Starting phenix.real_space_refine on Thu Feb 13 20:35:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nbi_0412/02_2025/6nbi_0412.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbi_0412/02_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_0412/02_2025/6nbi_0412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbi_0412/02_2025/6nbi_0412.map" model { file = "/net/cci-nas-00/data/ceres_data/6nbi_0412/02_2025/6nbi_0412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbi_0412/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.70, per 1000 atoms: 0.62 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: 2.18 Conformation dependent library (CDL) restraints added in 1.1 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: 1.23 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: 2.80 Time building geometry restraints manager: 2.52 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: 2.370 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.520 Find NCS groups from input model: 0.110 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- 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 : 1.001 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: 0.2753 time to fit residues: 187.0425 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 : 1.070 ------------------------------------------------------------------------------- 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 = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090149 restraints weight = 30268.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.092505 restraints weight = 19875.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094113 restraints weight = 14575.297| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 1.001 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: 0.9412 (tp40) cc_final: 0.9188 (tp40) REVERT: R 438 GLN cc_start: 0.7766 (pt0) cc_final: 0.7554 (pt0) REVERT: A 17 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8878 (mmtt) REVERT: A 218 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7996 (p0) REVERT: A 240 ASP cc_start: 0.8543 (p0) cc_final: 0.8085 (p0) REVERT: A 264 ASN cc_start: 0.8381 (t0) cc_final: 0.8149 (t0) REVERT: A 340 PHE cc_start: 0.8719 (t80) cc_final: 0.8382 (t80) REVERT: B 12 GLU cc_start: 0.8970 (tp30) cc_final: 0.8767 (tp30) REVERT: B 16 ASN cc_start: 0.9358 (m-40) cc_final: 0.8918 (m-40) REVERT: B 51 LEU cc_start: 0.9568 (mt) cc_final: 0.9184 (mp) REVERT: B 184 THR cc_start: 0.8640 (p) cc_final: 0.8109 (t) REVERT: B 252 LEU cc_start: 0.9736 (tp) cc_final: 0.9510 (tt) REVERT: B 275 SER cc_start: 0.9463 (t) cc_final: 0.9259 (m) REVERT: B 308 LEU cc_start: 0.9045 (mp) cc_final: 0.8787 (tp) REVERT: G 11 GLN cc_start: 0.8799 (pt0) cc_final: 0.8465 (pp30) REVERT: N 20 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.6216 (mt) REVERT: N 38 ARG cc_start: 0.8712 (ptt180) cc_final: 0.8458 (ptm160) REVERT: N 81 LEU cc_start: 0.6776 (tp) cc_final: 0.6287 (tt) outliers start: 39 outliers final: 22 residues processed: 346 average time/residue: 0.2458 time to fit residues: 113.9497 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 : 1.086 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** P 25 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.117429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.096329 restraints weight = 29352.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.098388 restraints weight = 19764.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.099781 restraints weight = 14802.170| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9403 Z= 0.191 Angle : 0.636 10.551 12746 Z= 0.327 Chirality : 0.043 0.332 1416 Planarity : 0.004 0.060 1604 Dihedral : 5.155 46.656 1449 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.12 % Allowed : 19.55 % Favored : 76.34 % 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: 0.08 (0.24), residues: 1115 helix: 1.23 (0.25), residues: 431 sheet: -0.07 (0.31), residues: 244 loop : -1.01 (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 G 13 *********************** 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 327 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 1.035 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 391 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7628 (mp0) REVERT: R 440 GLN cc_start: 0.9017 (pp30) cc_final: 0.8405 (pp30) REVERT: R 442 HIS cc_start: 0.8342 (m90) cc_final: 0.8114 (m90) REVERT: R 445 MET cc_start: 0.7736 (mmp) cc_final: 0.6756 (mmp) REVERT: P 10 GLN cc_start: 0.8314 (pp30) cc_final: 0.8108 (pp30) REVERT: P 11 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7867 (mmm-85) REVERT: A 240 ASP cc_start: 0.8536 (p0) cc_final: 0.7966 (p0) REVERT: A 270 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9507 (mm) REVERT: B 6 GLN cc_start: 0.9411 (pp30) cc_final: 0.9108 (pm20) REVERT: B 12 GLU cc_start: 0.8915 (tp30) cc_final: 0.8656 (tp30) REVERT: B 16 ASN cc_start: 0.9299 (m-40) cc_final: 0.8841 (m-40) REVERT: B 124 TYR cc_start: 0.8909 (m-80) cc_final: 0.8522 (m-80) REVERT: B 184 THR cc_start: 0.8476 (p) cc_final: 0.7902 (t) REVERT: G 11 GLN cc_start: 0.8874 (pt0) cc_final: 0.8532 (pp30) REVERT: N 4 LEU cc_start: 0.8764 (mm) cc_final: 0.8451 (mm) REVERT: N 20 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6304 (mp) REVERT: N 50 ASP cc_start: 0.8767 (p0) cc_final: 0.8439 (p0) REVERT: N 81 LEU cc_start: 0.6665 (tp) cc_final: 0.6175 (tt) REVERT: N 122 THR cc_start: 0.7946 (t) cc_final: 0.7551 (t) outliers start: 40 outliers final: 28 residues processed: 307 average time/residue: 0.2400 time to fit residues: 101.3387 Evaluate side-chains 282 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 P residue 11 ARG 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 228 ASP 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: 7.9990 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS A 31 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.113388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.090535 restraints weight = 30964.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.092586 restraints weight = 21090.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.094033 restraints weight = 16114.068| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9403 Z= 0.268 Angle : 0.657 9.592 12746 Z= 0.346 Chirality : 0.042 0.250 1416 Planarity : 0.004 0.048 1604 Dihedral : 5.057 48.990 1449 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 6.38 % Allowed : 19.86 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.25), residues: 1115 helix: 1.07 (0.24), residues: 443 sheet: 0.05 (0.32), residues: 243 loop : -0.95 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 437 HIS 0.016 0.001 HIS P 9 PHE 0.015 0.002 PHE R 173 TYR 0.016 0.002 TYR N 80 ARG 0.009 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 330 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 268 time to evaluate : 0.841 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: A 240 ASP cc_start: 0.8684 (p0) cc_final: 0.7983 (p0) REVERT: A 365 CYS cc_start: 0.8046 (t) cc_final: 0.7574 (m) REVERT: A 386 MET cc_start: 0.8619 (tmm) cc_final: 0.8350 (tmm) REVERT: B 6 GLN cc_start: 0.9459 (pp30) cc_final: 0.9174 (pm20) REVERT: B 12 GLU cc_start: 0.8951 (tp30) cc_final: 0.8736 (tp30) REVERT: B 16 ASN cc_start: 0.9312 (m-40) cc_final: 0.8889 (m-40) REVERT: B 124 TYR cc_start: 0.8756 (m-80) cc_final: 0.8449 (m-80) REVERT: B 215 GLU cc_start: 0.8954 (mp0) cc_final: 0.8269 (mp0) REVERT: B 339 TRP cc_start: 0.7891 (m100) cc_final: 0.7300 (m100) REVERT: G 11 GLN cc_start: 0.8894 (pt0) cc_final: 0.8541 (pp30) REVERT: N 4 LEU cc_start: 0.8900 (mm) cc_final: 0.8587 (mm) REVERT: N 19 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7025 (ttp80) REVERT: N 20 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6766 (mp) REVERT: N 50 ASP cc_start: 0.8794 (p0) cc_final: 0.8482 (p0) REVERT: N 81 LEU cc_start: 0.6804 (tp) cc_final: 0.6529 (tt) REVERT: N 90 ASP cc_start: 0.7738 (m-30) cc_final: 0.7265 (m-30) REVERT: N 91 THR cc_start: 0.7639 (OUTLIER) cc_final: 0.7389 (t) outliers start: 62 outliers final: 48 residues processed: 303 average time/residue: 0.1997 time to fit residues: 83.4164 Evaluate side-chains 295 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 245 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 213 GLN 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 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 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 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 32 LYS 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 20 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 Chi-restraints excluded: chain N residue 93 VAL 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: 3.9990 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.114124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.091679 restraints weight = 31555.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.093851 restraints weight = 21333.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.095236 restraints weight = 16119.195| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6921 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= 0.187 Angle : 0.644 12.394 12746 Z= 0.334 Chirality : 0.043 0.350 1416 Planarity : 0.004 0.049 1604 Dihedral : 4.802 49.913 1449 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.45 % Allowed : 22.02 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1115 helix: 1.27 (0.25), residues: 437 sheet: 0.34 (0.33), residues: 234 loop : -0.99 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 437 HIS 0.009 0.001 HIS P 9 PHE 0.028 0.002 PHE R 184 TYR 0.028 0.002 TYR R 191 ARG 0.006 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 324 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 1.079 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: R 220 ASN cc_start: 0.9125 (m-40) cc_final: 0.8904 (m-40) REVERT: R 240 LYS cc_start: 0.9371 (tppt) cc_final: 0.9133 (tppt) REVERT: R 324 PHE cc_start: 0.8465 (m-80) cc_final: 0.8196 (m-80) REVERT: R 368 LEU cc_start: 0.9144 (mm) cc_final: 0.8851 (mm) REVERT: R 440 GLN cc_start: 0.8998 (pp30) cc_final: 0.8591 (pp30) REVERT: A 240 ASP cc_start: 0.8570 (p0) cc_final: 0.7861 (p0) REVERT: A 365 CYS cc_start: 0.8029 (t) cc_final: 0.7529 (m) REVERT: A 386 MET cc_start: 0.8590 (tmm) cc_final: 0.8286 (tmm) REVERT: B 6 GLN cc_start: 0.9452 (pp30) cc_final: 0.9127 (pm20) REVERT: B 12 GLU cc_start: 0.8958 (tp30) cc_final: 0.8309 (tp30) REVERT: B 15 LYS cc_start: 0.9415 (ptpt) cc_final: 0.9057 (pttp) REVERT: B 16 ASN cc_start: 0.9320 (m-40) cc_final: 0.8793 (m-40) REVERT: B 124 TYR cc_start: 0.8671 (m-80) cc_final: 0.8448 (m-80) REVERT: B 127 LYS cc_start: 0.9120 (ptmm) cc_final: 0.8910 (ptmm) REVERT: B 215 GLU cc_start: 0.8886 (mp0) cc_final: 0.8162 (mp0) REVERT: B 339 TRP cc_start: 0.7798 (m100) cc_final: 0.7581 (m-10) REVERT: G 11 GLN cc_start: 0.8896 (pt0) cc_final: 0.8554 (pp30) REVERT: G 17 GLU cc_start: 0.9100 (pp20) cc_final: 0.8660 (pp20) REVERT: N 4 LEU cc_start: 0.8845 (mm) cc_final: 0.8456 (mm) REVERT: N 50 ASP cc_start: 0.8772 (p0) cc_final: 0.8447 (p0) REVERT: N 81 LEU cc_start: 0.6927 (tp) cc_final: 0.6445 (tt) REVERT: N 90 ASP cc_start: 0.7684 (m-30) cc_final: 0.7253 (m-30) REVERT: N 91 THR cc_start: 0.7451 (OUTLIER) cc_final: 0.7222 (t) outliers start: 53 outliers final: 40 residues processed: 302 average time/residue: 0.2199 time to fit residues: 90.3931 Evaluate side-chains 288 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET 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 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 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 158 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 22 GLU 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 51 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 86 LEU 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: 0.7980 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 295 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.114997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.092188 restraints weight = 31469.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.094324 restraints weight = 21394.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.095735 restraints weight = 16233.226| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.7215 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= 0.183 Angle : 0.646 9.758 12746 Z= 0.336 Chirality : 0.042 0.269 1416 Planarity : 0.004 0.050 1604 Dihedral : 4.698 51.184 1449 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.45 % Allowed : 22.43 % Favored : 72.12 % 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: 0.25 (0.25), residues: 1115 helix: 1.25 (0.25), residues: 435 sheet: 0.31 (0.33), residues: 231 loop : -0.94 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 437 HIS 0.012 0.001 HIS P 9 PHE 0.026 0.001 PHE R 184 TYR 0.018 0.001 TYR R 245 ARG 0.006 0.000 ARG A 38 *********************** 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 317 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 ILE cc_start: 0.8237 (mm) cc_final: 0.7866 (pt) REVERT: R 177 GLU cc_start: 0.9286 (mm-30) cc_final: 0.9007 (mm-30) REVERT: R 220 ASN cc_start: 0.9123 (m-40) cc_final: 0.8878 (m-40) REVERT: R 322 TRP cc_start: 0.7153 (OUTLIER) cc_final: 0.6944 (m100) REVERT: R 324 PHE cc_start: 0.8456 (m-80) cc_final: 0.8149 (m-80) REVERT: R 368 LEU cc_start: 0.9189 (mm) cc_final: 0.8961 (mm) REVERT: R 467 GLN cc_start: 0.8480 (mt0) cc_final: 0.8199 (mt0) REVERT: P 6 GLN cc_start: 0.8529 (mt0) cc_final: 0.8249 (mp10) REVERT: A 240 ASP cc_start: 0.8557 (p0) cc_final: 0.7840 (p0) REVERT: A 365 CYS cc_start: 0.8104 (t) cc_final: 0.7509 (m) REVERT: A 386 MET cc_start: 0.8642 (tmm) cc_final: 0.8361 (tmm) REVERT: B 6 GLN cc_start: 0.9459 (pp30) cc_final: 0.9122 (pm20) REVERT: B 12 GLU cc_start: 0.8977 (tp30) cc_final: 0.8388 (tp30) REVERT: B 15 LYS cc_start: 0.9442 (ptpt) cc_final: 0.9077 (pttp) REVERT: B 16 ASN cc_start: 0.9311 (m-40) cc_final: 0.8819 (m-40) REVERT: B 124 TYR cc_start: 0.8545 (m-80) cc_final: 0.8317 (m-80) REVERT: B 215 GLU cc_start: 0.8865 (mp0) cc_final: 0.8198 (mp0) REVERT: B 339 TRP cc_start: 0.7805 (m100) cc_final: 0.7395 (m100) REVERT: G 11 GLN cc_start: 0.8849 (pt0) cc_final: 0.8528 (pp30) REVERT: G 28 ILE cc_start: 0.9026 (tp) cc_final: 0.8597 (mp) REVERT: N 4 LEU cc_start: 0.8780 (mm) cc_final: 0.8288 (mm) REVERT: N 5 GLN cc_start: 0.8143 (tp40) cc_final: 0.7801 (tp40) REVERT: N 90 ASP cc_start: 0.7739 (m-30) cc_final: 0.7061 (m-30) REVERT: N 91 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7251 (t) outliers start: 53 outliers final: 44 residues processed: 296 average time/residue: 0.2235 time to fit residues: 90.4500 Evaluate side-chains 289 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 A residue 371 ASN Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 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 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 86 LEU Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 225 HIS ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.111968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089365 restraints weight = 31907.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.091492 restraints weight = 21565.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.092713 restraints weight = 16320.451| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.7603 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= 0.223 Angle : 0.680 10.699 12746 Z= 0.353 Chirality : 0.043 0.236 1416 Planarity : 0.004 0.050 1604 Dihedral : 4.791 52.897 1449 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.86 % Allowed : 23.97 % 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: 0.22 (0.25), residues: 1115 helix: 1.23 (0.24), residues: 440 sheet: 0.15 (0.33), residues: 231 loop : -0.92 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 437 HIS 0.011 0.001 HIS P 9 PHE 0.026 0.002 PHE R 184 TYR 0.029 0.002 TYR R 191 ARG 0.008 0.001 ARG R 147 *********************** 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 317 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 177 GLU cc_start: 0.9231 (mm-30) cc_final: 0.9025 (mm-30) REVERT: R 220 ASN cc_start: 0.9128 (m-40) cc_final: 0.8925 (m-40) REVERT: R 324 PHE cc_start: 0.8558 (m-80) cc_final: 0.8249 (m-80) REVERT: R 467 GLN cc_start: 0.8454 (mt0) cc_final: 0.8176 (mt0) REVERT: P 6 GLN cc_start: 0.8669 (mt0) cc_final: 0.8256 (mp10) REVERT: A 365 CYS cc_start: 0.8206 (t) cc_final: 0.7609 (m) REVERT: A 386 MET cc_start: 0.8770 (tmm) cc_final: 0.8513 (tmm) REVERT: B 6 GLN cc_start: 0.9444 (pp30) cc_final: 0.9116 (pm20) REVERT: B 12 GLU cc_start: 0.9000 (tp30) cc_final: 0.8461 (tp30) REVERT: B 15 LYS cc_start: 0.9440 (ptpt) cc_final: 0.9090 (pttp) REVERT: B 16 ASN cc_start: 0.9316 (m-40) cc_final: 0.8870 (m-40) REVERT: B 124 TYR cc_start: 0.8651 (m-80) cc_final: 0.8382 (m-80) REVERT: B 215 GLU cc_start: 0.8921 (mp0) cc_final: 0.8253 (mp0) REVERT: G 11 GLN cc_start: 0.8844 (pt0) cc_final: 0.8533 (pp30) REVERT: N 4 LEU cc_start: 0.8799 (mm) cc_final: 0.8276 (mm) REVERT: N 5 GLN cc_start: 0.8193 (tp40) cc_final: 0.7877 (tp40) REVERT: N 50 ASP cc_start: 0.8888 (p0) cc_final: 0.8603 (p0) REVERT: N 87 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8080 (ttpt) REVERT: N 90 ASP cc_start: 0.8093 (m-30) cc_final: 0.7477 (m-30) REVERT: N 91 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7774 (t) outliers start: 57 outliers final: 48 residues processed: 293 average time/residue: 0.2212 time to fit residues: 89.0060 Evaluate side-chains 291 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 140 HIS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 422 ILE 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 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 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 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 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 86 LEU Chi-restraints excluded: chain N residue 91 THR 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: 2.9990 chunk 68 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.116091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.092681 restraints weight = 32758.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094954 restraints weight = 21397.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.096522 restraints weight = 15959.238| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.7774 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= 0.193 Angle : 0.704 9.940 12746 Z= 0.364 Chirality : 0.042 0.190 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.645 52.963 1449 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.53 % Allowed : 26.75 % Favored : 68.72 % 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: 0.30 (0.25), residues: 1115 helix: 1.30 (0.25), residues: 441 sheet: 0.28 (0.34), residues: 223 loop : -0.91 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 322 HIS 0.014 0.001 HIS P 9 PHE 0.020 0.001 PHE R 184 TYR 0.020 0.001 TYR R 421 ARG 0.009 0.001 ARG A 38 *********************** 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 309 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.0997 (mmt) cc_final: 0.0377 (mmt) REVERT: R 115 ILE cc_start: 0.8315 (mm) cc_final: 0.7960 (pt) REVERT: R 177 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9119 (mm-30) REVERT: R 324 PHE cc_start: 0.8607 (m-80) cc_final: 0.8280 (m-80) REVERT: R 364 GLN cc_start: 0.9252 (tp40) cc_final: 0.9021 (tp40) REVERT: R 467 GLN cc_start: 0.8528 (mt0) cc_final: 0.8256 (mt0) REVERT: P 2 VAL cc_start: 0.9497 (t) cc_final: 0.8922 (m) REVERT: P 6 GLN cc_start: 0.8730 (mt0) cc_final: 0.8253 (mp10) REVERT: A 365 CYS cc_start: 0.8273 (t) cc_final: 0.7603 (m) REVERT: A 386 MET cc_start: 0.8833 (tmm) cc_final: 0.8498 (tmm) REVERT: B 12 GLU cc_start: 0.8973 (tp30) cc_final: 0.8397 (tp30) REVERT: B 15 LYS cc_start: 0.9451 (ptpt) cc_final: 0.9101 (pttp) REVERT: B 16 ASN cc_start: 0.9334 (m-40) cc_final: 0.8867 (m-40) REVERT: B 124 TYR cc_start: 0.8682 (m-80) cc_final: 0.8442 (m-80) REVERT: B 215 GLU cc_start: 0.8924 (mp0) cc_final: 0.8237 (mp0) REVERT: B 339 TRP cc_start: 0.7937 (m100) cc_final: 0.7593 (m100) REVERT: G 11 GLN cc_start: 0.8874 (pt0) cc_final: 0.8555 (pp30) REVERT: N 4 LEU cc_start: 0.8684 (mm) cc_final: 0.8159 (mm) REVERT: N 5 GLN cc_start: 0.8077 (tp40) cc_final: 0.7794 (tp40) REVERT: N 87 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8216 (ttpt) REVERT: N 90 ASP cc_start: 0.7965 (m-30) cc_final: 0.7434 (m-30) outliers start: 44 outliers final: 38 residues processed: 291 average time/residue: 0.2207 time to fit residues: 87.5924 Evaluate side-chains 280 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 140 HIS 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 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 391 TYR 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 146 LEU 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 G residue 51 LEU Chi-restraints excluded: chain N residue 86 LEU 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: 0.8980 chunk 39 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 8 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.116433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.093352 restraints weight = 32093.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.095707 restraints weight = 21285.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.097269 restraints weight = 15744.858| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.7927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9403 Z= 0.190 Angle : 0.718 12.125 12746 Z= 0.367 Chirality : 0.042 0.170 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.548 53.589 1449 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.12 % Allowed : 27.26 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.25), residues: 1115 helix: 1.18 (0.25), residues: 442 sheet: 0.19 (0.33), residues: 232 loop : -0.94 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 322 HIS 0.012 0.001 HIS P 9 PHE 0.010 0.001 PHE A 212 TYR 0.030 0.002 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 294 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.0874 (mmt) cc_final: 0.0486 (mmt) REVERT: R 115 ILE cc_start: 0.8257 (mm) cc_final: 0.7912 (pt) REVERT: R 177 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9105 (mm-30) REVERT: R 324 PHE cc_start: 0.8533 (m-80) cc_final: 0.8172 (m-80) REVERT: R 467 GLN cc_start: 0.8563 (mt0) cc_final: 0.8263 (mt0) REVERT: P 6 GLN cc_start: 0.8703 (mt0) cc_final: 0.8212 (mp10) REVERT: A 270 LEU cc_start: 0.9804 (OUTLIER) cc_final: 0.9455 (mm) REVERT: A 358 TYR cc_start: 0.7038 (m-80) cc_final: 0.6629 (m-80) REVERT: A 365 CYS cc_start: 0.8269 (t) cc_final: 0.7559 (m) REVERT: A 386 MET cc_start: 0.8771 (tmm) cc_final: 0.8524 (tmm) REVERT: B 12 GLU cc_start: 0.8937 (tp30) cc_final: 0.8274 (tp30) REVERT: B 15 LYS cc_start: 0.9454 (ptpt) cc_final: 0.9101 (pttp) REVERT: B 16 ASN cc_start: 0.9318 (m-40) cc_final: 0.8806 (m-40) REVERT: B 124 TYR cc_start: 0.8667 (m-80) cc_final: 0.8455 (m-80) REVERT: B 215 GLU cc_start: 0.8849 (mp0) cc_final: 0.8180 (mp0) REVERT: B 339 TRP cc_start: 0.7838 (m100) cc_final: 0.7511 (m100) REVERT: G 11 GLN cc_start: 0.8841 (pt0) cc_final: 0.8526 (pp30) REVERT: N 4 LEU cc_start: 0.8637 (mm) cc_final: 0.8117 (mm) REVERT: N 5 GLN cc_start: 0.8050 (tp40) cc_final: 0.7830 (tp40) REVERT: N 19 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7265 (ttp80) REVERT: N 87 LYS cc_start: 0.8779 (ttpp) cc_final: 0.8223 (ttpt) REVERT: N 90 ASP cc_start: 0.7984 (m-30) cc_final: 0.7460 (m-30) outliers start: 40 outliers final: 36 residues processed: 279 average time/residue: 0.2060 time to fit residues: 79.1796 Evaluate side-chains 283 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 140 HIS 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 421 TYR Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 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 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 146 LEU 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 260 GLU 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 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 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 = 0.115018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.092241 restraints weight = 32552.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094563 restraints weight = 21111.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.096026 restraints weight = 15605.822| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.8119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9403 Z= 0.207 Angle : 0.747 12.230 12746 Z= 0.384 Chirality : 0.043 0.203 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.615 54.241 1449 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.81 % Allowed : 27.78 % Favored : 68.42 % 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: 0.10 (0.25), residues: 1115 helix: 1.05 (0.25), residues: 444 sheet: 0.20 (0.33), residues: 232 loop : -0.98 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 322 HIS 0.014 0.001 HIS P 9 PHE 0.012 0.001 PHE R 447 TYR 0.019 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: 37 poor density : 249 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 ILE cc_start: 0.8253 (mm) cc_final: 0.7893 (pt) REVERT: R 177 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9107 (mm-30) REVERT: R 324 PHE cc_start: 0.8490 (m-80) cc_final: 0.8227 (m-80) REVERT: R 368 LEU cc_start: 0.9413 (mm) cc_final: 0.9102 (mm) REVERT: R 441 MET cc_start: 0.8842 (tpp) cc_final: 0.8254 (tpp) REVERT: R 467 GLN cc_start: 0.8554 (mt0) cc_final: 0.8244 (mt0) REVERT: P 2 VAL cc_start: 0.9436 (t) cc_final: 0.8798 (m) REVERT: P 6 GLN cc_start: 0.8730 (mt0) cc_final: 0.8274 (mp10) REVERT: A 240 ASP cc_start: 0.8668 (p0) cc_final: 0.8009 (p0) REVERT: A 270 LEU cc_start: 0.9789 (OUTLIER) cc_final: 0.9444 (mm) REVERT: A 365 CYS cc_start: 0.8275 (t) cc_final: 0.7578 (m) REVERT: A 386 MET cc_start: 0.8965 (tmm) cc_final: 0.8681 (tmm) REVERT: B 10 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8983 (tm-30) REVERT: B 16 ASN cc_start: 0.9326 (m-40) cc_final: 0.8918 (m-40) REVERT: B 124 TYR cc_start: 0.8672 (m-80) cc_final: 0.8460 (m-80) REVERT: B 215 GLU cc_start: 0.8891 (mp0) cc_final: 0.8206 (mp0) REVERT: B 337 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8687 (mmmt) REVERT: B 339 TRP cc_start: 0.7881 (m100) cc_final: 0.7474 (m100) REVERT: G 11 GLN cc_start: 0.8859 (pt0) cc_final: 0.8570 (pp30) REVERT: G 36 ASP cc_start: 0.9076 (m-30) cc_final: 0.8796 (p0) REVERT: N 4 LEU cc_start: 0.8619 (mm) cc_final: 0.8076 (mm) REVERT: N 19 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7209 (ttp80) REVERT: N 87 LYS cc_start: 0.8738 (ttpp) cc_final: 0.8186 (ttpt) REVERT: N 90 ASP cc_start: 0.7899 (m-30) cc_final: 0.7379 (m-30) outliers start: 37 outliers final: 35 residues processed: 273 average time/residue: 0.2108 time to fit residues: 79.5880 Evaluate side-chains 276 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 140 HIS 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 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 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 146 LEU 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 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 80 optimal weight: 0.0030 chunk 9 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 HIS ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 451 GLN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.115962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.094010 restraints weight = 31826.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.096233 restraints weight = 21241.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.097593 restraints weight = 15871.605| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.8241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9403 Z= 0.197 Angle : 0.772 12.484 12746 Z= 0.394 Chirality : 0.043 0.199 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.472 54.614 1449 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.70 % Allowed : 28.70 % Favored : 67.59 % 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: 0.12 (0.25), residues: 1115 helix: 1.06 (0.25), residues: 439 sheet: 0.10 (0.33), residues: 228 loop : -0.85 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 322 HIS 0.016 0.001 HIS P 9 PHE 0.038 0.001 PHE R 184 TYR 0.041 0.002 TYR R 191 ARG 0.007 0.001 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.53 seconds wall clock time: 58 minutes 32.40 seconds (3512.40 seconds total)