REVERT: B 12 GLU cc_start: 0.8901 (tp30) cc_final: 0.8245 (tp30) REVERT: B 15 LYS cc_start: 0.9439 (ptpp) cc_final: 0.9157 (pttp) REVERT: B 124 TYR cc_start: 0.8698 (m-80) cc_final: 0.8416 (m-80) REVERT: B 138 GLU cc_start: 0.8241 (pp20) cc_final: 0.8017 (pp20) REVERT: B 222 PHE cc_start: 0.8174 (m-80) cc_final: 0.7686 (m-10) REVERT: B 308 LEU cc_start: 0.8999 (mp) cc_final: 0.8435 (tp) REVERT: B 339 TRP cc_start: 0.7847 (m100) cc_final: 0.7165 (m100) REVERT: G 11 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8532 (pp30) REVERT: N 90 ASP cc_start: 0.7854 (m-30) cc_final: 0.7459 (m-30) REVERT: N 91 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7684 (t) outliers start: 60 outliers final: 45 residues processed: 307 average time/residue: 0.0930 time to fit residues: 39.9811 Evaluate side-chains 281 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 225 HIS ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.109658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.086867 restraints weight = 32114.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.088950 restraints weight = 21575.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.090337 restraints weight = 16260.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091196 restraints weight = 13331.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.091919 restraints weight = 11659.443| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9409 Z= 0.184 Angle : 0.660 9.458 12758 Z= 0.348 Chirality : 0.044 0.313 1416 Planarity : 0.004 0.048 1604 Dihedral : 4.852 48.079 1281 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.28 % Allowed : 20.16 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1115 helix: 1.00 (0.24), residues: 443 sheet: 0.13 (0.31), residues: 235 loop : -0.99 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.021 0.002 TYR R 191 PHE 0.020 0.002 PHE R 378 TRP 0.015 0.002 TRP R 118 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 9403) covalent geometry : angle 0.65823 / 0.35 (12746) SS BOND : bond 0.00378 / 0.19 ( 6) SS BOND : angle 1.72151 / 0.90 ( 12) hydrogen bonds : bond 0.04406 / 3.01 ( 421) hydrogen bonds : angle 5.15814 / 3.73 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 252 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 220 ASN cc_start: 0.8958 (m-40) cc_final: 0.8531 (m-40) REVERT: R 324 PHE cc_start: 0.8402 (m-10) cc_final: 0.8178 (m-80) REVERT: R 440 GLN cc_start: 0.9015 (pp30) cc_final: 0.8708 (pp30) REVERT: P 2 VAL cc_start: 0.9399 (t) cc_final: 0.9095 (m) REVERT: P 9 HIS cc_start: 0.8052 (m90) cc_final: 0.7553 (m-70) REVERT: A 33 ASP cc_start: 0.7912 (p0) cc_final: 0.7687 (t0) REVERT: A 339 TYR cc_start: 0.8768 (m-10) cc_final: 0.8559 (m-10) REVERT: A 365 CYS cc_start: 0.7978 (t) cc_final: 0.7760 (m) REVERT: B 6 GLN cc_start: 0.9441 (pp30) cc_final: 0.9154 (pm20) REVERT: B 12 GLU cc_start: 0.8940 (tp30) cc_final: 0.8339 (tp30) REVERT: B 15 LYS cc_start: 0.9430 (ptpp) cc_final: 0.9144 (pttp) REVERT: B 16 ASN cc_start: 0.9268 (m-40) cc_final: 0.8718 (m-40) REVERT: B 124 TYR cc_start: 0.8607 (m-80) cc_final: 0.8241 (m-80) REVERT: B 222 PHE cc_start: 0.8170 (m-80) cc_final: 0.7480 (m-10) REVERT: B 308 LEU cc_start: 0.8933 (mp) cc_final: 0.8421 (tp) REVERT: B 339 TRP cc_start: 0.7984 (m100) cc_final: 0.7200 (m100) REVERT: G 11 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8515 (pp30) REVERT: G 28 ILE cc_start: 0.8695 (mp) cc_final: 0.8472 (mp) REVERT: G 29 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7890 (ttmm) REVERT: N 20 LEU cc_start: 0.7353 (mt) cc_final: 0.6747 (mt) REVERT: N 50 ASP cc_start: 0.8882 (p0) cc_final: 0.8609 (p0) REVERT: N 81 LEU cc_start: 0.7742 (tt) cc_final: 0.7312 (tt) REVERT: N 90 ASP cc_start: 0.7952 (m-30) cc_final: 0.7213 (m-30) REVERT: N 91 THR cc_start: 0.7832 (OUTLIER) cc_final: 0.7625 (t) REVERT: N 94 TYR cc_start: 0.8787 (m-80) cc_final: 0.8520 (m-80) outliers start: 61 outliers final: 47 residues processed: 291 average time/residue: 0.0932 time to fit residues: 38.1890 Evaluate side-chains 281 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 4 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 19 optimal weight: 0.0000 chunk 98 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 45 GLN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.110334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.087743 restraints weight = 30186.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090010 restraints weight = 19378.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.091537 restraints weight = 14181.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.092620 restraints weight = 11356.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.093308 restraints weight = 9666.835| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.7223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9409 Z= 0.115 Angle : 0.626 10.552 12758 Z= 0.323 Chirality : 0.043 0.294 1416 Planarity : 0.004 0.052 1604 Dihedral : 4.655 50.409 1281 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.35 % Allowed : 22.22 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1115 helix: 1.19 (0.25), residues: 438 sheet: 0.33 (0.32), residues: 229 loop : -0.93 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 19 TYR 0.027 0.001 TYR R 421 PHE 0.015 0.001 PHE R 378 TRP 0.017 0.001 TRP R 437 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9403) covalent geometry : angle 0.62485 / 0.32 (12746) SS BOND : bond 0.00287 / 0.15 ( 6) SS BOND : angle 1.28035 / 0.68 ( 12) hydrogen bonds : bond 0.03943 / 2.71 ( 421) hydrogen bonds : angle 4.91190 / 3.56 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 135 ILE cc_start: 0.3501 (OUTLIER) cc_final: 0.3292 (tp) REVERT: R 220 ASN cc_start: 0.8932 (m-40) cc_final: 0.8514 (m-40) REVERT: R 368 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9101 (mm) REVERT: P 2 VAL cc_start: 0.9315 (t) cc_final: 0.9083 (m) REVERT: P 5 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9084 (mp) REVERT: P 8 MET cc_start: 0.8494 (tmm) cc_final: 0.8215 (tmm) REVERT: A 220 HIS cc_start: 0.7731 (m-70) cc_final: 0.7446 (m-70) REVERT: A 358 TYR cc_start: 0.7269 (m-80) cc_final: 0.7062 (m-10) REVERT: A 360 TYR cc_start: 0.8257 (m-80) cc_final: 0.7775 (m-80) REVERT: A 365 CYS cc_start: 0.8221 (t) cc_final: 0.7848 (m) REVERT: A 385 ARG cc_start: 0.8739 (mtp180) cc_final: 0.8174 (mtp85) REVERT: A 391 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: B 6 GLN cc_start: 0.9438 (pp30) cc_final: 0.9090 (pm20) REVERT: B 12 GLU cc_start: 0.8960 (tp30) cc_final: 0.8392 (tp30) REVERT: B 15 LYS cc_start: 0.9453 (ptpp) cc_final: 0.9190 (pttp) REVERT: B 16 ASN cc_start: 0.9274 (m-40) cc_final: 0.8786 (m-40) REVERT: B 124 TYR cc_start: 0.8873 (m-80) cc_final: 0.8450 (m-80) REVERT: B 215 GLU cc_start: 0.8807 (mp0) cc_final: 0.8204 (mp0) REVERT: B 222 PHE cc_start: 0.8160 (m-80) cc_final: 0.7544 (m-10) REVERT: B 308 LEU cc_start: 0.9020 (mp) cc_final: 0.8535 (tp) REVERT: B 339 TRP cc_start: 0.7891 (m100) cc_final: 0.7131 (m100) REVERT: G 11 GLN cc_start: 0.9022 (pt0) cc_final: 0.8584 (pp30) REVERT: G 25 ILE cc_start: 0.8512 (mt) cc_final: 0.8273 (mt) REVERT: N 19 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7486 (ttp80) REVERT: N 20 LEU cc_start: 0.7408 (mt) cc_final: 0.7187 (mp) REVERT: N 50 ASP cc_start: 0.8882 (p0) cc_final: 0.8541 (p0) REVERT: N 87 LYS cc_start: 0.8765 (ttpp) cc_final: 0.7748 (ptmm) REVERT: N 90 ASP cc_start: 0.7933 (m-30) cc_final: 0.7203 (m-30) outliers start: 52 outliers final: 32 residues processed: 294 average time/residue: 0.0886 time to fit residues: 36.9556 Evaluate side-chains 280 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 445 MET Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 295 ASN P 6 GLN ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.110684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.088156 restraints weight = 30845.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.090427 restraints weight = 19818.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.091955 restraints weight = 14470.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.093001 restraints weight = 11584.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.093673 restraints weight = 9903.895| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9409 Z= 0.118 Angle : 0.641 9.991 12758 Z= 0.332 Chirality : 0.042 0.259 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.522 52.140 1281 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.14 % Allowed : 23.35 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1115 helix: 1.22 (0.25), residues: 437 sheet: 0.43 (0.33), residues: 229 loop : -0.95 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 19 TYR 0.028 0.002 TYR R 191 PHE 0.014 0.001 PHE R 378 TRP 0.018 0.001 TRP R 437 HIS 0.009 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9403) covalent geometry : angle 0.64012 / 0.33 (12746) SS BOND : bond 0.00279 / 0.15 ( 6) SS BOND : angle 1.15234 / 0.60 ( 12) hydrogen bonds : bond 0.03965 / 2.68 ( 421) hydrogen bonds : angle 4.89119 / 3.58 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 260 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 220 ASN cc_start: 0.8859 (m-40) cc_final: 0.8380 (m-40) REVERT: R 324 PHE cc_start: 0.8499 (m-80) cc_final: 0.8228 (m-80) REVERT: R 368 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9116 (mm) REVERT: R 442 HIS cc_start: 0.8274 (m90) cc_final: 0.8064 (m90) REVERT: P 6 GLN cc_start: 0.8613 (mm110) cc_final: 0.8374 (mm110) REVERT: P 9 HIS cc_start: 0.8182 (m-70) cc_final: 0.7225 (m-70) REVERT: A 270 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9527 (mm) REVERT: A 360 TYR cc_start: 0.8244 (m-80) cc_final: 0.7645 (m-80) REVERT: A 365 CYS cc_start: 0.8188 (t) cc_final: 0.7698 (m) REVERT: A 381 ASP cc_start: 0.8491 (t0) cc_final: 0.8239 (t0) REVERT: A 385 ARG cc_start: 0.8757 (mtp180) cc_final: 0.8123 (mtp85) REVERT: B 6 GLN cc_start: 0.9443 (pp30) cc_final: 0.9125 (pm20) REVERT: B 12 GLU cc_start: 0.8969 (tp30) cc_final: 0.8735 (tp30) REVERT: B 16 ASN cc_start: 0.9270 (m-40) cc_final: 0.8788 (m-40) REVERT: B 124 TYR cc_start: 0.8826 (m-80) cc_final: 0.8488 (m-80) REVERT: B 184 THR cc_start: 0.8118 (p) cc_final: 0.7506 (t) REVERT: B 222 PHE cc_start: 0.8114 (m-10) cc_final: 0.7601 (m-10) REVERT: G 11 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8618 (pp30) REVERT: G 17 GLU cc_start: 0.9131 (pp20) cc_final: 0.8928 (pp20) REVERT: G 25 ILE cc_start: 0.8474 (mt) cc_final: 0.8213 (mt) REVERT: N 20 LEU cc_start: 0.7332 (mt) cc_final: 0.6773 (mp) REVERT: N 50 ASP cc_start: 0.8869 (p0) cc_final: 0.8574 (p0) REVERT: N 70 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8827 (mp) REVERT: N 90 ASP cc_start: 0.7954 (m-30) cc_final: 0.7483 (m-30) outliers start: 50 outliers final: 36 residues processed: 287 average time/residue: 0.0896 time to fit residues: 36.2725 Evaluate side-chains 281 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 0.0270 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 216 HIS R 295 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.109242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.086796 restraints weight = 31033.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.089034 restraints weight = 19872.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.090542 restraints weight = 14574.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.091495 restraints weight = 11727.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.092244 restraints weight = 10104.028| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.7727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9409 Z= 0.135 Angle : 0.669 11.438 12758 Z= 0.347 Chirality : 0.043 0.223 1416 Planarity : 0.004 0.050 1604 Dihedral : 4.639 53.289 1279 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.35 % Allowed : 24.38 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1115 helix: 1.22 (0.25), residues: 437 sheet: 0.45 (0.34), residues: 230 loop : -0.90 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 8 TYR 0.016 0.001 TYR N 80 PHE 0.014 0.001 PHE R 378 TRP 0.013 0.001 TRP R 322 HIS 0.013 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 9403) covalent geometry : angle 0.66874 / 0.35 (12746) SS BOND : bond 0.00247 / 0.13 ( 6) SS BOND : angle 1.09528 / 0.57 ( 12) hydrogen bonds : bond 0.04094 / 2.72 ( 421) hydrogen bonds : angle 4.92829 / 3.62 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 220 ASN cc_start: 0.8823 (m-40) cc_final: 0.8382 (m-40) REVERT: R 324 PHE cc_start: 0.8474 (m-80) cc_final: 0.8187 (m-80) REVERT: R 368 LEU cc_start: 0.9370 (mm) cc_final: 0.9103 (mm) REVERT: R 441 MET cc_start: 0.8637 (tpp) cc_final: 0.8254 (tpp) REVERT: R 442 HIS cc_start: 0.8309 (m90) cc_final: 0.8056 (m90) REVERT: R 445 MET cc_start: 0.7445 (mmp) cc_final: 0.7192 (mmp) REVERT: R 467 GLN cc_start: 0.8503 (mt0) cc_final: 0.8243 (mt0) REVERT: A 270 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9412 (mm) REVERT: A 278 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8174 (t0) REVERT: A 358 TYR cc_start: 0.7061 (m-80) cc_final: 0.5487 (m-80) REVERT: A 365 CYS cc_start: 0.8174 (t) cc_final: 0.7706 (m) REVERT: A 375 VAL cc_start: 0.9344 (t) cc_final: 0.9013 (p) REVERT: B 12 GLU cc_start: 0.8910 (tp30) cc_final: 0.8667 (tp30) REVERT: B 16 ASN cc_start: 0.9283 (m-40) cc_final: 0.8816 (m-40) REVERT: B 124 TYR cc_start: 0.8835 (m-80) cc_final: 0.8513 (m-80) REVERT: B 184 THR cc_start: 0.8164 (p) cc_final: 0.7571 (t) REVERT: B 222 PHE cc_start: 0.8066 (m-10) cc_final: 0.7583 (m-10) REVERT: G 11 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8515 (pp30) REVERT: G 17 GLU cc_start: 0.9119 (pp20) cc_final: 0.8902 (pp20) REVERT: G 25 ILE cc_start: 0.8453 (mt) cc_final: 0.8223 (mt) REVERT: N 50 ASP cc_start: 0.8877 (p0) cc_final: 0.8672 (p0) REVERT: N 70 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8830 (pt) REVERT: N 87 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8334 (tmmt) outliers start: 52 outliers final: 46 residues processed: 286 average time/residue: 0.0901 time to fit residues: 36.4220 Evaluate side-chains 281 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.108135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085692 restraints weight = 30793.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087929 restraints weight = 20018.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.089409 restraints weight = 14751.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.090467 restraints weight = 11880.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091124 restraints weight = 10208.473| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.7953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9409 Z= 0.147 Angle : 0.699 12.031 12758 Z= 0.357 Chirality : 0.044 0.289 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.774 54.321 1279 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.25 % Allowed : 26.13 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1115 helix: 1.02 (0.24), residues: 448 sheet: 0.39 (0.34), residues: 228 loop : -0.91 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 38 TYR 0.019 0.002 TYR A 358 PHE 0.015 0.001 PHE R 447 TRP 0.015 0.001 TRP R 361 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 9403) covalent geometry : angle 0.69813 / 0.36 (12746) SS BOND : bond 0.00239 / 0.12 ( 6) SS BOND : angle 1.08359 / 0.56 ( 12) hydrogen bonds : bond 0.04007 / 2.71 ( 421) hydrogen bonds : angle 4.95883 / 3.68 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 220 ASN cc_start: 0.8792 (m-40) cc_final: 0.8393 (m-40) REVERT: R 324 PHE cc_start: 0.8477 (m-80) cc_final: 0.8178 (m-80) REVERT: R 368 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9128 (mm) REVERT: R 442 HIS cc_start: 0.8332 (m90) cc_final: 0.8056 (m90) REVERT: P 10 GLN cc_start: 0.8133 (pp30) cc_final: 0.7926 (pp30) REVERT: A 270 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9381 (mm) REVERT: A 278 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8170 (t0) REVERT: A 365 CYS cc_start: 0.8196 (t) cc_final: 0.7722 (m) REVERT: B 8 ARG cc_start: 0.7814 (mpp80) cc_final: 0.7600 (mpp80) REVERT: B 12 GLU cc_start: 0.8934 (tp30) cc_final: 0.8709 (tp30) REVERT: B 16 ASN cc_start: 0.9315 (m-40) cc_final: 0.8850 (m-40) REVERT: B 124 TYR cc_start: 0.8861 (m-80) cc_final: 0.8564 (m-80) REVERT: B 222 PHE cc_start: 0.8044 (m-10) cc_final: 0.7623 (m-10) REVERT: G 11 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8587 (pp30) REVERT: G 17 GLU cc_start: 0.9123 (pp20) cc_final: 0.8907 (pp20) REVERT: G 25 ILE cc_start: 0.8447 (mt) cc_final: 0.8188 (mt) REVERT: N 50 ASP cc_start: 0.8915 (p0) cc_final: 0.8641 (p0) REVERT: N 87 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8358 (tmmt) REVERT: N 95 TYR cc_start: 0.8775 (m-80) cc_final: 0.8463 (m-80) outliers start: 51 outliers final: 42 residues processed: 281 average time/residue: 0.0921 time to fit residues: 36.5360 Evaluate side-chains 281 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 58 optimal weight: 0.0060 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 451 GLN P 16 GLN A 220 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.110175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.087155 restraints weight = 31368.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.089473 restraints weight = 20262.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091021 restraints weight = 14893.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.091983 restraints weight = 11987.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.092725 restraints weight = 10376.344| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.8129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9409 Z= 0.126 Angle : 0.716 12.853 12758 Z= 0.360 Chirality : 0.044 0.283 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.643 54.590 1279 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.73 % Allowed : 27.06 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1115 helix: 1.18 (0.25), residues: 442 sheet: 0.30 (0.34), residues: 238 loop : -0.82 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 38 TYR 0.026 0.001 TYR R 429 PHE 0.013 0.001 PHE R 447 TRP 0.020 0.001 TRP B 339 HIS 0.008 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9403) covalent geometry : angle 0.71544 / 0.36 (12746) SS BOND : bond 0.00227 / 0.12 ( 6) SS BOND : angle 0.96630 / 0.50 ( 12) hydrogen bonds : bond 0.03886 / 2.62 ( 421) hydrogen bonds : angle 4.97875 / 3.69 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.1321 (mmt) cc_final: 0.0964 (mmt) REVERT: R 220 ASN cc_start: 0.8819 (m-40) cc_final: 0.8429 (m-40) REVERT: R 324 PHE cc_start: 0.8453 (m-80) cc_final: 0.8179 (m-80) REVERT: R 368 LEU cc_start: 0.9362 (mm) cc_final: 0.9119 (mm) REVERT: R 442 HIS cc_start: 0.8308 (m90) cc_final: 0.8015 (m90) REVERT: A 230 GLU cc_start: 0.6481 (mp0) cc_final: 0.6089 (mp0) REVERT: A 270 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9351 (mm) REVERT: A 278 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8198 (t0) REVERT: A 358 TYR cc_start: 0.7184 (m-80) cc_final: 0.6812 (m-80) REVERT: A 365 CYS cc_start: 0.8213 (t) cc_final: 0.7671 (m) REVERT: B 12 GLU cc_start: 0.8967 (tp30) cc_final: 0.8731 (tp30) REVERT: B 16 ASN cc_start: 0.9303 (m-40) cc_final: 0.8848 (m-40) REVERT: B 124 TYR cc_start: 0.8849 (m-80) cc_final: 0.8583 (m-80) REVERT: B 222 PHE cc_start: 0.7851 (m-10) cc_final: 0.7576 (m-10) REVERT: B 295 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8055 (t0) REVERT: G 11 GLN cc_start: 0.9034 (pt0) cc_final: 0.8623 (pp30) REVERT: G 17 GLU cc_start: 0.9146 (pp20) cc_final: 0.8929 (pp20) REVERT: G 25 ILE cc_start: 0.8397 (mt) cc_final: 0.8145 (mt) REVERT: N 80 TYR cc_start: 0.7327 (t80) cc_final: 0.6974 (t80) REVERT: N 81 LEU cc_start: 0.6925 (tt) cc_final: 0.6589 (tt) REVERT: N 87 LYS cc_start: 0.8689 (ttpp) cc_final: 0.8354 (tmmt) outliers start: 46 outliers final: 42 residues processed: 277 average time/residue: 0.0945 time to fit residues: 36.9167 Evaluate side-chains 281 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 76 optimal weight: 0.0670 chunk 98 optimal weight: 0.0670 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.112989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.090051 restraints weight = 32158.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.092237 restraints weight = 21083.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.093510 restraints weight = 15760.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.094656 restraints weight = 13101.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.095319 restraints weight = 11220.268| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.8324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9409 Z= 0.159 Angle : 0.748 12.902 12758 Z= 0.381 Chirality : 0.044 0.260 1416 Planarity : 0.004 0.052 1604 Dihedral : 4.831 55.582 1279 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.25 % Allowed : 26.95 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1115 helix: 1.02 (0.25), residues: 441 sheet: 0.22 (0.33), residues: 238 loop : -0.87 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 38 TYR 0.032 0.002 TYR R 191 PHE 0.020 0.002 PHE R 184 TRP 0.036 0.002 TRP B 339 HIS 0.004 0.001 HIS R 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 9403) covalent geometry : angle 0.74577 / 0.38 (12746) SS BOND : bond 0.00250 / 0.13 ( 6) SS BOND : angle 2.04740 / 1.07 ( 12) hydrogen bonds : bond 0.04098 / 2.77 ( 421) hydrogen bonds : angle 5.08037 / 3.76 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.1476 (mmt) cc_final: 0.1199 (mmt) REVERT: R 220 ASN cc_start: 0.8801 (m-40) cc_final: 0.8470 (m-40) REVERT: R 324 PHE cc_start: 0.8602 (m-80) cc_final: 0.8272 (m-80) REVERT: R 368 LEU cc_start: 0.9463 (mm) cc_final: 0.9235 (mm) REVERT: R 442 HIS cc_start: 0.8437 (m90) cc_final: 0.8155 (m90) REVERT: A 43 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8883 (mm) REVERT: A 230 GLU cc_start: 0.6488 (mp0) cc_final: 0.6088 (mp0) REVERT: A 270 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9429 (mm) REVERT: A 278 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8305 (t0) REVERT: A 365 CYS cc_start: 0.8269 (t) cc_final: 0.7624 (m) REVERT: B 10 GLU cc_start: 0.9313 (tm-30) cc_final: 0.9087 (tm-30) REVERT: B 12 GLU cc_start: 0.8972 (tp30) cc_final: 0.8759 (tp30) REVERT: B 16 ASN cc_start: 0.9300 (m-40) cc_final: 0.8875 (m-40) REVERT: B 75 GLN cc_start: 0.8577 (mp10) cc_final: 0.8152 (mp10) REVERT: B 124 TYR cc_start: 0.8766 (m-80) cc_final: 0.8505 (m-80) REVERT: B 222 PHE cc_start: 0.7871 (m-10) cc_final: 0.7552 (m-10) REVERT: B 295 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8229 (t0) REVERT: B 337 LYS cc_start: 0.8866 (tppt) cc_final: 0.8561 (tppt) REVERT: B 339 TRP cc_start: 0.7870 (m100) cc_final: 0.7125 (m100) REVERT: G 11 GLN cc_start: 0.9015 (pt0) cc_final: 0.8615 (pp30) REVERT: G 17 GLU cc_start: 0.9150 (pp20) cc_final: 0.8935 (pp20) REVERT: G 25 ILE cc_start: 0.8423 (mt) cc_final: 0.8172 (mt) REVERT: N 87 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8376 (tmmt) REVERT: N 95 TYR cc_start: 0.8793 (m-80) cc_final: 0.8529 (m-80) outliers start: 51 outliers final: 41 residues processed: 269 average time/residue: 0.0920 time to fit residues: 35.1563 Evaluate side-chains 276 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.112994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.090068 restraints weight = 32485.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.092170 restraints weight = 21830.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.093608 restraints weight = 16519.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094626 restraints weight = 13554.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.095181 restraints weight = 11736.896| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.8349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 9409 Z= 0.198 Angle : 1.033 59.200 12758 Z= 0.573 Chirality : 0.046 0.475 1416 Planarity : 0.004 0.059 1604 Dihedral : 4.833 55.585 1279 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.94 % Allowed : 27.57 % Favored : 67.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1115 helix: 0.97 (0.25), residues: 441 sheet: 0.25 (0.34), residues: 238 loop : -0.87 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 19 TYR 0.022 0.002 TYR R 429 PHE 0.020 0.001 PHE A 345 TRP 0.029 0.002 TRP B 339 HIS 0.041 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 ( 9403) covalent geometry : angle 1.03190 / 0.57 (12746) SS BOND : bond 0.00243 / 0.14 ( 6) SS BOND : angle 1.82209 / 0.95 ( 12) hydrogen bonds : bond 0.04116 / 2.79 ( 421) hydrogen bonds : angle 5.13106 / 3.82 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.26 seconds wall clock time: 32 minutes 11.34 seconds (1931.34 seconds total)