Starting phenix.real_space_refine on Sat Aug 23 03:10:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nbi_0412/08_2025/6nbi_0412.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbi_0412/08_2025/6nbi_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_0412/08_2025/6nbi_0412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbi_0412/08_2025/6nbi_0412.map" model { file = "/net/cci-nas-00/data/ceres_data/6nbi_0412/08_2025/6nbi_0412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbi_0412/08_2025/6nbi_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-2.0-5787/lib/python3.9/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: 2.26, per 1000 atoms: 0.25 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: 0.99 Conformation dependent library (CDL) restraints added in 380.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.32 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: 1.54 Time building geometry restraints manager: 1.25 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: 5337 13.33 - 26.67: 297 26.67 - 40.00: 53 40.00 - 53.33: 15 53.33 - 66.66: 6 Dihedral angle restraints: 5708 sinusoidal: 2391 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 5705 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.410 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 8.927 66.664 3544 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 aren 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 covalent geometry : bond 0.00525 ( 9403) covalent geometry : angle 0.87594 (12746) SS BOND : bond 0.00647 ( 6) SS BOND : angle 2.78457 ( 12) hydrogen bonds : bond 0.17252 ( 421) hydrogen bonds : angle 7.22663 ( 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 : 0.370 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: 0.7616 (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: 0.7769 (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: 0.7406 (t) cc_final: 0.6807 (p) outliers start: 3 outliers final: 2 residues processed: 530 average time/residue: 0.1268 time to fit residues: 87.0183 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 : 0.350 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3882 r_free = 0.3882 target = 0.111576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.088305 restraints weight = 30428.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.090713 restraints weight = 19411.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.092343 restraints weight = 14116.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093492 restraints weight = 11197.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094241 restraints weight = 9443.799| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5121 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= 0.166 Angle : 0.689 9.853 12758 Z= 0.361 Chirality : 0.044 0.339 1416 Planarity : 0.005 0.047 1604 Dihedral : 5.579 43.613 1449 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 5.04 % Allowed : 15.64 % Favored : 79.32 % 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 aren not related in a simple way. whole: -0.19 (0.24), residues: 1115 helix: 1.09 (0.25), residues: 437 sheet: -0.29 (0.31), residues: 236 loop : -1.23 (0.27), residues: 442 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 0.018 0.002 PHE B 222 TRP 0.014 0.002 TRP R 118 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9403) covalent geometry : angle 0.68593 (12746) SS BOND : bond 0.00887 ( 6) SS BOND : angle 2.15332 ( 12) hydrogen bonds : bond 0.04781 ( 421) hydrogen bonds : angle 5.27753 ( 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 366 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 317 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: 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 364 GLN cc_start: 0.9370 (tp40) cc_final: 0.9097 (mm-40) REVERT: R 440 GLN cc_start: 0.9106 (pp30) cc_final: 0.8570 (pp30) REVERT: R 442 HIS cc_start: 0.8861 (m90) cc_final: 0.8639 (m90) REVERT: P 9 HIS cc_start: 0.8472 (m90) cc_final: 0.8127 (m-70) REVERT: A 17 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8872 (mmtt) REVERT: A 218 ASN cc_start: 0.8326 (p0) cc_final: 0.8061 (p0) REVERT: A 240 ASP cc_start: 0.8673 (p0) cc_final: 0.8275 (p0) REVERT: A 264 ASN cc_start: 0.8525 (t0) cc_final: 0.7736 (t0) REVERT: B 12 GLU cc_start: 0.8974 (tp30) cc_final: 0.8771 (tp30) REVERT: B 16 ASN cc_start: 0.9315 (m-40) cc_final: 0.8876 (m-40) REVERT: B 51 LEU cc_start: 0.9580 (mt) cc_final: 0.9219 (mp) REVERT: B 184 THR cc_start: 0.8668 (p) cc_final: 0.8131 (t) REVERT: B 219 ARG cc_start: 0.8361 (mtt180) cc_final: 0.8143 (mmt180) REVERT: B 308 LEU cc_start: 0.9105 (mp) cc_final: 0.8782 (tp) REVERT: B 325 MET cc_start: 0.8326 (tpp) cc_final: 0.8124 (tpt) REVERT: G 11 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8659 (pp30) REVERT: G 27 ARG cc_start: 0.8721 (mtt90) cc_final: 0.8520 (mmt90) REVERT: N 51 ILE cc_start: 0.8150 (tt) cc_final: 0.7013 (tp) outliers start: 49 outliers final: 28 residues processed: 345 average time/residue: 0.1075 time to fit residues: 50.2458 Evaluate side-chains 299 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 51 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: 1.9990 chunk 97 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 52 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN R 307 HIS ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN A 29 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 271 ASN A 377 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.107643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.084205 restraints weight = 30830.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086674 restraints weight = 19246.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.088324 restraints weight = 13845.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089441 restraints weight = 10956.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090167 restraints weight = 9261.573| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9409 Z= 0.176 Angle : 0.649 10.101 12758 Z= 0.338 Chirality : 0.044 0.365 1416 Planarity : 0.005 0.072 1604 Dihedral : 5.309 46.857 1449 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.76 % Allowed : 17.80 % 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 aren not related in a simple way. whole: 0.08 (0.24), residues: 1115 helix: 1.25 (0.25), residues: 431 sheet: -0.03 (0.31), residues: 233 loop : -1.03 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 11 TYR 0.022 0.002 TYR R 191 PHE 0.020 0.002 PHE R 327 TRP 0.012 0.002 TRP R 118 HIS 0.004 0.001 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9403) covalent geometry : angle 0.64740 (12746) SS BOND : bond 0.00336 ( 6) SS BOND : angle 1.80658 ( 12) hydrogen bonds : bond 0.04379 ( 421) hydrogen bonds : angle 5.16892 ( 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 336 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 280 time to evaluate : 0.373 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: R 217 CYS cc_start: 0.7340 (t) cc_final: 0.7049 (m) REVERT: R 237 ILE cc_start: 0.9413 (mm) cc_final: 0.9132 (mm) REVERT: R 241 ASP cc_start: 0.8821 (m-30) cc_final: 0.8615 (p0) REVERT: R 324 PHE cc_start: 0.8750 (m-10) cc_final: 0.8381 (m-80) REVERT: R 442 HIS cc_start: 0.8905 (m90) cc_final: 0.8619 (m90) REVERT: R 445 MET cc_start: 0.8032 (mmp) cc_final: 0.7796 (mmp) REVERT: P 6 GLN cc_start: 0.8417 (tp40) cc_final: 0.8044 (tp40) REVERT: P 8 MET cc_start: 0.8630 (tmm) cc_final: 0.8397 (tmm) REVERT: P 9 HIS cc_start: 0.8731 (m90) cc_final: 0.7982 (m-70) REVERT: P 10 GLN cc_start: 0.8778 (pp30) cc_final: 0.8468 (pp30) REVERT: A 14 ASN cc_start: 0.9069 (m110) cc_final: 0.8616 (p0) REVERT: A 240 ASP cc_start: 0.8964 (p0) cc_final: 0.8390 (p0) REVERT: A 264 ASN cc_start: 0.8509 (t0) cc_final: 0.7963 (t0) REVERT: A 358 TYR cc_start: 0.7492 (m-80) cc_final: 0.7231 (m-10) REVERT: A 365 CYS cc_start: 0.8358 (t) cc_final: 0.7921 (m) REVERT: B 6 GLN cc_start: 0.9489 (pp30) cc_final: 0.9199 (pm20) REVERT: B 12 GLU cc_start: 0.8965 (tp30) cc_final: 0.8410 (tp30) REVERT: B 15 LYS cc_start: 0.9468 (ptpp) cc_final: 0.9200 (pttp) REVERT: B 124 TYR cc_start: 0.9287 (m-80) cc_final: 0.8722 (m-80) REVERT: B 222 PHE cc_start: 0.8398 (m-80) cc_final: 0.7826 (m-80) REVERT: B 308 LEU cc_start: 0.9159 (mp) cc_final: 0.8942 (tp) REVERT: G 11 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8554 (pp30) REVERT: G 27 ARG cc_start: 0.8858 (mtt90) cc_final: 0.8651 (mmt90) REVERT: N 4 LEU cc_start: 0.8952 (mm) cc_final: 0.8695 (mm) REVERT: N 50 ASP cc_start: 0.8921 (p0) cc_final: 0.8688 (p0) REVERT: N 51 ILE cc_start: 0.7855 (tt) cc_final: 0.7543 (pt) REVERT: N 90 ASP cc_start: 0.7806 (m-30) cc_final: 0.7332 (m-30) REVERT: N 91 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7295 (t) REVERT: N 94 TYR cc_start: 0.9108 (m-10) cc_final: 0.8881 (m-80) outliers start: 56 outliers final: 40 residues processed: 311 average time/residue: 0.1034 time to fit residues: 44.0757 Evaluate side-chains 293 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 436 LEU 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 P residue 11 ARG 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 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 320 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL 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: 0.0770 chunk 109 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 225 HIS ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.105476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.082387 restraints weight = 31359.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.084842 restraints weight = 19192.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.086540 restraints weight = 13656.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087659 restraints weight = 10700.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.088377 restraints weight = 8992.563| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9409 Z= 0.179 Angle : 0.654 9.352 12758 Z= 0.343 Chirality : 0.043 0.296 1416 Planarity : 0.004 0.048 1604 Dihedral : 5.073 49.494 1449 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.28 % Allowed : 19.96 % Favored : 73.77 % 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 aren not related in a simple way. whole: 0.07 (0.25), residues: 1115 helix: 1.01 (0.24), residues: 444 sheet: 0.15 (0.32), residues: 233 loop : -0.96 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 11 TYR 0.021 0.002 TYR R 191 PHE 0.018 0.002 PHE R 327 TRP 0.015 0.002 TRP R 322 HIS 0.004 0.001 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9403) covalent geometry : angle 0.65227 (12746) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.51902 ( 12) hydrogen bonds : bond 0.04356 ( 421) hydrogen bonds : angle 5.14803 ( 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 328 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 267 time to evaluate : 0.358 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: R 322 TRP cc_start: 0.7192 (OUTLIER) cc_final: 0.6829 (m100) REVERT: R 324 PHE cc_start: 0.8803 (m-10) cc_final: 0.8454 (m-80) REVERT: R 364 GLN cc_start: 0.9385 (tp40) cc_final: 0.9108 (tp40) REVERT: R 367 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9129 (tp) REVERT: R 442 HIS cc_start: 0.8883 (m90) cc_final: 0.8643 (m90) REVERT: R 465 GLU cc_start: 0.8490 (mp0) cc_final: 0.8263 (pm20) REVERT: R 469 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8795 (pp20) REVERT: P 2 VAL cc_start: 0.9444 (t) cc_final: 0.9164 (m) REVERT: A 230 GLU cc_start: 0.6825 (mp0) cc_final: 0.6616 (mp0) REVERT: A 264 ASN cc_start: 0.8768 (t0) cc_final: 0.8211 (t0) REVERT: A 365 CYS cc_start: 0.8385 (t) cc_final: 0.7977 (m) REVERT: A 386 MET cc_start: 0.9058 (tmm) cc_final: 0.8780 (tmm) REVERT: B 6 GLN cc_start: 0.9474 (pp30) cc_final: 0.9191 (pm20) REVERT: B 12 GLU cc_start: 0.8985 (tp30) cc_final: 0.8449 (tp30) REVERT: B 15 LYS cc_start: 0.9461 (ptpp) cc_final: 0.9166 (pttp) REVERT: B 16 ASN cc_start: 0.9262 (m-40) cc_final: 0.8787 (m-40) REVERT: B 58 ILE cc_start: 0.9600 (OUTLIER) cc_final: 0.9373 (mp) REVERT: B 124 TYR cc_start: 0.9282 (m-80) cc_final: 0.8685 (m-80) REVERT: B 219 ARG cc_start: 0.8530 (mtt180) cc_final: 0.8059 (ttm170) REVERT: B 222 PHE cc_start: 0.8427 (m-80) cc_final: 0.7969 (m-80) REVERT: G 11 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8559 (pp30) REVERT: G 27 ARG cc_start: 0.8822 (mtt90) cc_final: 0.8486 (mmt90) REVERT: N 4 LEU cc_start: 0.8985 (mm) cc_final: 0.8662 (mm) REVERT: N 50 ASP cc_start: 0.8960 (p0) cc_final: 0.8695 (p0) REVERT: N 51 ILE cc_start: 0.7816 (tt) cc_final: 0.7371 (pt) REVERT: N 90 ASP cc_start: 0.7974 (m-30) cc_final: 0.7436 (m-30) REVERT: N 91 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7322 (t) REVERT: N 94 TYR cc_start: 0.9195 (m-10) cc_final: 0.8842 (m-80) REVERT: N 124 VAL cc_start: 0.9118 (p) cc_final: 0.8912 (p) outliers start: 61 outliers final: 44 residues processed: 302 average time/residue: 0.0966 time to fit residues: 40.6557 Evaluate side-chains 286 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 322 TRP Chi-restraints excluded: chain R residue 367 ILE 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 430 THR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 469 GLU Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 6 GLN 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 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 30 LEU Chi-restraints excluded: chain B residue 58 ILE 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 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 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 G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL 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: 9.9990 chunk 76 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 74 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS A 14 ASN ** B 44 GLN ** 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 = 0.3988 r_free = 0.3988 target = 0.111070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.088337 restraints weight = 31074.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.090629 restraints weight = 20470.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.092074 restraints weight = 15140.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.093019 restraints weight = 12269.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.093707 restraints weight = 10608.071| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.7221 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= 0.148 Angle : 0.638 8.893 12758 Z= 0.334 Chirality : 0.043 0.293 1416 Planarity : 0.004 0.050 1604 Dihedral : 4.885 52.164 1449 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 6.38 % Allowed : 21.40 % Favored : 72.22 % 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 aren not related in a simple way. whole: 0.17 (0.25), residues: 1115 helix: 1.09 (0.24), residues: 438 sheet: 0.33 (0.32), residues: 233 loop : -0.95 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 11 TYR 0.024 0.001 TYR R 421 PHE 0.016 0.001 PHE R 378 TRP 0.016 0.001 TRP R 322 HIS 0.003 0.001 HIS R 307 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9403) covalent geometry : angle 0.63589 (12746) SS BOND : bond 0.00454 ( 6) SS BOND : angle 1.78963 ( 12) hydrogen bonds : bond 0.04207 ( 421) hydrogen bonds : angle 5.03173 ( 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 314 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 252 time to evaluate : 0.360 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: 0.9216 (m-40) cc_final: 0.8998 (m-40) REVERT: R 322 TRP cc_start: 0.7253 (OUTLIER) cc_final: 0.7048 (m100) REVERT: R 364 GLN cc_start: 0.9155 (tp40) cc_final: 0.8916 (tp40) REVERT: R 368 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9152 (mm) REVERT: R 429 TYR cc_start: 0.6341 (m-10) cc_final: 0.6040 (m-10) REVERT: R 467 GLN cc_start: 0.8517 (mt0) cc_final: 0.8203 (mt0) REVERT: R 469 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8682 (pp20) REVERT: R 472 LYS cc_start: 0.9258 (mmtt) cc_final: 0.9040 (mmmt) REVERT: P 2 VAL cc_start: 0.9273 (t) cc_final: 0.9012 (m) REVERT: A 365 CYS cc_start: 0.8140 (t) cc_final: 0.7812 (m) REVERT: A 386 MET cc_start: 0.8909 (tmm) cc_final: 0.8603 (tmm) REVERT: B 6 GLN cc_start: 0.9453 (pp30) cc_final: 0.9127 (pm20) REVERT: B 8 ARG cc_start: 0.7711 (mpp80) cc_final: 0.7498 (mpp80) REVERT: B 12 GLU cc_start: 0.8967 (tp30) cc_final: 0.8411 (tp30) REVERT: B 15 LYS cc_start: 0.9454 (ptpp) cc_final: 0.9179 (pttp) REVERT: B 16 ASN cc_start: 0.9279 (m-40) cc_final: 0.8771 (m-40) REVERT: B 124 TYR cc_start: 0.8815 (m-80) cc_final: 0.8458 (m-80) REVERT: G 11 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8532 (pp30) REVERT: G 18 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8491 (pp30) REVERT: N 4 LEU cc_start: 0.8961 (mm) cc_final: 0.8621 (mm) REVERT: N 50 ASP cc_start: 0.8925 (p0) cc_final: 0.8697 (p0) REVERT: N 51 ILE cc_start: 0.8098 (tt) cc_final: 0.7716 (pt) REVERT: N 90 ASP cc_start: 0.7970 (m-30) cc_final: 0.7196 (m-30) REVERT: N 91 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7670 (t) REVERT: N 124 VAL cc_start: 0.9164 (p) cc_final: 0.8938 (p) outliers start: 62 outliers final: 45 residues processed: 288 average time/residue: 0.1012 time to fit residues: 40.4079 Evaluate side-chains 290 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 322 TRP Chi-restraints excluded: chain R residue 354 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 445 MET Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 469 GLU Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 15 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 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 30 LEU 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 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 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 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 38 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** N 3 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 = 0.3971 r_free = 0.3971 target = 0.110135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.087062 restraints weight = 32169.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089215 restraints weight = 21517.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.090605 restraints weight = 16224.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.091541 restraints weight = 13318.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.092095 restraints weight = 11608.020| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.7579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9409 Z= 0.159 Angle : 0.655 9.843 12758 Z= 0.341 Chirality : 0.043 0.297 1416 Planarity : 0.004 0.055 1604 Dihedral : 4.946 53.956 1449 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 6.28 % Allowed : 22.22 % 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 aren not related in a simple way. whole: 0.12 (0.25), residues: 1115 helix: 1.04 (0.24), residues: 437 sheet: 0.41 (0.32), residues: 226 loop : -1.01 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 11 TYR 0.019 0.001 TYR R 245 PHE 0.015 0.001 PHE R 378 TRP 0.018 0.001 TRP R 437 HIS 0.004 0.001 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9403) covalent geometry : angle 0.65376 (12746) SS BOND : bond 0.00305 ( 6) SS BOND : angle 1.46254 ( 12) hydrogen bonds : bond 0.04197 ( 421) hydrogen bonds : angle 5.03730 ( 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 326 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 265 time to evaluate : 0.339 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: R 220 ASN cc_start: 0.9121 (m-40) cc_final: 0.8812 (m-40) REVERT: R 324 PHE cc_start: 0.8496 (m-80) cc_final: 0.8274 (m-80) REVERT: R 364 GLN cc_start: 0.9089 (tp40) cc_final: 0.8827 (tp40) REVERT: R 368 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9161 (mm) REVERT: R 467 GLN cc_start: 0.8555 (mt0) cc_final: 0.8256 (mt0) REVERT: R 469 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8679 (tm-30) REVERT: R 472 LYS cc_start: 0.9266 (mmtt) cc_final: 0.9041 (mmmt) REVERT: P 2 VAL cc_start: 0.9292 (t) cc_final: 0.8985 (m) REVERT: A 270 LEU cc_start: 0.9781 (OUTLIER) cc_final: 0.9476 (mm) REVERT: A 365 CYS cc_start: 0.8061 (t) cc_final: 0.7687 (m) REVERT: A 386 MET cc_start: 0.8890 (tmm) cc_final: 0.8580 (tmm) REVERT: B 6 GLN cc_start: 0.9451 (pp30) cc_final: 0.9163 (pm20) REVERT: B 12 GLU cc_start: 0.8950 (tp30) cc_final: 0.8400 (tp30) REVERT: B 15 LYS cc_start: 0.9411 (ptpp) cc_final: 0.9133 (pttp) REVERT: B 16 ASN cc_start: 0.9275 (m-40) cc_final: 0.8793 (m-40) REVERT: B 124 TYR cc_start: 0.8731 (m-80) cc_final: 0.8433 (m-80) REVERT: B 222 PHE cc_start: 0.7859 (m-10) cc_final: 0.7501 (m-10) REVERT: B 339 TRP cc_start: 0.7754 (m100) cc_final: 0.7380 (m100) REVERT: G 11 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8534 (pp30) REVERT: G 18 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8661 (pp30) REVERT: N 4 LEU cc_start: 0.8945 (mm) cc_final: 0.8585 (mm) REVERT: N 50 ASP cc_start: 0.8982 (p0) cc_final: 0.8707 (p0) REVERT: N 81 LEU cc_start: 0.7620 (tt) cc_final: 0.7167 (tt) REVERT: N 90 ASP cc_start: 0.8132 (m-30) cc_final: 0.7628 (m-30) REVERT: N 91 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8050 (t) REVERT: N 94 TYR cc_start: 0.8875 (m-80) cc_final: 0.8640 (m-80) REVERT: N 95 TYR cc_start: 0.8762 (m-80) cc_final: 0.8362 (m-80) outliers start: 61 outliers final: 45 residues processed: 303 average time/residue: 0.0946 time to fit residues: 39.9672 Evaluate side-chains 294 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 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 466 VAL Chi-restraints excluded: chain R residue 469 GLU 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 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 30 LEU 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 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 276 VAL 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 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 91 THR 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: 0.9990 chunk 104 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.106240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084130 restraints weight = 31724.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.086282 restraints weight = 20835.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087713 restraints weight = 15483.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088601 restraints weight = 12547.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.089315 restraints weight = 10883.533| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.7896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9409 Z= 0.157 Angle : 0.682 10.995 12758 Z= 0.353 Chirality : 0.043 0.275 1416 Planarity : 0.004 0.058 1604 Dihedral : 4.918 55.507 1449 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 6.48 % Allowed : 22.53 % Favored : 70.99 % 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 aren not related in a simple way. whole: 0.04 (0.25), residues: 1115 helix: 0.95 (0.24), residues: 448 sheet: 0.32 (0.33), residues: 222 loop : -1.02 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 19 TYR 0.016 0.001 TYR N 80 PHE 0.016 0.001 PHE R 447 TRP 0.022 0.002 TRP R 322 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9403) covalent geometry : angle 0.68045 (12746) SS BOND : bond 0.00294 ( 6) SS BOND : angle 1.50766 ( 12) hydrogen bonds : bond 0.04165 ( 421) hydrogen bonds : angle 5.08029 ( 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 316 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 253 time to evaluate : 0.403 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: R 220 ASN cc_start: 0.9108 (m-40) cc_final: 0.8832 (m-40) REVERT: R 324 PHE cc_start: 0.8466 (m-80) cc_final: 0.8188 (m-80) REVERT: R 368 LEU cc_start: 0.9438 (mm) cc_final: 0.9219 (mm) REVERT: R 442 HIS cc_start: 0.8391 (m90) cc_final: 0.8188 (m90) REVERT: R 467 GLN cc_start: 0.8533 (mt0) cc_final: 0.8211 (mt0) REVERT: P 9 HIS cc_start: 0.7931 (m-70) cc_final: 0.7469 (m-70) REVERT: A 270 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9433 (mm) REVERT: A 365 CYS cc_start: 0.8189 (t) cc_final: 0.7774 (m) REVERT: A 386 MET cc_start: 0.8961 (tmm) cc_final: 0.8636 (tmm) REVERT: B 6 GLN cc_start: 0.9411 (pp30) cc_final: 0.9122 (pm20) REVERT: B 12 GLU cc_start: 0.8906 (tp30) cc_final: 0.8696 (tp30) REVERT: B 16 ASN cc_start: 0.9259 (m-40) cc_final: 0.8812 (m-40) REVERT: B 124 TYR cc_start: 0.8922 (m-80) cc_final: 0.8541 (m-80) REVERT: B 295 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8160 (t0) REVERT: G 11 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8489 (pp30) REVERT: G 17 GLU cc_start: 0.9059 (pp20) cc_final: 0.8803 (pp20) REVERT: G 18 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8670 (pp30) REVERT: G 21 MET cc_start: 0.8251 (tpt) cc_final: 0.7874 (ttm) REVERT: N 4 LEU cc_start: 0.8939 (mm) cc_final: 0.8522 (mm) REVERT: N 19 ARG cc_start: 0.7631 (ttp80) cc_final: 0.7007 (ttp80) REVERT: N 87 LYS cc_start: 0.8553 (ttpp) cc_final: 0.7466 (ptmm) REVERT: N 90 ASP cc_start: 0.8033 (m-30) cc_final: 0.7242 (m-30) REVERT: N 91 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.8054 (t) REVERT: N 94 TYR cc_start: 0.8986 (m-80) cc_final: 0.8783 (m-80) REVERT: N 95 TYR cc_start: 0.8803 (m-80) cc_final: 0.8405 (m-80) outliers start: 63 outliers final: 49 residues processed: 293 average time/residue: 0.0922 time to fit residues: 38.0173 Evaluate side-chains 291 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 189 MET 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 301 VAL Chi-restraints excluded: chain R residue 354 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 421 TYR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL 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 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 79 LEU 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 295 ASN 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 36 ASP 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 91 THR 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: 6.9990 chunk 96 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.110705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.088193 restraints weight = 32874.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.090282 restraints weight = 21787.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.091578 restraints weight = 16429.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.092562 restraints weight = 13530.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.093161 restraints weight = 11756.327| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.8163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9409 Z= 0.159 Angle : 0.698 10.752 12758 Z= 0.360 Chirality : 0.043 0.212 1416 Planarity : 0.004 0.050 1604 Dihedral : 4.927 56.657 1449 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.97 % Allowed : 25.51 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.25), residues: 1115 helix: 1.07 (0.24), residues: 439 sheet: 0.18 (0.34), residues: 221 loop : -0.98 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 19 TYR 0.017 0.001 TYR N 80 PHE 0.024 0.002 PHE R 184 TRP 0.025 0.002 TRP R 322 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9403) covalent geometry : angle 0.69654 (12746) SS BOND : bond 0.00369 ( 6) SS BOND : angle 1.43521 ( 12) hydrogen bonds : bond 0.04266 ( 421) hydrogen bonds : angle 5.01945 ( 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 307 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 0.339 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: R 220 ASN cc_start: 0.9077 (m-40) cc_final: 0.8776 (m-40) REVERT: R 225 HIS cc_start: 0.7887 (m-70) cc_final: 0.7660 (m-70) REVERT: R 240 LYS cc_start: 0.9076 (tppt) cc_final: 0.8858 (tppt) REVERT: R 324 PHE cc_start: 0.8470 (m-80) cc_final: 0.8265 (m-80) REVERT: R 442 HIS cc_start: 0.8370 (m90) cc_final: 0.8150 (m90) REVERT: R 467 GLN cc_start: 0.8422 (mt0) cc_final: 0.8156 (mt0) REVERT: P 9 HIS cc_start: 0.7986 (m-70) cc_final: 0.7457 (m-70) REVERT: A 270 LEU cc_start: 0.9757 (OUTLIER) cc_final: 0.9347 (mm) REVERT: A 278 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8218 (t0) REVERT: A 317 ARG cc_start: 0.8568 (ptt-90) cc_final: 0.8234 (ptt-90) REVERT: A 365 CYS cc_start: 0.8135 (t) cc_final: 0.7667 (m) REVERT: A 386 MET cc_start: 0.8887 (tmm) cc_final: 0.8615 (tmm) REVERT: B 6 GLN cc_start: 0.9395 (pp30) cc_final: 0.9116 (pm20) REVERT: B 12 GLU cc_start: 0.8898 (tp30) cc_final: 0.8506 (tp30) REVERT: B 15 LYS cc_start: 0.9387 (ptpp) cc_final: 0.9111 (ptpt) REVERT: B 16 ASN cc_start: 0.9263 (m-40) cc_final: 0.8782 (m-40) REVERT: B 124 TYR cc_start: 0.8703 (m-80) cc_final: 0.8451 (m-80) REVERT: B 222 PHE cc_start: 0.7928 (m-10) cc_final: 0.7586 (m-10) REVERT: B 295 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8407 (t0) REVERT: G 11 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8570 (pp30) REVERT: G 17 GLU cc_start: 0.9063 (pp20) cc_final: 0.8822 (pp20) REVERT: G 18 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8650 (pp30) REVERT: G 21 MET cc_start: 0.8238 (tpt) cc_final: 0.7889 (ttm) REVERT: N 4 LEU cc_start: 0.8873 (mm) cc_final: 0.8437 (mm) REVERT: N 19 ARG cc_start: 0.7471 (ttp80) cc_final: 0.7164 (ttp80) REVERT: N 20 LEU cc_start: 0.7648 (mt) cc_final: 0.7402 (mt) REVERT: N 51 ILE cc_start: 0.7860 (tp) cc_final: 0.7561 (mt) REVERT: N 87 LYS cc_start: 0.8636 (ttpp) cc_final: 0.7523 (ptmm) REVERT: N 90 ASP cc_start: 0.8083 (m-30) cc_final: 0.7272 (m-30) REVERT: N 91 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8266 (t) REVERT: N 95 TYR cc_start: 0.8802 (m-80) cc_final: 0.8425 (m-80) outliers start: 58 outliers final: 50 residues processed: 287 average time/residue: 0.0927 time to fit residues: 37.5977 Evaluate side-chains 293 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 238 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 145 TYR Chi-restraints excluded: chain R residue 189 MET 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 301 VAL Chi-restraints excluded: chain R residue 354 LEU 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 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 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 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 79 LEU 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 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 318 LEU 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 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: 6.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 48 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 451 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 GLN ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.111954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.089604 restraints weight = 32232.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.091733 restraints weight = 21090.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.093191 restraints weight = 15797.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.094171 restraints weight = 12897.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.094724 restraints weight = 11186.666| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.8240 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 : 0.697 11.884 12758 Z= 0.356 Chirality : 0.043 0.204 1416 Planarity : 0.004 0.050 1604 Dihedral : 4.710 56.946 1447 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.14 % Allowed : 26.65 % 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 aren not related in a simple way. whole: 0.12 (0.26), residues: 1115 helix: 1.10 (0.25), residues: 442 sheet: 0.06 (0.34), residues: 237 loop : -0.90 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 38 TYR 0.037 0.001 TYR R 191 PHE 0.014 0.001 PHE R 447 TRP 0.031 0.001 TRP R 322 HIS 0.003 0.001 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9403) covalent geometry : angle 0.69601 (12746) SS BOND : bond 0.00284 ( 6) SS BOND : angle 1.16760 ( 12) hydrogen bonds : bond 0.04010 ( 421) hydrogen bonds : angle 4.93853 ( 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 303 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 0.391 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 189 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7662 (tpp) REVERT: R 220 ASN cc_start: 0.9036 (m-40) cc_final: 0.8738 (m-40) REVERT: R 240 LYS cc_start: 0.9061 (tppt) cc_final: 0.8833 (tppt) REVERT: R 324 PHE cc_start: 0.8454 (m-80) cc_final: 0.8211 (m-80) REVERT: R 368 LEU cc_start: 0.9426 (mm) cc_final: 0.9193 (mm) REVERT: R 421 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: R 442 HIS cc_start: 0.8346 (m90) cc_final: 0.8080 (m90) REVERT: R 467 GLN cc_start: 0.8552 (mt0) cc_final: 0.8272 (mt0) REVERT: P 9 HIS cc_start: 0.7900 (m-70) cc_final: 0.7471 (m-70) REVERT: A 221 MET cc_start: 0.8628 (tpp) cc_final: 0.8417 (tpt) REVERT: A 270 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9341 (mm) REVERT: A 278 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8112 (t0) REVERT: A 365 CYS cc_start: 0.8162 (t) cc_final: 0.7529 (m) REVERT: A 386 MET cc_start: 0.8889 (tmm) cc_final: 0.8617 (tmm) REVERT: B 6 GLN cc_start: 0.9419 (pp30) cc_final: 0.9115 (pm20) REVERT: B 12 GLU cc_start: 0.8907 (tp30) cc_final: 0.8701 (tp30) REVERT: B 16 ASN cc_start: 0.9298 (m-40) cc_final: 0.8849 (m-40) REVERT: B 124 TYR cc_start: 0.8722 (m-80) cc_final: 0.8470 (m-80) REVERT: B 215 GLU cc_start: 0.8697 (mp0) cc_final: 0.8287 (mp0) REVERT: B 222 PHE cc_start: 0.7853 (m-10) cc_final: 0.7452 (m-10) REVERT: B 295 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8567 (t0) REVERT: B 339 TRP cc_start: 0.7761 (m100) cc_final: 0.7402 (m100) REVERT: G 11 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8562 (pp30) REVERT: G 17 GLU cc_start: 0.9076 (pp20) cc_final: 0.8835 (pp20) REVERT: G 18 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8654 (pp30) REVERT: G 21 MET cc_start: 0.8289 (tpt) cc_final: 0.7908 (ttm) REVERT: N 4 LEU cc_start: 0.8864 (mm) cc_final: 0.8431 (mm) REVERT: N 19 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7339 (ttp80) REVERT: N 20 LEU cc_start: 0.7733 (mt) cc_final: 0.7511 (mt) REVERT: N 50 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8247 (p0) REVERT: N 90 ASP cc_start: 0.8089 (m-30) cc_final: 0.7555 (m-30) REVERT: N 91 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8083 (t) REVERT: N 95 TYR cc_start: 0.8801 (m-80) cc_final: 0.8422 (m-80) outliers start: 50 outliers final: 37 residues processed: 284 average time/residue: 0.0934 time to fit residues: 37.2638 Evaluate side-chains 291 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 189 MET 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 331 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 389 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 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 B residue 71 VAL 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 286 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU 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 50 ASP Chi-restraints excluded: chain N residue 91 THR 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: 0.9980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS R 295 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.111838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.089204 restraints weight = 32206.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.091407 restraints weight = 21216.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.092774 restraints weight = 15841.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.093802 restraints weight = 13020.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.094477 restraints weight = 11308.211| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.8351 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= 0.130 Angle : 0.715 11.694 12758 Z= 0.364 Chirality : 0.043 0.198 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.648 57.314 1447 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.04 % Allowed : 27.88 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.25), residues: 1115 helix: 1.06 (0.25), residues: 441 sheet: 0.08 (0.33), residues: 237 loop : -0.91 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 317 TYR 0.015 0.001 TYR N 80 PHE 0.014 0.001 PHE R 447 TRP 0.028 0.001 TRP R 322 HIS 0.004 0.001 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9403) covalent geometry : angle 0.71446 (12746) SS BOND : bond 0.00275 ( 6) SS BOND : angle 1.12255 ( 12) hydrogen bonds : bond 0.04089 ( 421) hydrogen bonds : angle 4.91016 ( 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 291 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 0.372 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 32 MET cc_start: 0.1476 (mmt) cc_final: 0.1031 (mmt) REVERT: R 155 GLU cc_start: 0.5018 (OUTLIER) cc_final: 0.4407 (pm20) REVERT: R 189 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7816 (tpp) REVERT: R 220 ASN cc_start: 0.9028 (m-40) cc_final: 0.8751 (m-40) REVERT: R 241 ASP cc_start: 0.8526 (m-30) cc_final: 0.8284 (p0) REVERT: R 291 PHE cc_start: 0.8762 (m-80) cc_final: 0.8291 (m-80) REVERT: R 324 PHE cc_start: 0.8416 (m-80) cc_final: 0.8171 (m-80) REVERT: R 421 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: R 442 HIS cc_start: 0.8373 (m90) cc_final: 0.8106 (m90) REVERT: R 467 GLN cc_start: 0.8502 (mt0) cc_final: 0.8204 (mt0) REVERT: P 9 HIS cc_start: 0.8063 (m-70) cc_final: 0.7729 (m-70) REVERT: A 221 MET cc_start: 0.8567 (tpp) cc_final: 0.8357 (tpt) REVERT: A 270 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9331 (mm) REVERT: A 278 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8098 (t0) REVERT: A 317 ARG cc_start: 0.8670 (mpp-170) cc_final: 0.7600 (mpp-170) REVERT: A 360 TYR cc_start: 0.8307 (m-80) cc_final: 0.8101 (m-80) REVERT: A 365 CYS cc_start: 0.8200 (t) cc_final: 0.7572 (m) REVERT: A 386 MET cc_start: 0.8875 (tmm) cc_final: 0.8627 (tmm) REVERT: B 12 GLU cc_start: 0.8883 (tp30) cc_final: 0.8677 (tp30) REVERT: B 16 ASN cc_start: 0.9301 (m-40) cc_final: 0.8844 (m-40) REVERT: B 124 TYR cc_start: 0.8658 (m-80) cc_final: 0.8413 (m-80) REVERT: B 215 GLU cc_start: 0.8813 (mp0) cc_final: 0.8325 (mp0) REVERT: B 222 PHE cc_start: 0.7852 (m-10) cc_final: 0.7427 (m-10) REVERT: B 339 TRP cc_start: 0.7723 (m100) cc_final: 0.7324 (m100) REVERT: G 11 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8585 (pp30) REVERT: G 17 GLU cc_start: 0.9085 (pp20) cc_final: 0.8846 (pp20) REVERT: G 18 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8601 (pp30) REVERT: G 21 MET cc_start: 0.8371 (tpt) cc_final: 0.8037 (ttm) REVERT: N 4 LEU cc_start: 0.8857 (mm) cc_final: 0.8444 (mm) REVERT: N 20 LEU cc_start: 0.7707 (mt) cc_final: 0.7504 (mt) REVERT: N 50 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8400 (p0) REVERT: N 90 ASP cc_start: 0.8049 (m-30) cc_final: 0.7450 (m-30) REVERT: N 91 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8312 (t) outliers start: 49 outliers final: 36 residues processed: 276 average time/residue: 0.0935 time to fit residues: 36.2273 Evaluate side-chains 279 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 155 GLU Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 225 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 385 LEU Chi-restraints excluded: chain R residue 389 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 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 71 VAL 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 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 N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 91 THR 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: 1.9990 chunk 7 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.0570 chunk 12 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS ** P 6 GLN ** 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 B 295 ASN ** B 340 ASN ** 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 = 0.3977 r_free = 0.3977 target = 0.111270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.088198 restraints weight = 32422.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.090547 restraints weight = 21539.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.091957 restraints weight = 15801.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.093013 restraints weight = 12789.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.093518 restraints weight = 11004.353| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.8543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9409 Z= 0.157 Angle : 0.737 12.399 12758 Z= 0.376 Chirality : 0.043 0.203 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.822 58.207 1447 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.04 % Allowed : 28.29 % Favored : 66.67 % 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 aren not related in a simple way. whole: -0.03 (0.25), residues: 1115 helix: 0.94 (0.24), residues: 446 sheet: -0.02 (0.34), residues: 235 loop : -0.96 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.044 0.002 TYR R 191 PHE 0.018 0.001 PHE R 447 TRP 0.025 0.001 TRP R 322 HIS 0.008 0.001 HIS R 225 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9403) covalent geometry : angle 0.73609 (12746) SS BOND : bond 0.00278 ( 6) SS BOND : angle 1.18556 ( 12) hydrogen bonds : bond 0.04189 ( 421) hydrogen bonds : angle 4.91424 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1863.63 seconds wall clock time: 33 minutes 5.87 seconds (1985.87 seconds total)