Starting phenix.real_space_refine on Thu Mar 14 18:52:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbh_0411/03_2024/6nbh_0411_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbh_0411/03_2024/6nbh_0411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbh_0411/03_2024/6nbh_0411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbh_0411/03_2024/6nbh_0411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbh_0411/03_2024/6nbh_0411_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbh_0411/03_2024/6nbh_0411_updated.pdb" } resolution = 3.5 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= 0.004 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 6121 2.51 5 N 1627 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9502 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3098 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 11, 'TRANS': 367} Chain breaks: 3 Chain: "P" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 283 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1873 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} 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: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 250 Unusual residues: {'CLR': 7, 'PLM': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 5.45, per 1000 atoms: 0.57 Number of scatterers: 9502 At special positions: 0 Unit cell: (125.736, 99.372, 150.072, 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 1697 8.00 N 1627 7.00 C 6121 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=2.03 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 - 3.50 Amino acid : False - 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 36.9% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'R' and resid 34 through 55 Processing helix chain 'R' and resid 178 through 211 removed outlier: 3.755A pdb=" N MET R 189 " --> pdb=" O ASP R 185 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE R 190 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU R 199 " --> pdb=" O TYR R 195 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU R 202 " --> pdb=" O SER R 198 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL R 206 " --> pdb=" O LEU R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 238 removed outlier: 3.700A pdb=" N HIS R 223 " --> pdb=" O ARG R 219 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET R 224 " --> pdb=" O ASN R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 249 removed outlier: 3.601A pdb=" N LEU R 244 " --> pdb=" O LYS R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 277 No H-bonds generated for 'chain 'R' and resid 274 through 277' Processing helix chain 'R' and resid 279 through 311 removed outlier: 3.633A pdb=" N VAL R 283 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE R 287 " --> pdb=" O ALA R 284 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE R 291 " --> pdb=" O PHE R 288 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU R 292 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR R 294 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR R 296 " --> pdb=" O ALA R 293 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE R 299 " --> pdb=" O TYR R 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU R 302 " --> pdb=" O ILE R 299 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU R 306 " --> pdb=" O GLY R 303 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU R 309 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE R 310 " --> pdb=" O HIS R 307 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE R 311 " --> pdb=" O SER R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 346 removed outlier: 3.612A pdb=" N THR R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL R 326 " --> pdb=" O TRP R 322 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE R 327 " --> pdb=" O GLY R 323 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.725A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 370 removed outlier: 3.851A pdb=" N ILE R 363 " --> pdb=" O LYS R 360 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL R 365 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 4.221A pdb=" N ALA R 369 " --> pdb=" O PRO R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 372 through 380 Processing helix chain 'R' and resid 384 through 390 Processing helix chain 'R' and resid 400 through 411 Processing helix chain 'R' and resid 414 through 417 No H-bonds generated for 'chain 'R' and resid 414 through 417' Processing helix chain 'R' and resid 420 through 423 No H-bonds generated for 'chain 'R' and resid 420 through 423' Processing helix chain 'R' and resid 435 through 459 removed outlier: 3.514A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR R 459 " --> pdb=" O VAL R 455 " (cutoff:3.500A) Processing helix chain 'R' and resid 464 through 480 Processing helix chain 'P' and resid 3 through 31 removed outlier: 3.720A pdb=" N ARG P 20 " --> pdb=" O GLN P 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 37 removed outlier: 3.735A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.616A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 4.583A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.707A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.844A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'R' and resid 126 through 130 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.026A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.229A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.568A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.850A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.304A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.586A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.801A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.002A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.566A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.091A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1011 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: 2.64 Time building geometry restraints manager: 3.61 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: 3015 1.35 - 1.47: 2338 1.47 - 1.59: 4290 1.59 - 1.71: 0 1.71 - 1.83: 80 Bond restraints: 9723 Sorted by residual: bond pdb=" N HIS R 114 " pdb=" CA HIS R 114 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.54e+00 bond pdb=" C MET R 414 " pdb=" N PRO R 415 " ideal model delta sigma weight residual 1.335 1.364 -0.028 1.36e-02 5.41e+03 4.30e+00 bond pdb=" C THR A 320 " pdb=" N PRO A 321 " ideal model delta sigma weight residual 1.331 1.356 -0.025 1.20e-02 6.94e+03 4.20e+00 bond pdb=" C ASP G 48 " pdb=" N PRO G 49 " ideal model delta sigma weight residual 1.332 1.348 -0.016 8.90e-03 1.26e+04 3.12e+00 bond pdb=" C LEU R 331 " pdb=" N PRO R 332 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.28e-02 6.10e+03 2.42e+00 ... (remaining 9718 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.69: 236 106.69 - 113.58: 5350 113.58 - 120.47: 3870 120.47 - 127.37: 3644 127.37 - 134.26: 89 Bond angle restraints: 13189 Sorted by residual: angle pdb=" CA ASP A 354 " pdb=" CB ASP A 354 " pdb=" CG ASP A 354 " ideal model delta sigma weight residual 112.60 116.94 -4.34 1.00e+00 1.00e+00 1.89e+01 angle pdb=" N VAL R 382 " pdb=" CA VAL R 382 " pdb=" C VAL R 382 " ideal model delta sigma weight residual 112.43 108.49 3.94 9.20e-01 1.18e+00 1.84e+01 angle pdb=" C LYS N 76 " pdb=" N ASN N 77 " pdb=" CA ASN N 77 " ideal model delta sigma weight residual 122.07 126.86 -4.79 1.43e+00 4.89e-01 1.12e+01 angle pdb=" N PRO B 236 " pdb=" CA PRO B 236 " pdb=" C PRO B 236 " ideal model delta sigma weight residual 112.47 119.34 -6.87 2.06e+00 2.36e-01 1.11e+01 angle pdb=" CA ASN N 77 " pdb=" CB ASN N 77 " pdb=" CG ASN N 77 " ideal model delta sigma weight residual 112.60 115.91 -3.31 1.00e+00 1.00e+00 1.10e+01 ... (remaining 13184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.71: 5792 13.71 - 27.43: 233 27.43 - 41.14: 59 41.14 - 54.85: 11 54.85 - 68.57: 3 Dihedral angle restraints: 6098 sinusoidal: 2728 harmonic: 3370 Sorted by residual: dihedral pdb=" CA ILE R 381 " pdb=" C ILE R 381 " pdb=" N VAL R 382 " pdb=" CA VAL R 382 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 128.88 -35.88 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CA LEU R 202 " pdb=" C LEU R 202 " pdb=" N THR R 203 " pdb=" CA THR R 203 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 6095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1025 0.052 - 0.104: 364 0.104 - 0.157: 67 0.157 - 0.209: 14 0.209 - 0.261: 3 Chirality restraints: 1473 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 -2.58 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C14 CLR R 603 " pdb=" C13 CLR R 603 " pdb=" C15 CLR R 603 " pdb=" C8 CLR R 603 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1470 not shown) Planarity restraints: 1633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.030 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO G 49 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 414 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO R 415 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 415 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 415 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 376 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C PHE A 376 " -0.021 2.00e-02 2.50e+03 pdb=" O PHE A 376 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN A 377 " 0.007 2.00e-02 2.50e+03 ... (remaining 1630 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 3055 2.87 - 3.37: 8186 3.37 - 3.88: 14807 3.88 - 4.39: 16393 4.39 - 4.90: 28772 Nonbonded interactions: 71213 Sorted by model distance: nonbonded pdb=" OH TYR A 360 " pdb=" OD2 ASP A 381 " model vdw 2.357 2.440 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.390 2.440 nonbonded pdb=" O ARG A 42 " pdb=" OG1 THR A 242 " model vdw 2.399 2.440 nonbonded pdb=" O VAL R 412 " pdb=" OH TYR R 459 " model vdw 2.400 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.407 2.440 ... (remaining 71208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.520 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.660 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 0.028 9723 Z= 0.342 Angle : 0.865 6.871 13189 Z= 0.567 Chirality : 0.054 0.261 1473 Planarity : 0.003 0.046 1633 Dihedral : 8.431 68.568 3900 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.20 % Allowed : 0.71 % Favored : 99.09 % 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: -1.51 (0.22), residues: 1135 helix: -0.27 (0.22), residues: 446 sheet: -0.70 (0.33), residues: 210 loop : -1.78 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 437 HIS 0.009 0.001 HIS R 114 PHE 0.013 0.002 PHE R 138 TYR 0.016 0.002 TYR N 80 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 444 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.7194 (mtp) cc_final: 0.6646 (ppp) REVERT: R 348 ASN cc_start: 0.6392 (t0) cc_final: 0.6170 (t0) REVERT: R 404 ARG cc_start: 0.7618 (mtt180) cc_final: 0.6903 (tpt170) REVERT: R 408 LYS cc_start: 0.8141 (tttt) cc_final: 0.7918 (tttm) REVERT: R 433 SER cc_start: 0.7747 (t) cc_final: 0.7402 (p) REVERT: R 474 TRP cc_start: 0.6368 (t60) cc_final: 0.5924 (t60) REVERT: A 31 GLN cc_start: 0.8784 (mm-40) cc_final: 0.7642 (tm-30) REVERT: B 65 THR cc_start: 0.8859 (p) cc_final: 0.8609 (t) REVERT: B 123 ILE cc_start: 0.8181 (mt) cc_final: 0.7958 (mt) REVERT: B 184 THR cc_start: 0.8151 (p) cc_final: 0.7918 (t) REVERT: B 303 ASP cc_start: 0.9190 (t70) cc_final: 0.8773 (p0) REVERT: N 29 PHE cc_start: 0.8684 (t80) cc_final: 0.8320 (t80) REVERT: N 31 ASN cc_start: 0.8484 (m-40) cc_final: 0.8281 (t0) REVERT: N 57 SER cc_start: 0.9014 (t) cc_final: 0.8760 (m) REVERT: N 68 PHE cc_start: 0.7194 (m-10) cc_final: 0.6686 (m-10) REVERT: N 93 VAL cc_start: 0.8190 (t) cc_final: 0.7810 (p) REVERT: N 124 VAL cc_start: 0.8660 (t) cc_final: 0.8449 (m) outliers start: 2 outliers final: 1 residues processed: 445 average time/residue: 0.2480 time to fit residues: 144.5099 Evaluate side-chains 247 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 140 HIS R 295 ASN R 364 GLN R 402 GLN R 451 GLN A 23 ASN B 88 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9723 Z= 0.204 Angle : 0.597 9.507 13189 Z= 0.311 Chirality : 0.042 0.192 1473 Planarity : 0.005 0.062 1633 Dihedral : 5.816 46.599 1768 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.35 % Allowed : 14.57 % Favored : 81.07 % 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: 1135 helix: 1.00 (0.25), residues: 440 sheet: -0.17 (0.33), residues: 213 loop : -1.16 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 298 HIS 0.005 0.001 HIS R 114 PHE 0.021 0.002 PHE B 235 TYR 0.017 0.001 TYR R 191 ARG 0.008 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 256 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 404 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7107 (tpt170) REVERT: R 408 LYS cc_start: 0.8346 (tttt) cc_final: 0.8074 (tttm) REVERT: R 474 TRP cc_start: 0.6532 (t60) cc_final: 0.6003 (t60) REVERT: A 31 GLN cc_start: 0.8747 (mm-40) cc_final: 0.7844 (tm-30) REVERT: A 315 PHE cc_start: 0.7664 (t80) cc_final: 0.7323 (t80) REVERT: B 127 LYS cc_start: 0.8450 (mmmt) cc_final: 0.7823 (mttp) REVERT: B 235 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8372 (t80) REVERT: B 333 ASP cc_start: 0.8457 (p0) cc_final: 0.8156 (t0) REVERT: N 31 ASN cc_start: 0.8683 (m-40) cc_final: 0.8431 (t0) REVERT: N 123 GLN cc_start: 0.8769 (tp40) cc_final: 0.8340 (tp-100) outliers start: 43 outliers final: 25 residues processed: 286 average time/residue: 0.2285 time to fit residues: 87.8399 Evaluate side-chains 244 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN A 59 GLN A 271 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9723 Z= 0.228 Angle : 0.580 6.626 13189 Z= 0.301 Chirality : 0.042 0.156 1473 Planarity : 0.004 0.045 1633 Dihedral : 5.566 42.654 1767 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.86 % Allowed : 16.60 % Favored : 78.54 % 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: 0.28 (0.25), residues: 1135 helix: 1.34 (0.25), residues: 443 sheet: 0.27 (0.34), residues: 211 loop : -0.93 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 298 HIS 0.004 0.001 HIS A 357 PHE 0.023 0.002 PHE B 235 TYR 0.019 0.002 TYR R 191 ARG 0.009 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 239 time to evaluate : 1.069 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: 0.5549 (ttp) cc_final: 0.4835 (ttt) REVERT: R 288 PHE cc_start: 0.7921 (t80) cc_final: 0.7683 (t80) REVERT: R 321 LEU cc_start: 0.7956 (tp) cc_final: 0.7685 (tt) REVERT: R 404 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7209 (tpt170) REVERT: R 411 LEU cc_start: 0.8828 (mt) cc_final: 0.8307 (tt) REVERT: R 472 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8412 (ttmt) REVERT: R 474 TRP cc_start: 0.6564 (t60) cc_final: 0.5962 (t60) REVERT: R 476 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7702 (ttm170) REVERT: A 31 GLN cc_start: 0.8694 (mm-40) cc_final: 0.7941 (tm-30) REVERT: A 229 ASP cc_start: 0.8076 (m-30) cc_final: 0.7603 (p0) REVERT: B 58 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8731 (mp) REVERT: B 235 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8397 (t80) REVERT: B 333 ASP cc_start: 0.8601 (p0) cc_final: 0.8281 (t0) REVERT: N 31 ASN cc_start: 0.8857 (m-40) cc_final: 0.8414 (t0) REVERT: N 43 LYS cc_start: 0.7017 (mmmt) cc_final: 0.6804 (mmmt) REVERT: N 47 TRP cc_start: 0.7654 (t60) cc_final: 0.7406 (t60) REVERT: N 76 LYS cc_start: 0.8920 (tttt) cc_final: 0.8648 (tttp) REVERT: N 93 VAL cc_start: 0.8127 (t) cc_final: 0.7883 (p) REVERT: N 123 GLN cc_start: 0.8854 (tp40) cc_final: 0.8277 (tp-100) outliers start: 48 outliers final: 31 residues processed: 272 average time/residue: 0.2136 time to fit residues: 79.5532 Evaluate side-chains 252 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 219 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 GLU Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN A 14 ASN A 23 ASN B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9723 Z= 0.234 Angle : 0.568 9.573 13189 Z= 0.294 Chirality : 0.042 0.175 1473 Planarity : 0.004 0.043 1633 Dihedral : 5.389 34.880 1767 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.57 % Allowed : 18.32 % Favored : 76.11 % 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: 0.29 (0.25), residues: 1135 helix: 1.32 (0.25), residues: 443 sheet: 0.22 (0.34), residues: 213 loop : -0.85 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 352 HIS 0.004 0.001 HIS R 114 PHE 0.023 0.001 PHE B 235 TYR 0.019 0.001 TYR R 191 ARG 0.009 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 226 time to evaluate : 1.124 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: 0.5669 (ttp) cc_final: 0.4774 (ttt) REVERT: R 192 THR cc_start: 0.8124 (p) cc_final: 0.7894 (t) REVERT: R 404 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7158 (tpt170) REVERT: R 411 LEU cc_start: 0.8895 (mt) cc_final: 0.8447 (tt) REVERT: R 474 TRP cc_start: 0.6572 (t60) cc_final: 0.6165 (t60) REVERT: A 31 GLN cc_start: 0.8676 (mm-40) cc_final: 0.7967 (tm-30) REVERT: A 229 ASP cc_start: 0.8168 (m-30) cc_final: 0.7612 (p0) REVERT: A 268 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8356 (tp30) REVERT: B 58 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8749 (mp) REVERT: B 235 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8348 (t80) REVERT: B 273 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8720 (mp) REVERT: B 312 ASP cc_start: 0.7304 (p0) cc_final: 0.6773 (p0) REVERT: B 333 ASP cc_start: 0.8663 (p0) cc_final: 0.8287 (t0) REVERT: N 31 ASN cc_start: 0.8878 (m110) cc_final: 0.8265 (t0) REVERT: N 47 TRP cc_start: 0.7848 (t60) cc_final: 0.7393 (t60) REVERT: N 93 VAL cc_start: 0.8292 (t) cc_final: 0.8027 (p) REVERT: N 123 GLN cc_start: 0.8902 (tp40) cc_final: 0.8282 (tp-100) outliers start: 55 outliers final: 38 residues processed: 269 average time/residue: 0.2187 time to fit residues: 80.4602 Evaluate side-chains 247 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 425 MET Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 0.0010 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 402 GLN R 448 ASN B 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9723 Z= 0.168 Angle : 0.546 7.344 13189 Z= 0.284 Chirality : 0.040 0.156 1473 Planarity : 0.003 0.044 1633 Dihedral : 5.101 34.380 1767 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.85 % Allowed : 21.66 % Favored : 74.49 % 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: 0.45 (0.25), residues: 1135 helix: 1.43 (0.25), residues: 443 sheet: 0.42 (0.35), residues: 213 loop : -0.81 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 114 PHE 0.023 0.001 PHE B 235 TYR 0.021 0.001 TYR R 134 ARG 0.010 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 1.176 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: 0.5406 (ttp) cc_final: 0.4692 (ttt) REVERT: R 321 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7628 (tt) REVERT: R 404 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7122 (tpt170) REVERT: R 471 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8174 (mtpt) REVERT: R 474 TRP cc_start: 0.6503 (t60) cc_final: 0.6099 (t60) REVERT: R 476 ARG cc_start: 0.8003 (ttm170) cc_final: 0.7775 (ttm170) REVERT: A 31 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8129 (tm-30) REVERT: B 58 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8600 (mp) REVERT: B 235 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8385 (t80) REVERT: B 245 SER cc_start: 0.7110 (t) cc_final: 0.6683 (t) REVERT: B 273 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8644 (mp) REVERT: B 312 ASP cc_start: 0.7246 (p0) cc_final: 0.6656 (p0) REVERT: B 333 ASP cc_start: 0.8595 (p0) cc_final: 0.8225 (t0) REVERT: N 31 ASN cc_start: 0.8870 (m110) cc_final: 0.8177 (t0) REVERT: N 47 TRP cc_start: 0.7793 (t60) cc_final: 0.7299 (t60) REVERT: N 93 VAL cc_start: 0.8287 (t) cc_final: 0.7989 (p) REVERT: N 123 GLN cc_start: 0.8859 (tp40) cc_final: 0.8342 (tp-100) outliers start: 38 outliers final: 26 residues processed: 257 average time/residue: 0.2089 time to fit residues: 74.5682 Evaluate side-chains 230 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 HIS R 402 GLN R 448 ASN P 32 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9723 Z= 0.264 Angle : 0.606 7.293 13189 Z= 0.315 Chirality : 0.042 0.161 1473 Planarity : 0.004 0.048 1633 Dihedral : 5.468 37.603 1767 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.36 % Allowed : 20.34 % Favored : 74.29 % 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: 0.40 (0.25), residues: 1135 helix: 1.33 (0.25), residues: 450 sheet: 0.41 (0.34), residues: 226 loop : -0.85 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.026 0.002 PHE R 424 TYR 0.021 0.002 TYR R 134 ARG 0.010 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 211 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 404 ARG cc_start: 0.7824 (mtt180) cc_final: 0.7308 (tpt170) REVERT: R 472 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8535 (ttmt) REVERT: R 474 TRP cc_start: 0.6528 (t60) cc_final: 0.6089 (t60) REVERT: R 482 ASP cc_start: 0.5473 (t0) cc_final: 0.5206 (t0) REVERT: A 31 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8209 (tm-30) REVERT: A 229 ASP cc_start: 0.8176 (m-30) cc_final: 0.7754 (p0) REVERT: A 314 GLU cc_start: 0.8232 (pm20) cc_final: 0.8008 (mm-30) REVERT: B 235 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8384 (t80) REVERT: B 245 SER cc_start: 0.7373 (t) cc_final: 0.6891 (t) REVERT: B 273 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 312 ASP cc_start: 0.7291 (p0) cc_final: 0.6741 (p0) REVERT: B 333 ASP cc_start: 0.8655 (p0) cc_final: 0.8292 (t0) REVERT: G 21 MET cc_start: 0.7814 (mmm) cc_final: 0.7285 (mmt) REVERT: N 93 VAL cc_start: 0.8483 (t) cc_final: 0.8232 (p) REVERT: N 123 GLN cc_start: 0.8936 (tp40) cc_final: 0.8484 (tp-100) outliers start: 53 outliers final: 41 residues processed: 251 average time/residue: 0.2060 time to fit residues: 71.4620 Evaluate side-chains 246 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 203 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 362 ILE Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9723 Z= 0.182 Angle : 0.558 7.920 13189 Z= 0.289 Chirality : 0.040 0.156 1473 Planarity : 0.004 0.053 1633 Dihedral : 5.103 39.453 1767 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.25 % Allowed : 21.96 % Favored : 73.79 % 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: 0.50 (0.25), residues: 1135 helix: 1.43 (0.25), residues: 451 sheet: 0.43 (0.35), residues: 222 loop : -0.78 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS R 114 PHE 0.023 0.001 PHE B 235 TYR 0.021 0.001 TYR R 134 ARG 0.013 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 212 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 404 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7267 (tpt170) REVERT: R 471 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8154 (mtpt) REVERT: R 474 TRP cc_start: 0.6516 (t60) cc_final: 0.6049 (t60) REVERT: R 482 ASP cc_start: 0.5664 (t0) cc_final: 0.5445 (t0) REVERT: A 31 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8249 (tm-30) REVERT: A 229 ASP cc_start: 0.8193 (m-30) cc_final: 0.7922 (p0) REVERT: A 314 GLU cc_start: 0.8157 (pm20) cc_final: 0.7946 (mm-30) REVERT: B 188 MET cc_start: 0.7525 (mmm) cc_final: 0.7228 (mmm) REVERT: B 235 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8390 (t80) REVERT: B 245 SER cc_start: 0.7332 (t) cc_final: 0.6854 (t) REVERT: B 273 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8519 (mp) REVERT: B 301 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8190 (mmtt) REVERT: B 312 ASP cc_start: 0.7120 (p0) cc_final: 0.6563 (p0) REVERT: B 333 ASP cc_start: 0.8619 (p0) cc_final: 0.8215 (t0) REVERT: N 68 PHE cc_start: 0.7328 (m-10) cc_final: 0.6825 (m-10) REVERT: N 83 MET cc_start: 0.5646 (mmm) cc_final: 0.5405 (mmm) REVERT: N 93 VAL cc_start: 0.8456 (t) cc_final: 0.8153 (p) REVERT: N 123 GLN cc_start: 0.8935 (tp40) cc_final: 0.8204 (tp-100) outliers start: 42 outliers final: 35 residues processed: 245 average time/residue: 0.2097 time to fit residues: 71.3192 Evaluate side-chains 233 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 413 LEU Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 402 GLN A 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9723 Z= 0.181 Angle : 0.570 7.996 13189 Z= 0.294 Chirality : 0.040 0.154 1473 Planarity : 0.004 0.057 1633 Dihedral : 4.993 40.222 1767 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.35 % Allowed : 22.57 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.25), residues: 1135 helix: 1.50 (0.25), residues: 451 sheet: 0.47 (0.34), residues: 222 loop : -0.73 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.004 0.001 HIS R 114 PHE 0.023 0.001 PHE B 235 TYR 0.019 0.001 TYR R 134 ARG 0.013 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 211 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 321 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7729 (tt) REVERT: R 404 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7240 (tpt170) REVERT: R 411 LEU cc_start: 0.8922 (mt) cc_final: 0.8503 (tt) REVERT: R 471 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8147 (mtpt) REVERT: R 474 TRP cc_start: 0.6477 (t60) cc_final: 0.6028 (t60) REVERT: A 31 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8290 (tm-30) REVERT: A 229 ASP cc_start: 0.8210 (m-30) cc_final: 0.7916 (p0) REVERT: B 188 MET cc_start: 0.7520 (mmm) cc_final: 0.7243 (mmm) REVERT: B 235 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8401 (t80) REVERT: B 245 SER cc_start: 0.7324 (t) cc_final: 0.6845 (t) REVERT: B 273 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8451 (mp) REVERT: B 312 ASP cc_start: 0.7098 (p0) cc_final: 0.6541 (p0) REVERT: B 333 ASP cc_start: 0.8643 (p0) cc_final: 0.8220 (t0) REVERT: G 21 MET cc_start: 0.7478 (mmm) cc_final: 0.6873 (mmt) REVERT: N 68 PHE cc_start: 0.7395 (m-10) cc_final: 0.6948 (m-10) REVERT: N 83 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5413 (mmm) REVERT: N 93 VAL cc_start: 0.8429 (t) cc_final: 0.8163 (p) REVERT: N 123 GLN cc_start: 0.8882 (tp40) cc_final: 0.8164 (tp-100) outliers start: 43 outliers final: 31 residues processed: 242 average time/residue: 0.2047 time to fit residues: 68.4379 Evaluate side-chains 238 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 402 GLN R 420 HIS R 448 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9723 Z= 0.221 Angle : 0.595 8.839 13189 Z= 0.305 Chirality : 0.041 0.168 1473 Planarity : 0.004 0.058 1633 Dihedral : 5.110 40.813 1767 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.55 % Allowed : 22.87 % Favored : 72.57 % 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: 0.61 (0.25), residues: 1135 helix: 1.45 (0.25), residues: 450 sheet: 0.54 (0.34), residues: 227 loop : -0.68 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP R 298 HIS 0.007 0.001 HIS R 225 PHE 0.023 0.001 PHE B 235 TYR 0.019 0.001 TYR R 134 ARG 0.014 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 207 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 LEU cc_start: 0.9187 (mm) cc_final: 0.8960 (mm) REVERT: R 402 GLN cc_start: 0.8596 (mm110) cc_final: 0.8381 (mm-40) REVERT: R 404 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7283 (tpt170) REVERT: R 411 LEU cc_start: 0.8956 (mt) cc_final: 0.8547 (tt) REVERT: R 471 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8161 (mtpt) REVERT: R 474 TRP cc_start: 0.6511 (t60) cc_final: 0.6040 (t60) REVERT: P 20 ARG cc_start: 0.9168 (tmm-80) cc_final: 0.8899 (ttp80) REVERT: A 31 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8265 (tm-30) REVERT: A 229 ASP cc_start: 0.8243 (m-30) cc_final: 0.7966 (p0) REVERT: A 314 GLU cc_start: 0.8315 (pm20) cc_final: 0.8050 (mm-30) REVERT: B 188 MET cc_start: 0.7645 (mmm) cc_final: 0.7352 (mmm) REVERT: B 235 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8398 (t80) REVERT: B 245 SER cc_start: 0.7405 (t) cc_final: 0.6928 (t) REVERT: B 273 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8392 (mp) REVERT: B 312 ASP cc_start: 0.7209 (p0) cc_final: 0.6604 (p0) REVERT: B 333 ASP cc_start: 0.8687 (p0) cc_final: 0.8259 (t0) REVERT: G 21 MET cc_start: 0.7428 (mmm) cc_final: 0.6747 (mmt) REVERT: G 58 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8113 (mm-30) REVERT: N 65 LYS cc_start: 0.8063 (tppt) cc_final: 0.7725 (mmmt) REVERT: N 68 PHE cc_start: 0.7418 (m-10) cc_final: 0.6843 (m-10) REVERT: N 93 VAL cc_start: 0.8374 (t) cc_final: 0.8124 (p) REVERT: N 123 GLN cc_start: 0.8941 (tp40) cc_final: 0.8190 (tp-100) outliers start: 45 outliers final: 39 residues processed: 237 average time/residue: 0.1952 time to fit residues: 64.8199 Evaluate side-chains 245 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 440 GLN Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 30.0000 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 70 optimal weight: 0.0770 chunk 94 optimal weight: 0.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 448 ASN B 32 GLN N 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9723 Z= 0.196 Angle : 0.595 13.447 13189 Z= 0.305 Chirality : 0.041 0.162 1473 Planarity : 0.004 0.059 1633 Dihedral : 5.054 42.005 1767 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.25 % Allowed : 23.38 % Favored : 72.37 % 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: 0.58 (0.25), residues: 1135 helix: 1.44 (0.25), residues: 447 sheet: 0.49 (0.33), residues: 231 loop : -0.68 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP R 298 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.001 PHE B 235 TYR 0.021 0.001 TYR R 134 ARG 0.014 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.6652 (ptt) cc_final: 0.6237 (ptt) REVERT: R 40 LEU cc_start: 0.9174 (mm) cc_final: 0.8939 (mm) REVERT: R 404 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7237 (tpt170) REVERT: R 411 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8561 (tt) REVERT: R 427 THR cc_start: 0.8560 (m) cc_final: 0.8191 (p) REVERT: R 471 LYS cc_start: 0.8401 (mtpt) cc_final: 0.8178 (mtpt) REVERT: R 474 TRP cc_start: 0.6464 (t60) cc_final: 0.5996 (t60) REVERT: P 20 ARG cc_start: 0.9246 (tmm-80) cc_final: 0.8985 (ttp80) REVERT: A 31 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8307 (tm-30) REVERT: A 209 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 314 GLU cc_start: 0.8289 (pm20) cc_final: 0.7956 (mm-30) REVERT: A 327 GLU cc_start: 0.7683 (tp30) cc_final: 0.7083 (tm-30) REVERT: B 188 MET cc_start: 0.7621 (mmm) cc_final: 0.7313 (mmm) REVERT: B 235 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8400 (t80) REVERT: B 245 SER cc_start: 0.7440 (t) cc_final: 0.6975 (t) REVERT: B 273 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8355 (mp) REVERT: B 312 ASP cc_start: 0.7175 (p0) cc_final: 0.6626 (p0) REVERT: B 333 ASP cc_start: 0.8687 (p0) cc_final: 0.8259 (t0) REVERT: G 21 MET cc_start: 0.7352 (mmm) cc_final: 0.6953 (mmt) REVERT: N 65 LYS cc_start: 0.8047 (tppt) cc_final: 0.7717 (mmmt) REVERT: N 68 PHE cc_start: 0.7416 (m-10) cc_final: 0.7079 (m-10) REVERT: N 93 VAL cc_start: 0.8387 (t) cc_final: 0.8141 (p) REVERT: N 123 GLN cc_start: 0.8932 (tp40) cc_final: 0.8155 (tp-100) outliers start: 42 outliers final: 37 residues processed: 241 average time/residue: 0.2033 time to fit residues: 68.7613 Evaluate side-chains 241 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 440 GLN Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.0670 chunk 88 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 402 GLN B 32 GLN ** N 82 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 = 0.4020 r_free = 0.4020 target = 0.149596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.109051 restraints weight = 16043.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113283 restraints weight = 7439.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.116083 restraints weight = 4759.638| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.6894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 9723 Z= 0.276 Angle : 0.904 59.159 13189 Z= 0.518 Chirality : 0.044 0.497 1473 Planarity : 0.004 0.058 1633 Dihedral : 5.094 42.009 1767 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.35 % Allowed : 23.48 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1135 helix: 1.45 (0.25), residues: 447 sheet: 0.46 (0.33), residues: 230 loop : -0.72 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP R 298 HIS 0.012 0.001 HIS A 220 PHE 0.023 0.001 PHE B 235 TYR 0.021 0.001 TYR R 134 ARG 0.010 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2344.98 seconds wall clock time: 42 minutes 40.62 seconds (2560.62 seconds total)