Starting phenix.real_space_refine on Thu Mar 13 23:57:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nbi_0412/03_2025/6nbi_0412.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbi_0412/03_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_0412/03_2025/6nbi_0412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbi_0412/03_2025/6nbi_0412.map" model { file = "/net/cci-nas-00/data/ceres_data/6nbi_0412/03_2025/6nbi_0412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbi_0412/03_2025/6nbi_0412.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.22, per 1000 atoms: 0.57 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: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.00 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: 2.33 Time building geometry restraints manager: 2.58 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- 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 9403 Z= 0.341 Angle : 0.876 6.654 12746 Z= 0.593 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 : 2.35 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (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 TRP 0.024 0.002 TRP R 154 HIS 0.006 0.001 HIS A 387 PHE 0.014 0.002 PHE R 447 TYR 0.025 0.002 TYR R 191 ARG 0.003 0.000 ARG A 389 *********************** 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 : 1.002 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: R 307 HIS cc_start: 0.8222 (t-90) cc_final: 0.7726 (t-90) REVERT: R 445 MET cc_start: 0.8003 (mmp) cc_final: 0.7612 (mmp) REVERT: A 13 ARG cc_start: 0.8455 (mtt180) cc_final: 0.7537 (mpt180) REVERT: A 16 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8821 (pt0) REVERT: A 278 ASN cc_start: 0.8348 (m110) cc_final: 0.7768 (m-40) REVERT: A 286 SER cc_start: 0.9489 (t) cc_final: 0.9265 (p) REVERT: B 10 GLU cc_start: 0.9371 (tt0) cc_final: 0.9099 (tm-30) REVERT: B 20 ASP cc_start: 0.9095 (m-30) cc_final: 0.8651 (m-30) REVERT: B 51 LEU cc_start: 0.7980 (mt) cc_final: 0.7775 (mp) REVERT: B 184 THR cc_start: 0.8195 (p) cc_final: 0.7920 (t) REVERT: B 301 LYS cc_start: 0.8297 (mmmm) cc_final: 0.7861 (mmtp) REVERT: B 316 SER cc_start: 0.8935 (p) cc_final: 0.8730 (t) REVERT: G 38 MET cc_start: 0.9299 (mtm) cc_final: 0.9086 (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: 0.6816 (p) outliers start: 3 outliers final: 2 residues processed: 530 average time/residue: 0.2624 time to fit residues: 179.6680 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 : 1.036 ------------------------------------------------------------------------------- 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 93 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.0370 chunk 64 optimal weight: 0.0470 chunk 100 optimal weight: 20.0000 overall best weight: 1.2960 ------------------------------------------------------------------------------- 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 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS B 156 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.113156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090147 restraints weight = 30268.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.092506 restraints weight = 19883.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094112 restraints weight = 14579.586| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9403 Z= 0.210 Angle : 0.680 10.185 12746 Z= 0.354 Chirality : 0.044 0.353 1416 Planarity : 0.005 0.045 1604 Dihedral : 5.497 43.356 1449 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.01 % Allowed : 16.98 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1115 helix: 1.05 (0.25), residues: 437 sheet: -0.28 (0.32), residues: 224 loop : -1.20 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 14 HIS 0.005 0.001 HIS B 54 PHE 0.012 0.001 PHE R 315 TYR 0.013 0.002 TYR N 32 ARG 0.008 0.001 ARG A 38 *********************** 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 362 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 323 time to evaluate : 0.968 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 364 GLN cc_start: 0.9411 (tp40) cc_final: 0.9187 (tp40) REVERT: R 438 GLN cc_start: 0.7763 (pt0) cc_final: 0.7551 (pt0) REVERT: A 17 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8878 (mmtt) REVERT: A 218 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7995 (p0) REVERT: A 240 ASP cc_start: 0.8543 (p0) cc_final: 0.8089 (p0) REVERT: A 264 ASN cc_start: 0.8383 (t0) cc_final: 0.8152 (t0) REVERT: A 340 PHE cc_start: 0.8717 (t80) cc_final: 0.8381 (t80) REVERT: B 12 GLU cc_start: 0.8972 (tp30) cc_final: 0.8772 (tp30) REVERT: B 16 ASN cc_start: 0.9359 (m-40) cc_final: 0.8923 (m-40) REVERT: B 51 LEU cc_start: 0.9567 (mt) cc_final: 0.9184 (mp) REVERT: B 184 THR cc_start: 0.8644 (p) cc_final: 0.8114 (t) REVERT: B 252 LEU cc_start: 0.9737 (tp) cc_final: 0.9512 (tt) REVERT: B 275 SER cc_start: 0.9462 (t) cc_final: 0.9258 (m) REVERT: B 308 LEU cc_start: 0.9046 (mp) cc_final: 0.8788 (tp) REVERT: G 11 GLN cc_start: 0.8791 (pt0) cc_final: 0.8462 (pp30) REVERT: N 20 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.6210 (mt) REVERT: N 38 ARG cc_start: 0.8714 (ptt180) cc_final: 0.8456 (ptm160) REVERT: N 81 LEU cc_start: 0.6778 (tp) cc_final: 0.6290 (tt) outliers start: 39 outliers final: 22 residues processed: 346 average time/residue: 0.2455 time to fit residues: 113.9092 Evaluate side-chains 292 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 388 LYS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 367 VAL 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 191 SER 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 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 20 LEU 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 80 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 8 optimal weight: 0.0570 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 ** 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** A 14 ASN A 19 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN B 220 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.117653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.096616 restraints weight = 29369.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.098595 restraints weight = 19817.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.100015 restraints weight = 14939.785| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9403 Z= 0.189 Angle : 0.633 10.497 12746 Z= 0.325 Chirality : 0.043 0.327 1416 Planarity : 0.004 0.059 1604 Dihedral : 5.141 46.788 1449 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.81 % Allowed : 19.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1115 helix: 1.23 (0.25), residues: 431 sheet: -0.06 (0.31), residues: 244 loop : -1.00 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.015 0.001 HIS P 9 PHE 0.015 0.001 PHE R 378 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.001 ARG P 11 *********************** 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 324 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 1.044 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: R 440 GLN cc_start: 0.9024 (pp30) cc_final: 0.8414 (pp30) REVERT: R 442 HIS cc_start: 0.8329 (m90) cc_final: 0.8069 (m90) REVERT: R 445 MET cc_start: 0.7718 (mmp) cc_final: 0.6767 (mmp) REVERT: A 240 ASP cc_start: 0.8526 (p0) cc_final: 0.7967 (p0) REVERT: A 270 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9506 (mm) REVERT: A 360 TYR cc_start: 0.8548 (m-80) cc_final: 0.8102 (m-80) REVERT: B 6 GLN cc_start: 0.9405 (pp30) cc_final: 0.9109 (pm20) REVERT: B 12 GLU cc_start: 0.8907 (tp30) cc_final: 0.8654 (tp30) REVERT: B 124 TYR cc_start: 0.8906 (m-80) cc_final: 0.8519 (m-80) REVERT: B 184 THR cc_start: 0.8474 (p) cc_final: 0.7897 (t) REVERT: G 11 GLN cc_start: 0.8892 (pt0) cc_final: 0.8538 (pp30) REVERT: N 4 LEU cc_start: 0.8813 (mm) cc_final: 0.8517 (mm) REVERT: N 20 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6274 (mp) REVERT: N 50 ASP cc_start: 0.8759 (p0) cc_final: 0.8433 (p0) REVERT: N 81 LEU cc_start: 0.6645 (tp) cc_final: 0.6159 (tt) REVERT: N 122 THR cc_start: 0.7957 (t) cc_final: 0.7600 (t) outliers start: 37 outliers final: 27 residues processed: 306 average time/residue: 0.2445 time to fit residues: 102.7196 Evaluate side-chains 278 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 374 ASN Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR 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 158 VAL Chi-restraints excluded: chain B residue 191 SER 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 26 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 93 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 225 HIS R 295 ASN ** R 364 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** A 31 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 271 ASN B 142 HIS G 18 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.110615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.088062 restraints weight = 31260.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.090150 restraints weight = 21129.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.091480 restraints weight = 15988.103| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9403 Z= 0.314 Angle : 0.694 11.022 12746 Z= 0.366 Chirality : 0.043 0.250 1416 Planarity : 0.005 0.048 1604 Dihedral : 5.263 49.594 1449 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.89 % Allowed : 20.37 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1115 helix: 0.93 (0.24), residues: 444 sheet: -0.01 (0.31), residues: 239 loop : -0.99 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 352 HIS 0.020 0.001 HIS P 9 PHE 0.035 0.002 PHE R 184 TYR 0.017 0.002 TYR A 358 ARG 0.010 0.001 ARG N 19 *********************** 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 333 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 1.197 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 237 ILE cc_start: 0.9416 (mm) cc_final: 0.9143 (mm) REVERT: R 241 ASP cc_start: 0.8439 (m-30) cc_final: 0.8203 (p0) REVERT: R 306 LEU cc_start: 0.9549 (tp) cc_final: 0.9264 (tt) REVERT: R 364 GLN cc_start: 0.9066 (tp40) cc_final: 0.8770 (tp40) REVERT: R 367 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9017 (tp) REVERT: P 2 VAL cc_start: 0.9638 (t) cc_final: 0.9308 (m) REVERT: A 240 ASP cc_start: 0.8719 (p0) cc_final: 0.7978 (p0) REVERT: A 365 CYS cc_start: 0.7995 (t) cc_final: 0.7583 (m) REVERT: A 386 MET cc_start: 0.8640 (tmm) cc_final: 0.8421 (tmm) REVERT: B 6 GLN cc_start: 0.9457 (pp30) cc_final: 0.9166 (pm20) REVERT: B 12 GLU cc_start: 0.8931 (tp30) cc_final: 0.8465 (tp30) REVERT: B 15 LYS cc_start: 0.9399 (ptpt) cc_final: 0.9156 (ptpt) REVERT: B 124 TYR cc_start: 0.8715 (m-80) cc_final: 0.8432 (m-80) REVERT: B 127 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8898 (ptmm) REVERT: B 215 GLU cc_start: 0.8919 (mp0) cc_final: 0.8135 (mp0) REVERT: B 339 TRP cc_start: 0.7963 (m100) cc_final: 0.7412 (m100) REVERT: G 11 GLN cc_start: 0.8909 (pt0) cc_final: 0.8543 (pp30) REVERT: N 4 LEU cc_start: 0.8910 (mm) cc_final: 0.8618 (mm) REVERT: N 19 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7181 (ttp80) REVERT: N 50 ASP cc_start: 0.8891 (p0) cc_final: 0.8611 (p0) REVERT: N 81 LEU cc_start: 0.6902 (tp) cc_final: 0.6630 (tt) REVERT: N 90 ASP cc_start: 0.7860 (m-30) cc_final: 0.7465 (m-30) REVERT: N 91 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7573 (t) outliers start: 67 outliers final: 45 residues processed: 304 average time/residue: 0.3494 time to fit residues: 148.9747 Evaluate side-chains 280 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 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 288 PHE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 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 117 LEU 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 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 26 ASP 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 51 ILE Chi-restraints excluded: chain N residue 83 MET 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 14 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.114755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.091504 restraints weight = 32152.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.093735 restraints weight = 21303.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.095194 restraints weight = 15907.956| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9403 Z= 0.195 Angle : 0.654 10.126 12746 Z= 0.341 Chirality : 0.043 0.304 1416 Planarity : 0.004 0.049 1604 Dihedral : 4.892 50.529 1449 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.86 % Allowed : 22.74 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1115 helix: 1.18 (0.25), residues: 435 sheet: 0.30 (0.32), residues: 229 loop : -0.96 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 437 HIS 0.017 0.001 HIS P 9 PHE 0.023 0.002 PHE R 184 TYR 0.021 0.001 TYR R 421 ARG 0.005 0.000 ARG A 38 *********************** 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 315 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 0.940 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: 0.9220 (m-40) cc_final: 0.8965 (m-40) REVERT: R 237 ILE cc_start: 0.9515 (mm) cc_final: 0.9199 (mm) REVERT: R 324 PHE cc_start: 0.8598 (m-80) cc_final: 0.8311 (m-80) REVERT: R 364 GLN cc_start: 0.9006 (tp40) cc_final: 0.8723 (tp40) REVERT: R 368 LEU cc_start: 0.9326 (mm) cc_final: 0.9058 (mm) REVERT: R 440 GLN cc_start: 0.9112 (pp30) cc_final: 0.8772 (pp30) REVERT: R 467 GLN cc_start: 0.8427 (mt0) cc_final: 0.8073 (mt0) REVERT: P 2 VAL cc_start: 0.9438 (t) cc_final: 0.9121 (m) REVERT: P 6 GLN cc_start: 0.8653 (tp40) cc_final: 0.8008 (tp40) REVERT: P 10 GLN cc_start: 0.8708 (pp30) cc_final: 0.8424 (pp30) REVERT: A 240 ASP cc_start: 0.8704 (p0) cc_final: 0.7956 (p0) REVERT: A 365 CYS cc_start: 0.8077 (t) cc_final: 0.7580 (m) REVERT: A 386 MET cc_start: 0.8720 (tmm) cc_final: 0.8441 (tmm) REVERT: B 6 GLN cc_start: 0.9466 (pp30) cc_final: 0.9143 (pm20) REVERT: B 8 ARG cc_start: 0.7652 (mpp80) cc_final: 0.7443 (mpp80) REVERT: B 12 GLU cc_start: 0.8954 (tp30) cc_final: 0.8271 (tp30) REVERT: B 15 LYS cc_start: 0.9416 (ptpt) cc_final: 0.9055 (pttp) REVERT: B 16 ASN cc_start: 0.9290 (m-40) cc_final: 0.8783 (m-40) REVERT: B 215 GLU cc_start: 0.8789 (mp0) cc_final: 0.8169 (mp0) REVERT: G 11 GLN cc_start: 0.8920 (pt0) cc_final: 0.8560 (pp30) REVERT: G 17 GLU cc_start: 0.9059 (pp20) cc_final: 0.8656 (pp20) REVERT: N 4 LEU cc_start: 0.8870 (mm) cc_final: 0.8489 (mm) REVERT: N 50 ASP cc_start: 0.8859 (p0) cc_final: 0.8546 (p0) REVERT: N 81 LEU cc_start: 0.7055 (tp) cc_final: 0.6689 (tt) REVERT: N 91 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7342 (t) outliers start: 57 outliers final: 40 residues processed: 294 average time/residue: 0.2138 time to fit residues: 86.1526 Evaluate side-chains 284 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 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 B residue 25 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 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 307 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 MET 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 80 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** P 10 GLN ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 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 = 0.4033 r_free = 0.4033 target = 0.114481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.091589 restraints weight = 30977.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.093741 restraints weight = 20667.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.095132 restraints weight = 15584.270| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.7400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9403 Z= 0.169 Angle : 0.655 9.116 12746 Z= 0.339 Chirality : 0.042 0.252 1416 Planarity : 0.004 0.049 1604 Dihedral : 4.746 51.556 1449 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.45 % Allowed : 22.74 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1115 helix: 1.22 (0.25), residues: 437 sheet: 0.23 (0.33), residues: 225 loop : -0.90 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 437 HIS 0.016 0.001 HIS P 9 PHE 0.020 0.001 PHE R 184 TYR 0.020 0.001 TYR R 245 ARG 0.007 0.001 ARG N 19 *********************** 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 318 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 265 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 177 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8957 (mm-30) REVERT: R 220 ASN cc_start: 0.9116 (m-40) cc_final: 0.8817 (m-40) REVERT: R 322 TRP cc_start: 0.7292 (OUTLIER) cc_final: 0.7051 (m100) REVERT: R 324 PHE cc_start: 0.8515 (m-80) cc_final: 0.8194 (m-80) REVERT: R 467 GLN cc_start: 0.8508 (mt0) cc_final: 0.8161 (mt0) REVERT: A 240 ASP cc_start: 0.8557 (p0) cc_final: 0.7838 (p0) REVERT: A 365 CYS cc_start: 0.8190 (t) cc_final: 0.7596 (m) REVERT: A 386 MET cc_start: 0.8727 (tmm) cc_final: 0.8448 (tmm) REVERT: B 6 GLN cc_start: 0.9415 (pp30) cc_final: 0.9075 (pm20) REVERT: B 12 GLU cc_start: 0.8976 (tp30) cc_final: 0.8381 (tp30) REVERT: B 15 LYS cc_start: 0.9455 (ptpt) cc_final: 0.9078 (pttp) REVERT: B 16 ASN cc_start: 0.9307 (m-40) cc_final: 0.8797 (m-40) REVERT: B 215 GLU cc_start: 0.8878 (mp0) cc_final: 0.8171 (mp0) REVERT: B 308 LEU cc_start: 0.8832 (tp) cc_final: 0.8619 (tp) REVERT: B 339 TRP cc_start: 0.7888 (m100) cc_final: 0.7492 (m100) REVERT: G 11 GLN cc_start: 0.8868 (pt0) cc_final: 0.8517 (pp30) REVERT: N 4 LEU cc_start: 0.8837 (mm) cc_final: 0.8348 (mm) REVERT: N 5 GLN cc_start: 0.8232 (tp40) cc_final: 0.7901 (tp40) outliers start: 53 outliers final: 42 residues processed: 299 average time/residue: 0.2024 time to fit residues: 84.1750 Evaluate side-chains 276 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 189 MET 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 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.111020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.088296 restraints weight = 31987.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090326 restraints weight = 21740.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.091666 restraints weight = 16584.453| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.7776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9403 Z= 0.235 Angle : 0.706 11.056 12746 Z= 0.366 Chirality : 0.043 0.223 1416 Planarity : 0.004 0.049 1604 Dihedral : 4.829 52.651 1449 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.86 % Allowed : 22.84 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1115 helix: 1.09 (0.24), residues: 444 sheet: 0.13 (0.33), residues: 225 loop : -0.86 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 322 HIS 0.008 0.001 HIS P 9 PHE 0.024 0.002 PHE R 184 TYR 0.030 0.002 TYR R 191 ARG 0.008 0.001 ARG A 38 *********************** 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 296 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 220 ASN cc_start: 0.9009 (m-40) cc_final: 0.8781 (m-40) REVERT: R 240 LYS cc_start: 0.9318 (tppt) cc_final: 0.9095 (tppt) REVERT: R 324 PHE cc_start: 0.8434 (m-80) cc_final: 0.8186 (m-80) REVERT: R 364 GLN cc_start: 0.8935 (tp40) cc_final: 0.8676 (tp40) REVERT: R 440 GLN cc_start: 0.9036 (pp30) cc_final: 0.8646 (pp30) REVERT: R 467 GLN cc_start: 0.8543 (mt0) cc_final: 0.8252 (mt0) REVERT: P 2 VAL cc_start: 0.9363 (t) cc_final: 0.9155 (m) REVERT: P 6 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 43 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8720 (mm) REVERT: A 270 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9399 (mm) REVERT: A 365 CYS cc_start: 0.8081 (t) cc_final: 0.7501 (m) REVERT: A 375 VAL cc_start: 0.9287 (t) cc_final: 0.8944 (p) REVERT: A 386 MET cc_start: 0.8756 (tmm) cc_final: 0.8530 (tmm) REVERT: B 6 GLN cc_start: 0.9391 (pp30) cc_final: 0.9104 (pm20) REVERT: B 12 GLU cc_start: 0.8923 (tp30) cc_final: 0.8378 (tp30) REVERT: B 15 LYS cc_start: 0.9435 (ptpt) cc_final: 0.9081 (pttp) REVERT: B 16 ASN cc_start: 0.9309 (m-40) cc_final: 0.8835 (m-40) REVERT: B 215 GLU cc_start: 0.8812 (mp0) cc_final: 0.8208 (mp0) REVERT: B 337 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8840 (mmmt) REVERT: B 339 TRP cc_start: 0.7968 (m100) cc_final: 0.7566 (m100) REVERT: G 11 GLN cc_start: 0.8876 (pt0) cc_final: 0.8563 (pp30) REVERT: G 21 MET cc_start: 0.8148 (tpt) cc_final: 0.7812 (ttm) REVERT: N 4 LEU cc_start: 0.8790 (mm) cc_final: 0.8286 (mm) REVERT: N 5 GLN cc_start: 0.8134 (tp40) cc_final: 0.7846 (tp40) REVERT: N 19 ARG cc_start: 0.7323 (ttp80) cc_final: 0.7121 (ttp80) REVERT: N 50 ASP cc_start: 0.8877 (p0) cc_final: 0.8620 (p0) REVERT: N 90 ASP cc_start: 0.8227 (m-30) cc_final: 0.7668 (m-30) outliers start: 57 outliers final: 45 residues processed: 275 average time/residue: 0.1952 time to fit residues: 74.9606 Evaluate side-chains 275 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 288 PHE 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 430 THR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 9 HIS 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 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 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 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 0.0030 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 overall best weight: 1.0594 ------------------------------------------------------------------------------- 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 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.113399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.090968 restraints weight = 32051.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.093096 restraints weight = 21418.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.094499 restraints weight = 16126.604| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.7926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9403 Z= 0.185 Angle : 0.711 11.082 12746 Z= 0.363 Chirality : 0.043 0.279 1416 Planarity : 0.004 0.049 1604 Dihedral : 4.618 52.748 1449 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.25 % Allowed : 24.59 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1115 helix: 1.09 (0.25), residues: 450 sheet: 0.19 (0.33), residues: 226 loop : -0.92 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 322 HIS 0.011 0.001 HIS P 9 PHE 0.021 0.001 PHE R 227 TYR 0.022 0.001 TYR R 421 ARG 0.009 0.000 ARG P 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 ILE cc_start: 0.8317 (mm) cc_final: 0.8108 (pt) REVERT: R 220 ASN cc_start: 0.9067 (m-40) cc_final: 0.8835 (m-40) REVERT: R 240 LYS cc_start: 0.9302 (tppt) cc_final: 0.9021 (tppt) REVERT: R 324 PHE cc_start: 0.8418 (m-80) cc_final: 0.8138 (m-80) REVERT: R 467 GLN cc_start: 0.8460 (mt0) cc_final: 0.8207 (mt0) REVERT: P 2 VAL cc_start: 0.9374 (t) cc_final: 0.9077 (m) REVERT: P 6 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: A 30 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9344 (tt) REVERT: A 270 LEU cc_start: 0.9775 (OUTLIER) cc_final: 0.9385 (mm) REVERT: A 358 TYR cc_start: 0.6995 (m-80) cc_final: 0.5476 (m-80) REVERT: A 360 TYR cc_start: 0.8334 (m-80) cc_final: 0.7911 (m-80) REVERT: A 365 CYS cc_start: 0.8205 (t) cc_final: 0.7539 (m) REVERT: A 386 MET cc_start: 0.8817 (tmm) cc_final: 0.8527 (tmm) REVERT: B 10 GLU cc_start: 0.9233 (tm-30) cc_final: 0.9000 (tm-30) REVERT: B 12 GLU cc_start: 0.8926 (tp30) cc_final: 0.8380 (tp30) REVERT: B 15 LYS cc_start: 0.9438 (ptpt) cc_final: 0.9088 (pttp) REVERT: B 16 ASN cc_start: 0.9281 (m-40) cc_final: 0.8781 (m-40) REVERT: B 215 GLU cc_start: 0.8826 (mp0) cc_final: 0.8195 (mp0) REVERT: B 339 TRP cc_start: 0.7968 (m100) cc_final: 0.7636 (m100) REVERT: G 11 GLN cc_start: 0.8888 (pt0) cc_final: 0.8549 (pp30) REVERT: G 21 MET cc_start: 0.8149 (tpt) cc_final: 0.7777 (ttm) REVERT: N 4 LEU cc_start: 0.8717 (mm) cc_final: 0.8188 (mm) REVERT: N 5 GLN cc_start: 0.8131 (tp40) cc_final: 0.7870 (tp40) REVERT: N 90 ASP cc_start: 0.8167 (m-30) cc_final: 0.7619 (m-30) REVERT: N 95 TYR cc_start: 0.8481 (m-80) cc_final: 0.8201 (m-80) outliers start: 51 outliers final: 42 residues processed: 284 average time/residue: 0.2115 time to fit residues: 82.4752 Evaluate side-chains 274 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain A residue 30 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 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE 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 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 0.2980 chunk 108 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.113514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.091183 restraints weight = 31705.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.093302 restraints weight = 21367.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.094590 restraints weight = 16188.513| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.8050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9403 Z= 0.196 Angle : 0.730 10.467 12746 Z= 0.371 Chirality : 0.043 0.181 1416 Planarity : 0.004 0.079 1604 Dihedral : 4.613 53.336 1449 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.14 % Allowed : 25.72 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1115 helix: 0.94 (0.25), residues: 449 sheet: 0.20 (0.33), residues: 226 loop : -0.92 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 322 HIS 0.011 0.001 HIS P 9 PHE 0.024 0.002 PHE R 227 TYR 0.033 0.001 TYR R 191 ARG 0.010 0.001 ARG A 38 *********************** 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 296 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 177 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8989 (mm-30) REVERT: R 220 ASN cc_start: 0.9071 (m-40) cc_final: 0.8862 (m-40) REVERT: R 324 PHE cc_start: 0.8411 (m-80) cc_final: 0.8177 (m-80) REVERT: R 364 GLN cc_start: 0.8861 (tp40) cc_final: 0.8404 (tp-100) REVERT: R 368 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9187 (mm) REVERT: R 467 GLN cc_start: 0.8481 (mt0) cc_final: 0.8221 (mt0) REVERT: P 2 VAL cc_start: 0.9359 (t) cc_final: 0.9050 (m) REVERT: P 6 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: A 43 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 270 LEU cc_start: 0.9768 (OUTLIER) cc_final: 0.9380 (mm) REVERT: A 278 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8116 (t0) REVERT: A 365 CYS cc_start: 0.8228 (t) cc_final: 0.7574 (m) REVERT: A 386 MET cc_start: 0.8942 (tmm) cc_final: 0.8612 (tmm) REVERT: B 16 ASN cc_start: 0.9322 (m-40) cc_final: 0.8948 (m-40) REVERT: B 215 GLU cc_start: 0.8879 (mp0) cc_final: 0.8171 (mp0) REVERT: B 339 TRP cc_start: 0.7849 (m100) cc_final: 0.7509 (m100) REVERT: G 11 GLN cc_start: 0.8855 (pt0) cc_final: 0.8519 (pp30) REVERT: G 21 MET cc_start: 0.8272 (tpt) cc_final: 0.7898 (ttm) REVERT: G 31 SER cc_start: 0.8822 (p) cc_final: 0.8528 (p) REVERT: N 4 LEU cc_start: 0.8700 (mm) cc_final: 0.8192 (mm) REVERT: N 85 SER cc_start: 0.8457 (t) cc_final: 0.7982 (p) REVERT: N 90 ASP cc_start: 0.8217 (m-30) cc_final: 0.7581 (m-30) REVERT: N 95 TYR cc_start: 0.8558 (m-80) cc_final: 0.8259 (m-80) outliers start: 50 outliers final: 40 residues processed: 279 average time/residue: 0.1991 time to fit residues: 77.4455 Evaluate side-chains 273 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 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 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 7 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 270 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE 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 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL 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 46 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.112874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089373 restraints weight = 33468.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.091556 restraints weight = 21931.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.093119 restraints weight = 16425.267| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.8338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9403 Z= 0.251 Angle : 0.780 10.131 12746 Z= 0.401 Chirality : 0.045 0.241 1416 Planarity : 0.005 0.080 1604 Dihedral : 4.847 54.473 1447 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.84 % Allowed : 26.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1115 helix: 0.86 (0.24), residues: 444 sheet: 0.09 (0.34), residues: 229 loop : -0.92 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 322 HIS 0.010 0.001 HIS P 9 PHE 0.026 0.002 PHE R 227 TYR 0.022 0.001 TYR R 421 ARG 0.011 0.001 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 177 GLU cc_start: 0.9244 (mm-30) cc_final: 0.9022 (mm-30) REVERT: R 324 PHE cc_start: 0.8419 (m-80) cc_final: 0.8064 (m-80) REVERT: R 364 GLN cc_start: 0.8936 (tp40) cc_final: 0.8611 (tp40) REVERT: R 467 GLN cc_start: 0.8485 (mt0) cc_final: 0.8225 (mt0) REVERT: P 2 VAL cc_start: 0.9381 (t) cc_final: 0.9112 (m) REVERT: P 6 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8116 (mp10) REVERT: A 278 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8120 (t0) REVERT: A 365 CYS cc_start: 0.8215 (t) cc_final: 0.7589 (m) REVERT: A 386 MET cc_start: 0.9055 (tmm) cc_final: 0.8705 (tmm) REVERT: B 15 LYS cc_start: 0.9425 (ptpt) cc_final: 0.9153 (pttp) REVERT: B 16 ASN cc_start: 0.9318 (m-40) cc_final: 0.9076 (m110) REVERT: B 215 GLU cc_start: 0.8881 (mp0) cc_final: 0.8176 (mp0) REVERT: B 308 LEU cc_start: 0.8722 (tp) cc_final: 0.8417 (tp) REVERT: B 339 TRP cc_start: 0.7930 (m100) cc_final: 0.7551 (m100) REVERT: G 21 MET cc_start: 0.8259 (tpt) cc_final: 0.7889 (ttm) REVERT: N 4 LEU cc_start: 0.8628 (mm) cc_final: 0.8088 (mm) REVERT: N 19 ARG cc_start: 0.7314 (ttp80) cc_final: 0.6724 (ttp80) REVERT: N 50 ASP cc_start: 0.8875 (p0) cc_final: 0.8623 (p0) REVERT: N 90 ASP cc_start: 0.8356 (m-30) cc_final: 0.7714 (m-30) REVERT: N 95 TYR cc_start: 0.8581 (m-80) cc_final: 0.8303 (m-80) outliers start: 47 outliers final: 44 residues processed: 269 average time/residue: 0.1957 time to fit residues: 73.4125 Evaluate side-chains 275 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 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 430 THR Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 9 HIS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 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 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL 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 63 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.0470 chunk 109 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- 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** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 451 GLN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.110649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089312 restraints weight = 31024.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091330 restraints weight = 20508.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.092726 restraints weight = 15334.005| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.8441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9403 Z= 0.208 Angle : 0.788 10.666 12746 Z= 0.400 Chirality : 0.045 0.342 1416 Planarity : 0.004 0.077 1604 Dihedral : 4.684 54.574 1447 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.12 % Allowed : 28.50 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1115 helix: 0.78 (0.24), residues: 442 sheet: 0.14 (0.34), residues: 230 loop : -0.88 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 322 HIS 0.013 0.001 HIS P 9 PHE 0.027 0.002 PHE R 227 TYR 0.021 0.001 TYR R 421 ARG 0.011 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.29 seconds wall clock time: 63 minutes 4.54 seconds (3784.54 seconds total)