Starting phenix.real_space_refine on Fri Sep 11 18:07:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ot0_20190/09_2026/6ot0_20190.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ot0_20190/09_2026/6ot0_20190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ot0_20190/09_2026/6ot0_20190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ot0_20190/09_2026/6ot0_20190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ot0_20190/09_2026/6ot0_20190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ot0_20190/09_2026/6ot0_20190.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ot0_20190/09_2026/6ot0_20190.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ot0_20190/09_2026/6ot0_20190.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.067 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 71 5.16 5 C 6723 2.51 5 N 1792 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10572 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2887 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 13, 'TRANS': 350} Chain: "A" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2832 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 349} Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 995 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CO1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.84, per 1000 atoms: 0.27 Number of scatterers: 10572 At special positions: 0 Unit cell: (143.38, 131.61, 120.91, 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 71 16.00 O 1986 8.00 N 1792 7.00 C 6723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 213 " distance=2.03 Simple disulfide: pdb=" SG CYS R 490 " - pdb=" SG CYS R 507 " distance=2.02 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 320.6 milliseconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 36.7% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 223 through 255 removed outlier: 3.704A pdb=" N HIS R 227 " --> pdb=" O THR R 223 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR R 251 " --> pdb=" O PHE R 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE R 252 " --> pdb=" O THR R 248 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA R 254 " --> pdb=" O ALA R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 273 removed outlier: 3.594A pdb=" N LEU R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 281 removed outlier: 3.705A pdb=" N GLY R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 309 removed outlier: 3.919A pdb=" N SER R 308 " --> pdb=" O GLU R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 345 removed outlier: 3.682A pdb=" N PHE R 318 " --> pdb=" O CYS R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 376 removed outlier: 3.585A pdb=" N PHE R 360 " --> pdb=" O LYS R 356 " (cutoff:3.500A) Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 397 through 426 removed outlier: 4.676A pdb=" N GLY R 402 " --> pdb=" O ARG R 398 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE R 403 " --> pdb=" O TYR R 399 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL R 404 " --> pdb=" O ARG R 400 " (cutoff:3.500A) Proline residue: R 407 - end of helix Processing helix chain 'R' and resid 438 through 494 removed outlier: 3.682A pdb=" N LYS R 444 " --> pdb=" O LYS R 440 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL R 463 " --> pdb=" O ALA R 459 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU R 464 " --> pdb=" O PHE R 460 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR R 466 " --> pdb=" O PHE R 462 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE R 475 " --> pdb=" O PHE R 471 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN R 476 " --> pdb=" O TYR R 472 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA R 478 " --> pdb=" O PHE R 474 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU R 479 " --> pdb=" O PHE R 475 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA R 492 " --> pdb=" O VAL R 488 " (cutoff:3.500A) Processing helix chain 'R' and resid 517 through 532 removed outlier: 4.085A pdb=" N ASN R 521 " --> pdb=" O VAL R 517 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET R 532 " --> pdb=" O THR R 528 " (cutoff:3.500A) Processing helix chain 'R' and resid 540 through 551 removed outlier: 4.057A pdb=" N ILE R 544 " --> pdb=" O ALA R 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 25 removed outlier: 3.549A pdb=" N ALA A 7 " --> pdb=" O CYS A 3 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 65 through 91 Processing helix chain 'A' and resid 100 through 112 removed outlier: 3.904A pdb=" N LEU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 4.096A pdb=" N ARG A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 151 through 158 removed outlier: 4.662A pdb=" N TYR A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 164 removed outlier: 3.714A pdb=" N ILE A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 241 through 255 removed outlier: 4.268A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.807A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.593A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 352 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.048A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.650A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing sheet with id=AA1, first strand: chain 'R' and resid 197 through 199 Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 191 removed outlier: 6.893A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.369A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.413A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.611A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.403A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.163A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 234 removed outlier: 6.484A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 284 through 288 removed outlier: 3.878A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 7 through 9 Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.757A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 7 through 10 Processing sheet with id=AB4, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.347A pdb=" N GLY H 13 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER H 53 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER H 62 " --> pdb=" O SER H 53 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3036 1.34 - 1.45: 1735 1.45 - 1.57: 5923 1.57 - 1.69: 11 1.69 - 1.81: 101 Bond restraints: 10806 Sorted by residual: bond pdb=" C TYR R 262 " pdb=" O TYR R 262 " ideal model delta sigma weight residual 1.238 1.550 -0.312 1.28e-02 6.10e+03 5.95e+02 bond pdb=" C14 CO1 R 601 " pdb=" C7 CO1 R 601 " ideal model delta sigma weight residual 1.519 1.629 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C11 CO1 R 601 " pdb=" C5 CO1 R 601 " ideal model delta sigma weight residual 1.530 1.605 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" CA VAL R 195 " pdb=" CB VAL R 195 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.35e+01 bond pdb=" C12 CO1 R 601 " pdb=" C5 CO1 R 601 " ideal model delta sigma weight residual 1.532 1.605 -0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 10801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 14263 2.80 - 5.60: 369 5.60 - 8.41: 18 8.41 - 11.21: 2 11.21 - 14.01: 1 Bond angle restraints: 14653 Sorted by residual: angle pdb=" C TYR R 262 " pdb=" N PRO R 263 " pdb=" CA PRO R 263 " ideal model delta sigma weight residual 119.84 128.24 -8.40 1.25e+00 6.40e-01 4.51e+01 angle pdb=" C GLU R 305 " pdb=" N PRO R 306 " pdb=" CA PRO R 306 " ideal model delta sigma weight residual 119.19 125.75 -6.56 1.06e+00 8.90e-01 3.83e+01 angle pdb=" CA VAL R 195 " pdb=" C VAL R 195 " pdb=" N PRO R 196 " ideal model delta sigma weight residual 120.83 117.75 3.08 6.10e-01 2.69e+00 2.54e+01 angle pdb=" N GLY R 347 " pdb=" CA GLY R 347 " pdb=" C GLY R 347 " ideal model delta sigma weight residual 113.18 102.43 10.75 2.37e+00 1.78e-01 2.06e+01 angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 112.87 118.27 -5.40 1.20e+00 6.94e-01 2.03e+01 ... (remaining 14648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 5577 15.50 - 31.00: 589 31.00 - 46.49: 164 46.49 - 61.99: 29 61.99 - 77.49: 14 Dihedral angle restraints: 6373 sinusoidal: 2473 harmonic: 3900 Sorted by residual: dihedral pdb=" CA TYR R 262 " pdb=" C TYR R 262 " pdb=" N PRO R 263 " pdb=" CA PRO R 263 " ideal model delta harmonic sigma weight residual 180.00 -110.37 -69.63 0 5.00e+00 4.00e-02 1.94e+02 dihedral pdb=" CA GLY R 347 " pdb=" C GLY R 347 " pdb=" N THR R 348 " pdb=" CA THR R 348 " ideal model delta harmonic sigma weight residual -180.00 -145.34 -34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA LEU R 346 " pdb=" C LEU R 346 " pdb=" N GLY R 347 " pdb=" CA GLY R 347 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 6370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1322 0.085 - 0.171: 275 0.171 - 0.256: 30 0.256 - 0.341: 5 0.341 - 0.427: 3 Chirality restraints: 1635 Sorted by residual: chirality pdb=" C5 CO1 R 601 " pdb=" C10 CO1 R 601 " pdb=" C11 CO1 R 601 " pdb=" C2 CO1 R 601 " both_signs ideal model delta sigma weight residual False -2.93 -3.36 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" C7 CO1 R 601 " pdb=" C14 CO1 R 601 " pdb=" C15 CO1 R 601 " pdb=" C3 CO1 R 601 " both_signs ideal model delta sigma weight residual False 2.86 3.27 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C2 CO1 R 601 " pdb=" C1 CO1 R 601 " pdb=" C5 CO1 R 601 " pdb=" C6 CO1 R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 1632 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 262 " -0.055 2.00e-02 2.50e+03 1.01e-01 1.02e+02 pdb=" C TYR R 262 " 0.175 2.00e-02 2.50e+03 pdb=" O TYR R 262 " -0.056 2.00e-02 2.50e+03 pdb=" N PRO R 263 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 262 " 0.088 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO R 263 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO R 263 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO R 263 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS R 433 " -0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO R 434 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 434 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 434 " -0.038 5.00e-02 4.00e+02 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3100 2.84 - 3.35: 9933 3.35 - 3.87: 17327 3.87 - 4.38: 18362 4.38 - 4.90: 31332 Nonbonded interactions: 80054 Sorted by model distance: nonbonded pdb=" OD2 ASP A 231 " pdb=" NZ LYS A 277 " model vdw 2.324 3.120 nonbonded pdb=" ND2 ASN A 311 " pdb=" O LYS A 314 " model vdw 2.365 3.120 nonbonded pdb=" O VAL R 333 " pdb=" OG1 THR R 336 " model vdw 2.389 3.040 nonbonded pdb=" O THR R 245 " pdb=" OG1 THR R 248 " model vdw 2.405 3.040 nonbonded pdb=" NH2 ARG R 451 " pdb=" O THR R 534 " model vdw 2.421 3.120 ... (remaining 80049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.450 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.009 0.312 10809 Z= 0.622 Angle : 1.131 14.010 14659 Z= 0.726 Chirality : 0.070 0.427 1635 Planarity : 0.006 0.132 1857 Dihedral : 14.498 77.489 3858 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.79 % Allowed : 7.67 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.20), residues: 1333 helix: -1.55 (0.20), residues: 439 sheet: -1.21 (0.32), residues: 254 loop : -2.89 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 142 TYR 0.015 0.002 TYR A 302 PHE 0.016 0.002 PHE B 151 TRP 0.015 0.002 TRP R 206 HIS 0.007 0.002 HIS R 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00896 / 0.62 (10806) covalent geometry : angle 1.13045 / 0.73 (14653) SS BOND : bond 0.00441 / 0.21 ( 3) SS BOND : angle 1.36951 / 0.62 ( 6) hydrogen bonds : bond 0.15548 / 9.70 ( 442) hydrogen bonds : angle 6.93709 / 5.09 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 432 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8475 (mt0) cc_final: 0.8171 (mp10) REVERT: R 255 ASP cc_start: 0.8055 (t0) cc_final: 0.7718 (t0) REVERT: R 257 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7758 (mtt-85) REVERT: R 269 TYR cc_start: 0.9103 (m-80) cc_final: 0.8860 (m-10) REVERT: R 271 ASN cc_start: 0.8814 (p0) cc_final: 0.8606 (p0) REVERT: R 281 TRP cc_start: 0.8442 (m-10) cc_final: 0.7854 (m-10) REVERT: R 325 LEU cc_start: 0.8967 (pp) cc_final: 0.8679 (pp) REVERT: R 326 MET cc_start: 0.9046 (tpp) cc_final: 0.8763 (mmt) REVERT: R 343 PHE cc_start: 0.9212 (m-10) cc_final: 0.8375 (m-80) REVERT: R 344 LYS cc_start: 0.8491 (ttmt) cc_final: 0.7721 (mttp) REVERT: R 351 GLN cc_start: 0.8650 (tt0) cc_final: 0.8051 (tp-100) REVERT: R 400 ARG cc_start: 0.9277 (ttp80) cc_final: 0.9028 (ttp80) REVERT: R 485 ARG cc_start: 0.6033 (ttt180) cc_final: 0.4728 (tpp80) REVERT: R 491 GLN cc_start: 0.8927 (tt0) cc_final: 0.8632 (mm-40) REVERT: R 510 LYS cc_start: 0.8040 (tptm) cc_final: 0.6984 (ttpp) REVERT: A 18 MET cc_start: 0.7521 (mmm) cc_final: 0.6865 (tpp) REVERT: A 22 ASN cc_start: 0.8816 (m-40) cc_final: 0.8432 (m110) REVERT: A 36 LEU cc_start: 0.9106 (mp) cc_final: 0.8892 (mp) REVERT: A 47 ASN cc_start: 0.9253 (m-40) cc_final: 0.8965 (p0) REVERT: A 74 TYR cc_start: 0.8196 (m-10) cc_final: 0.7929 (m-80) REVERT: A 79 GLN cc_start: 0.9203 (tp-100) cc_final: 0.8683 (mt0) REVERT: A 147 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8892 (tm-30) REVERT: A 188 HIS cc_start: 0.8250 (p-80) cc_final: 0.7890 (p-80) REVERT: A 195 HIS cc_start: 0.8805 (m-70) cc_final: 0.8399 (m90) REVERT: A 211 TRP cc_start: 0.8902 (p-90) cc_final: 0.8550 (p-90) REVERT: A 243 MET cc_start: 0.8824 (ptt) cc_final: 0.8362 (ptt) REVERT: A 244 HIS cc_start: 0.9241 (m170) cc_final: 0.8931 (m170) REVERT: A 269 ASN cc_start: 0.7581 (p0) cc_final: 0.7262 (p0) REVERT: A 320 TYR cc_start: 0.8823 (m-10) cc_final: 0.8619 (m-10) REVERT: B 3 GLU cc_start: 0.8883 (pt0) cc_final: 0.8593 (tp30) REVERT: B 23 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7545 (ptpp) REVERT: B 80 ILE cc_start: 0.8524 (tt) cc_final: 0.8186 (tt) REVERT: B 82 TRP cc_start: 0.8946 (m100) cc_final: 0.8469 (m100) REVERT: B 127 LYS cc_start: 0.9258 (mmmm) cc_final: 0.8638 (mttt) REVERT: B 171 ILE cc_start: 0.9401 (pt) cc_final: 0.9142 (pt) REVERT: B 183 HIS cc_start: 0.7937 (m-70) cc_final: 0.7430 (m170) REVERT: B 211 TRP cc_start: 0.8798 (m100) cc_final: 0.8299 (m100) REVERT: B 212 ASP cc_start: 0.7020 (p0) cc_final: 0.5568 (p0) REVERT: B 215 GLU cc_start: 0.9183 (tp30) cc_final: 0.8809 (tp30) REVERT: B 289 TYR cc_start: 0.8824 (m-80) cc_final: 0.7956 (m-80) REVERT: B 295 ASN cc_start: 0.8392 (p0) cc_final: 0.8148 (p0) REVERT: B 301 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7080 (mmtt) REVERT: G 14 LYS cc_start: 0.9045 (mttm) cc_final: 0.8792 (mttm) REVERT: G 17 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8858 (mt-10) REVERT: L 37 TYR cc_start: 0.8607 (m-80) cc_final: 0.7363 (m-80) REVERT: L 59 VAL cc_start: 0.9373 (t) cc_final: 0.9119 (p) REVERT: L 97 ILE cc_start: 0.9480 (mm) cc_final: 0.8907 (mp) REVERT: L 104 LYS cc_start: 0.8983 (pttp) cc_final: 0.8758 (ptpt) REVERT: H 39 TRP cc_start: 0.9106 (m100) cc_final: 0.8891 (m100) REVERT: H 54 ILE cc_start: 0.8461 (tp) cc_final: 0.8017 (tt) REVERT: H 68 LYS cc_start: 0.9262 (pttt) cc_final: 0.9026 (ptpt) REVERT: H 103 PRO cc_start: 0.9106 (Cg_endo) cc_final: 0.8855 (Cg_exo) REVERT: H 128 THR cc_start: 0.9010 (p) cc_final: 0.8789 (t) outliers start: 9 outliers final: 3 residues processed: 436 average time/residue: 0.1067 time to fit residues: 64.4386 Evaluate side-chains 309 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain A residue 221 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 258 ASN R 309 ASN R 446 ASN A 68 GLN A 256 ASN A 294 ASN A 333 GLN B 16 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 340 ASN G 44 HIS L 80 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.106068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.087135 restraints weight = 35452.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.089715 restraints weight = 19835.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.091456 restraints weight = 13217.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092649 restraints weight = 9903.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093474 restraints weight = 8055.099| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10809 Z= 0.168 Angle : 0.682 10.839 14659 Z= 0.357 Chirality : 0.043 0.180 1635 Planarity : 0.005 0.104 1857 Dihedral : 5.999 50.191 1478 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 3.88 % Allowed : 16.39 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.21), residues: 1333 helix: -0.70 (0.22), residues: 455 sheet: -0.91 (0.31), residues: 269 loop : -2.70 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 261 TYR 0.018 0.002 TYR H 120 PHE 0.022 0.002 PHE B 235 TRP 0.024 0.002 TRP R 339 HIS 0.006 0.002 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (10806) covalent geometry : angle 0.68124 / 0.36 (14653) SS BOND : bond 0.00601 / 0.29 ( 3) SS BOND : angle 1.76357 / 0.91 ( 6) hydrogen bonds : bond 0.04416 / 2.95 ( 442) hydrogen bonds : angle 5.13183 / 3.76 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8422 (mt0) cc_final: 0.7977 (mp10) REVERT: R 228 GLN cc_start: 0.9221 (mt0) cc_final: 0.8915 (tp40) REVERT: R 257 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7667 (mmt90) REVERT: R 301 MET cc_start: 0.7419 (pmm) cc_final: 0.6671 (pmm) REVERT: R 340 HIS cc_start: 0.7183 (p-80) cc_final: 0.6686 (p-80) REVERT: R 351 GLN cc_start: 0.8424 (tt0) cc_final: 0.7720 (tp-100) REVERT: R 391 PHE cc_start: 0.5710 (OUTLIER) cc_final: 0.5490 (t80) REVERT: R 400 ARG cc_start: 0.8821 (ttp80) cc_final: 0.8444 (ttp80) REVERT: R 485 ARG cc_start: 0.6172 (ttt180) cc_final: 0.4794 (tpp80) REVERT: A 18 MET cc_start: 0.7687 (mmm) cc_final: 0.7245 (mmm) REVERT: A 79 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8754 (mt0) REVERT: A 106 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8416 (tp40) REVERT: A 147 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8916 (tm-30) REVERT: A 175 LEU cc_start: 0.8667 (mm) cc_final: 0.8369 (pp) REVERT: A 243 MET cc_start: 0.8391 (ptt) cc_final: 0.7920 (ptt) REVERT: B 51 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8611 (tp) REVERT: B 61 MET cc_start: 0.7845 (ppp) cc_final: 0.7485 (ppp) REVERT: B 82 TRP cc_start: 0.8898 (m100) cc_final: 0.8454 (m100) REVERT: B 127 LYS cc_start: 0.9097 (mmmm) cc_final: 0.8528 (mttt) REVERT: B 175 GLN cc_start: 0.8833 (tp40) cc_final: 0.8256 (tm-30) REVERT: B 237 ASN cc_start: 0.9325 (p0) cc_final: 0.9121 (p0) REVERT: B 289 TYR cc_start: 0.8867 (m-80) cc_final: 0.8249 (m-80) REVERT: B 295 ASN cc_start: 0.8391 (p0) cc_final: 0.8044 (p0) REVERT: B 301 LYS cc_start: 0.7542 (mtmt) cc_final: 0.6654 (mmtt) REVERT: B 325 MET cc_start: 0.7166 (mtm) cc_final: 0.6913 (ttp) REVERT: B 333 ASP cc_start: 0.8402 (p0) cc_final: 0.8109 (p0) REVERT: G 17 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8873 (mt-10) REVERT: G 21 MET cc_start: 0.7911 (mmt) cc_final: 0.7668 (mmt) REVERT: L 59 VAL cc_start: 0.9417 (t) cc_final: 0.9165 (p) REVERT: L 97 ILE cc_start: 0.9394 (mm) cc_final: 0.8962 (mm) REVERT: H 108 MET cc_start: 0.8814 (mtp) cc_final: 0.8326 (mtp) REVERT: H 118 MET cc_start: 0.8318 (mpp) cc_final: 0.7883 (mpp) REVERT: H 120 TYR cc_start: 0.8044 (m-10) cc_final: 0.7843 (m-80) REVERT: H 128 THR cc_start: 0.8697 (p) cc_final: 0.8481 (t) outliers start: 44 outliers final: 30 residues processed: 323 average time/residue: 0.0915 time to fit residues: 43.2605 Evaluate side-chains 301 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 466 THR Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 528 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 0.0020 chunk 66 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 155 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.106894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.088270 restraints weight = 35572.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090836 restraints weight = 19852.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092593 restraints weight = 13220.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.093783 restraints weight = 9878.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094535 restraints weight = 8026.457| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10809 Z= 0.125 Angle : 0.653 12.733 14659 Z= 0.331 Chirality : 0.042 0.201 1635 Planarity : 0.005 0.101 1857 Dihedral : 5.656 51.311 1477 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.23 % Allowed : 18.94 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.22), residues: 1333 helix: -0.23 (0.23), residues: 448 sheet: -0.64 (0.32), residues: 266 loop : -2.53 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 290 TYR 0.018 0.001 TYR A 69 PHE 0.021 0.001 PHE H 32 TRP 0.026 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10806) covalent geometry : angle 0.65123 / 0.33 (14653) SS BOND : bond 0.00351 / 0.17 ( 3) SS BOND : angle 2.48267 / 1.25 ( 6) hydrogen bonds : bond 0.03929 / 2.65 ( 442) hydrogen bonds : angle 4.86220 / 3.57 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8097 (m) cc_final: 0.7794 (p) REVERT: R 218 GLN cc_start: 0.8370 (mt0) cc_final: 0.7891 (mp10) REVERT: R 228 GLN cc_start: 0.9246 (mt0) cc_final: 0.9026 (tp40) REVERT: R 257 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7695 (mmt90) REVERT: R 271 ASN cc_start: 0.8432 (p0) cc_final: 0.8152 (p0) REVERT: R 301 MET cc_start: 0.7345 (pmm) cc_final: 0.6407 (pmm) REVERT: R 351 GLN cc_start: 0.8318 (tt0) cc_final: 0.7679 (tp-100) REVERT: R 400 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8385 (ttp80) REVERT: R 449 MET cc_start: 0.9234 (ttt) cc_final: 0.8716 (tpp) REVERT: R 485 ARG cc_start: 0.6307 (ttt180) cc_final: 0.4926 (tpp80) REVERT: A 74 TYR cc_start: 0.8258 (m-10) cc_final: 0.7969 (m-80) REVERT: A 79 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8730 (mt0) REVERT: A 147 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8919 (tm-30) REVERT: A 164 GLN cc_start: 0.8963 (pt0) cc_final: 0.8675 (tm-30) REVERT: A 175 LEU cc_start: 0.8627 (mm) cc_final: 0.8352 (pp) REVERT: A 198 MET cc_start: 0.8239 (tpt) cc_final: 0.7892 (tpt) REVERT: B 3 GLU cc_start: 0.8786 (tp30) cc_final: 0.8522 (pt0) REVERT: B 59 TYR cc_start: 0.8162 (m-80) cc_final: 0.7868 (m-80) REVERT: B 61 MET cc_start: 0.7829 (ppp) cc_final: 0.7115 (ppp) REVERT: B 95 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.8002 (pp) REVERT: B 127 LYS cc_start: 0.9096 (mmmm) cc_final: 0.8626 (mttt) REVERT: B 237 ASN cc_start: 0.9272 (p0) cc_final: 0.9046 (p0) REVERT: B 289 TYR cc_start: 0.8790 (m-80) cc_final: 0.8113 (m-80) REVERT: B 301 LYS cc_start: 0.7528 (mtmt) cc_final: 0.6702 (mmtt) REVERT: B 325 MET cc_start: 0.7061 (mtm) cc_final: 0.6840 (ttp) REVERT: B 333 ASP cc_start: 0.8493 (p0) cc_final: 0.8147 (p0) REVERT: G 17 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8910 (mt-10) REVERT: G 21 MET cc_start: 0.7791 (mmt) cc_final: 0.7524 (mmm) REVERT: G 36 ASP cc_start: 0.8712 (t0) cc_final: 0.8411 (m-30) REVERT: L 59 VAL cc_start: 0.9360 (t) cc_final: 0.9124 (p) REVERT: L 97 ILE cc_start: 0.9315 (mm) cc_final: 0.9030 (mp) REVERT: H 50 TRP cc_start: 0.7904 (t60) cc_final: 0.7693 (t60) REVERT: H 120 TYR cc_start: 0.8059 (m-10) cc_final: 0.7769 (m-80) outliers start: 48 outliers final: 33 residues processed: 306 average time/residue: 0.0865 time to fit residues: 39.1003 Evaluate side-chains 294 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 60 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 340 HIS R 361 HIS ** R 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN A 79 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.101611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083163 restraints weight = 36497.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.085553 restraints weight = 20507.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.087182 restraints weight = 13772.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.088284 restraints weight = 10363.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089054 restraints weight = 8480.491| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10809 Z= 0.249 Angle : 0.733 13.420 14659 Z= 0.380 Chirality : 0.045 0.175 1635 Planarity : 0.005 0.107 1857 Dihedral : 6.198 69.369 1477 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.10 % Rotamer: Outliers : 6.17 % Allowed : 20.62 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.22), residues: 1333 helix: -0.23 (0.23), residues: 459 sheet: -0.63 (0.31), residues: 276 loop : -2.60 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 400 TYR 0.020 0.002 TYR R 337 PHE 0.020 0.002 PHE H 32 TRP 0.035 0.002 TRP R 339 HIS 0.007 0.002 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (10806) covalent geometry : angle 0.73166 / 0.38 (14653) SS BOND : bond 0.01223 / 0.59 ( 3) SS BOND : angle 2.34490 / 1.22 ( 6) hydrogen bonds : bond 0.04315 / 2.89 ( 442) hydrogen bonds : angle 5.20993 / 3.81 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 254 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8439 (mt0) cc_final: 0.7870 (mp10) REVERT: R 228 GLN cc_start: 0.9353 (mt0) cc_final: 0.9060 (tp40) REVERT: R 257 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7727 (mmt90) REVERT: R 301 MET cc_start: 0.7552 (pmm) cc_final: 0.6636 (pmm) REVERT: R 400 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8511 (ttp80) REVERT: R 433 HIS cc_start: 0.6413 (OUTLIER) cc_final: 0.5878 (p-80) REVERT: R 485 ARG cc_start: 0.6441 (ttt180) cc_final: 0.5136 (tpp80) REVERT: A 33 GLU cc_start: 0.7895 (tp30) cc_final: 0.7616 (tp30) REVERT: A 283 LEU cc_start: 0.8402 (tt) cc_final: 0.8084 (tp) REVERT: B 61 MET cc_start: 0.7981 (ppp) cc_final: 0.7463 (ppp) REVERT: B 110 ASN cc_start: 0.8870 (p0) cc_final: 0.8378 (p0) REVERT: B 289 TYR cc_start: 0.8954 (m-80) cc_final: 0.8522 (m-80) REVERT: B 295 ASN cc_start: 0.8650 (p0) cc_final: 0.8215 (p0) REVERT: B 301 LYS cc_start: 0.7675 (mtmt) cc_final: 0.6861 (mmtt) REVERT: B 325 MET cc_start: 0.7563 (mtm) cc_final: 0.7356 (ttp) REVERT: B 333 ASP cc_start: 0.8661 (p0) cc_final: 0.8349 (p0) REVERT: G 17 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8825 (mt-10) REVERT: G 29 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8494 (ttmm) REVERT: G 32 LYS cc_start: 0.9531 (mmtt) cc_final: 0.9314 (mmtp) REVERT: L 59 VAL cc_start: 0.9446 (t) cc_final: 0.9158 (p) REVERT: L 97 ILE cc_start: 0.9457 (mm) cc_final: 0.8998 (mm) REVERT: H 30 PHE cc_start: 0.7442 (p90) cc_final: 0.7178 (p90) REVERT: H 118 MET cc_start: 0.8415 (mpp) cc_final: 0.8103 (mpp) REVERT: H 120 TYR cc_start: 0.8253 (m-10) cc_final: 0.7848 (m-10) outliers start: 70 outliers final: 55 residues processed: 294 average time/residue: 0.0872 time to fit residues: 38.1021 Evaluate side-chains 292 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 466 THR Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 0.0010 chunk 22 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 271 ASN R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN B 142 HIS B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.106114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.087374 restraints weight = 35026.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.089877 restraints weight = 19703.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091574 restraints weight = 13227.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.092720 restraints weight = 9940.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093530 restraints weight = 8113.423| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10809 Z= 0.117 Angle : 0.665 11.871 14659 Z= 0.334 Chirality : 0.042 0.189 1635 Planarity : 0.005 0.100 1857 Dihedral : 5.753 78.904 1477 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.29 % Allowed : 22.82 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.22), residues: 1333 helix: -0.04 (0.23), residues: 457 sheet: -0.47 (0.32), residues: 271 loop : -2.40 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 400 TYR 0.019 0.001 TYR A 69 PHE 0.023 0.001 PHE H 71 TRP 0.042 0.002 TRP R 339 HIS 0.007 0.001 HIS R 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10806) covalent geometry : angle 0.66441 / 0.33 (14653) SS BOND : bond 0.00434 / 0.22 ( 3) SS BOND : angle 1.56556 / 0.80 ( 6) hydrogen bonds : bond 0.03681 / 2.51 ( 442) hydrogen bonds : angle 4.81574 / 3.56 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8210 (m) cc_final: 0.7934 (p) REVERT: R 218 GLN cc_start: 0.8401 (mt0) cc_final: 0.7845 (mp10) REVERT: R 228 GLN cc_start: 0.9343 (mt0) cc_final: 0.9041 (tp40) REVERT: R 252 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8066 (t80) REVERT: R 257 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7706 (mmt90) REVERT: R 301 MET cc_start: 0.7467 (pmm) cc_final: 0.6541 (pmm) REVERT: R 339 TRP cc_start: 0.9114 (OUTLIER) cc_final: 0.8875 (m-90) REVERT: R 351 GLN cc_start: 0.7876 (tt0) cc_final: 0.7409 (tp-100) REVERT: R 433 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.5707 (p-80) REVERT: R 447 GLU cc_start: 0.7954 (tp30) cc_final: 0.7387 (tm-30) REVERT: R 485 ARG cc_start: 0.6334 (ttt180) cc_final: 0.5055 (tpp80) REVERT: A 18 MET cc_start: 0.7219 (mmm) cc_final: 0.6638 (tpp) REVERT: A 38 LEU cc_start: 0.9137 (tt) cc_final: 0.8597 (mt) REVERT: A 74 TYR cc_start: 0.8224 (m-10) cc_final: 0.7924 (m-80) REVERT: A 132 LYS cc_start: 0.9353 (mttt) cc_final: 0.8846 (mttm) REVERT: A 198 MET cc_start: 0.8294 (tpt) cc_final: 0.8016 (tpt) REVERT: A 283 LEU cc_start: 0.8457 (tt) cc_final: 0.8219 (tp) REVERT: B 3 GLU cc_start: 0.8752 (tp30) cc_final: 0.8372 (pt0) REVERT: B 46 ARG cc_start: 0.7685 (tpp80) cc_final: 0.7472 (tpp80) REVERT: B 61 MET cc_start: 0.7913 (ppp) cc_final: 0.7566 (ppp) REVERT: B 127 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8550 (mttt) REVERT: B 209 LYS cc_start: 0.8088 (mmtp) cc_final: 0.7750 (mttt) REVERT: B 289 TYR cc_start: 0.8840 (m-80) cc_final: 0.8240 (m-80) REVERT: B 301 LYS cc_start: 0.7621 (mtmt) cc_final: 0.6951 (mmtt) REVERT: B 333 ASP cc_start: 0.8603 (p0) cc_final: 0.8260 (p0) REVERT: G 14 LYS cc_start: 0.9317 (mtpp) cc_final: 0.9053 (mtmm) REVERT: L 59 VAL cc_start: 0.9307 (t) cc_final: 0.9026 (p) REVERT: L 97 ILE cc_start: 0.9308 (mm) cc_final: 0.8997 (mp) REVERT: H 32 PHE cc_start: 0.8626 (t80) cc_final: 0.8346 (t80) REVERT: H 120 TYR cc_start: 0.8276 (m-10) cc_final: 0.7906 (m-10) outliers start: 60 outliers final: 46 residues processed: 305 average time/residue: 0.0872 time to fit residues: 39.4451 Evaluate side-chains 298 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 249 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 271 ASN Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 111 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 340 HIS ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 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 = 0.3759 r_free = 0.3759 target = 0.106083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.087205 restraints weight = 35414.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.089717 restraints weight = 19978.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.091433 restraints weight = 13406.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.092594 restraints weight = 10056.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.093411 restraints weight = 8199.867| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10809 Z= 0.133 Angle : 0.678 11.345 14659 Z= 0.345 Chirality : 0.043 0.226 1635 Planarity : 0.005 0.100 1857 Dihedral : 5.738 82.850 1477 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.46 % Allowed : 24.23 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.22), residues: 1333 helix: 0.11 (0.24), residues: 454 sheet: -0.53 (0.32), residues: 257 loop : -2.36 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.019 0.001 TYR A 69 PHE 0.016 0.001 PHE H 71 TRP 0.042 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10806) covalent geometry : angle 0.67704 / 0.34 (14653) SS BOND : bond 0.00348 / 0.17 ( 3) SS BOND : angle 1.42764 / 0.74 ( 6) hydrogen bonds : bond 0.03671 / 2.52 ( 442) hydrogen bonds : angle 4.81419 / 3.55 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 268 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8240 (m) cc_final: 0.7962 (p) REVERT: R 218 GLN cc_start: 0.8458 (mt0) cc_final: 0.7927 (mp10) REVERT: R 228 GLN cc_start: 0.9381 (mt0) cc_final: 0.9044 (tp40) REVERT: R 257 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7718 (mmt180) REVERT: R 301 MET cc_start: 0.7508 (pmm) cc_final: 0.6598 (pmm) REVERT: R 339 TRP cc_start: 0.9124 (OUTLIER) cc_final: 0.8842 (m-90) REVERT: R 351 GLN cc_start: 0.7821 (tt0) cc_final: 0.7382 (tp-100) REVERT: R 433 HIS cc_start: 0.6217 (OUTLIER) cc_final: 0.5654 (p-80) REVERT: R 447 GLU cc_start: 0.7971 (tp30) cc_final: 0.7400 (tm-30) REVERT: R 485 ARG cc_start: 0.6421 (ttt180) cc_final: 0.5221 (tpp80) REVERT: A 38 LEU cc_start: 0.9246 (tt) cc_final: 0.8666 (mt) REVERT: A 74 TYR cc_start: 0.8162 (m-10) cc_final: 0.7889 (m-80) REVERT: A 132 LYS cc_start: 0.9360 (mttt) cc_final: 0.8849 (mttm) REVERT: A 198 MET cc_start: 0.8206 (tpt) cc_final: 0.7937 (tpt) REVERT: A 243 MET cc_start: 0.8694 (ptt) cc_final: 0.8470 (ptt) REVERT: A 283 LEU cc_start: 0.8501 (tt) cc_final: 0.8290 (tp) REVERT: B 3 GLU cc_start: 0.8646 (tp30) cc_final: 0.8382 (tp30) REVERT: B 46 ARG cc_start: 0.7764 (tpp80) cc_final: 0.7532 (tpp80) REVERT: B 61 MET cc_start: 0.7888 (ppp) cc_final: 0.7673 (ppp) REVERT: B 127 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8754 (mttp) REVERT: B 289 TYR cc_start: 0.8770 (m-80) cc_final: 0.8225 (m-80) REVERT: B 301 LYS cc_start: 0.7650 (mtmt) cc_final: 0.6960 (mmtt) REVERT: B 325 MET cc_start: 0.7147 (mtm) cc_final: 0.6905 (ttm) REVERT: B 333 ASP cc_start: 0.8635 (p0) cc_final: 0.8248 (p0) REVERT: G 17 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8857 (mt-10) REVERT: G 21 MET cc_start: 0.7700 (mmt) cc_final: 0.7498 (mmt) REVERT: G 36 ASP cc_start: 0.8734 (t0) cc_final: 0.8475 (m-30) REVERT: L 59 VAL cc_start: 0.9290 (t) cc_final: 0.9016 (p) REVERT: H 112 TYR cc_start: 0.8582 (m-10) cc_final: 0.8216 (m-10) REVERT: H 120 TYR cc_start: 0.8315 (m-10) cc_final: 0.7948 (m-10) outliers start: 62 outliers final: 52 residues processed: 305 average time/residue: 0.0866 time to fit residues: 39.1540 Evaluate side-chains 305 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 47 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 = 0.3724 r_free = 0.3724 target = 0.103806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.085082 restraints weight = 35638.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.087499 restraints weight = 20209.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089139 restraints weight = 13668.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.090263 restraints weight = 10330.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091029 restraints weight = 8462.364| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10809 Z= 0.182 Angle : 0.692 11.196 14659 Z= 0.359 Chirality : 0.044 0.224 1635 Planarity : 0.005 0.100 1857 Dihedral : 5.944 85.982 1477 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 6.17 % Allowed : 23.52 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.22), residues: 1333 helix: 0.12 (0.24), residues: 457 sheet: -0.59 (0.32), residues: 262 loop : -2.41 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.018 0.001 TYR A 69 PHE 0.027 0.002 PHE H 32 TRP 0.043 0.002 TRP R 339 HIS 0.007 0.002 HIS R 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (10806) covalent geometry : angle 0.69185 / 0.36 (14653) SS BOND : bond 0.00404 / 0.20 ( 3) SS BOND : angle 1.02934 / 0.55 ( 6) hydrogen bonds : bond 0.03938 / 2.67 ( 442) hydrogen bonds : angle 4.96258 / 3.64 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 250 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8276 (m) cc_final: 0.7983 (p) REVERT: R 218 GLN cc_start: 0.8462 (mt0) cc_final: 0.7868 (mp10) REVERT: R 228 GLN cc_start: 0.9395 (mt0) cc_final: 0.9071 (tp40) REVERT: R 257 ARG cc_start: 0.8289 (mtp180) cc_final: 0.7759 (mmt180) REVERT: R 301 MET cc_start: 0.7531 (pmm) cc_final: 0.6719 (pmm) REVERT: R 339 TRP cc_start: 0.9173 (OUTLIER) cc_final: 0.8892 (m-90) REVERT: R 433 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.5782 (p-80) REVERT: R 447 GLU cc_start: 0.8066 (tp30) cc_final: 0.7476 (tm-30) REVERT: R 485 ARG cc_start: 0.6600 (ttt180) cc_final: 0.5401 (tpp80) REVERT: R 491 GLN cc_start: 0.7807 (tp40) cc_final: 0.7367 (tp40) REVERT: B 3 GLU cc_start: 0.8686 (tp30) cc_final: 0.8463 (tp30) REVERT: B 46 ARG cc_start: 0.7803 (tpp80) cc_final: 0.7576 (tpp80) REVERT: B 110 ASN cc_start: 0.8504 (p0) cc_final: 0.8190 (p0) REVERT: B 136 SER cc_start: 0.8718 (m) cc_final: 0.8492 (t) REVERT: B 289 TYR cc_start: 0.8735 (m-80) cc_final: 0.8263 (m-80) REVERT: B 295 ASN cc_start: 0.8416 (p0) cc_final: 0.8145 (p0) REVERT: B 333 ASP cc_start: 0.8701 (p0) cc_final: 0.8343 (p0) REVERT: G 36 ASP cc_start: 0.8774 (t0) cc_final: 0.8503 (m-30) REVERT: L 59 VAL cc_start: 0.9338 (t) cc_final: 0.9037 (p) REVERT: H 68 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8416 (ptpp) REVERT: H 120 TYR cc_start: 0.8344 (m-10) cc_final: 0.7968 (m-10) outliers start: 70 outliers final: 53 residues processed: 294 average time/residue: 0.0869 time to fit residues: 38.1260 Evaluate side-chains 296 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 340 HIS ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 = 0.3765 r_free = 0.3765 target = 0.106494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087561 restraints weight = 35101.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.090041 restraints weight = 19920.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.091707 restraints weight = 13419.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092889 restraints weight = 10136.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093690 restraints weight = 8269.062| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10809 Z= 0.128 Angle : 0.704 14.215 14659 Z= 0.354 Chirality : 0.043 0.204 1635 Planarity : 0.005 0.098 1857 Dihedral : 5.769 87.641 1477 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.20 % Allowed : 24.93 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.23), residues: 1333 helix: 0.18 (0.24), residues: 456 sheet: -0.44 (0.33), residues: 257 loop : -2.38 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.019 0.001 TYR A 69 PHE 0.024 0.001 PHE H 32 TRP 0.056 0.002 TRP H 50 HIS 0.005 0.001 HIS R 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10806) covalent geometry : angle 0.70436 / 0.35 (14653) SS BOND : bond 0.00200 / 0.10 ( 3) SS BOND : angle 0.70962 / 0.38 ( 6) hydrogen bonds : bond 0.03692 / 2.56 ( 442) hydrogen bonds : angle 4.84872 / 3.57 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 268 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8215 (m) cc_final: 0.7936 (p) REVERT: R 218 GLN cc_start: 0.8437 (mt0) cc_final: 0.7851 (mp10) REVERT: R 228 GLN cc_start: 0.9373 (mt0) cc_final: 0.9045 (tp40) REVERT: R 257 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7755 (mmt180) REVERT: R 301 MET cc_start: 0.7414 (pmm) cc_final: 0.6614 (pmm) REVERT: R 339 TRP cc_start: 0.9126 (OUTLIER) cc_final: 0.8896 (m-90) REVERT: R 433 HIS cc_start: 0.6332 (OUTLIER) cc_final: 0.5747 (p-80) REVERT: R 447 GLU cc_start: 0.8026 (tp30) cc_final: 0.7465 (tm-30) REVERT: R 449 MET cc_start: 0.9240 (ttt) cc_final: 0.8663 (tpp) REVERT: R 485 ARG cc_start: 0.6692 (ttt180) cc_final: 0.5634 (tpp80) REVERT: R 491 GLN cc_start: 0.7790 (tp40) cc_final: 0.7416 (tp40) REVERT: A 18 MET cc_start: 0.7300 (mmm) cc_final: 0.6736 (tpp) REVERT: A 74 TYR cc_start: 0.8171 (m-10) cc_final: 0.7916 (m-80) REVERT: A 232 LEU cc_start: 0.8639 (mp) cc_final: 0.8025 (tt) REVERT: B 3 GLU cc_start: 0.8634 (tp30) cc_final: 0.8426 (tp30) REVERT: B 110 ASN cc_start: 0.8565 (p0) cc_final: 0.8277 (p0) REVERT: B 136 SER cc_start: 0.8653 (m) cc_final: 0.8433 (t) REVERT: B 289 TYR cc_start: 0.8626 (m-80) cc_final: 0.8182 (m-80) REVERT: B 301 LYS cc_start: 0.7519 (mtmt) cc_final: 0.6855 (mmtt) REVERT: B 325 MET cc_start: 0.7325 (ttm) cc_final: 0.7027 (ttm) REVERT: B 333 ASP cc_start: 0.8643 (p0) cc_final: 0.8252 (p0) REVERT: L 59 VAL cc_start: 0.9291 (t) cc_final: 0.9006 (p) REVERT: H 120 TYR cc_start: 0.8309 (m-10) cc_final: 0.7957 (m-10) outliers start: 59 outliers final: 50 residues processed: 303 average time/residue: 0.0886 time to fit residues: 39.8312 Evaluate side-chains 304 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 340 HIS ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 = 0.3770 r_free = 0.3770 target = 0.106860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.087953 restraints weight = 35205.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.090469 restraints weight = 20062.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.092155 restraints weight = 13526.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093339 restraints weight = 10200.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094155 restraints weight = 8319.566| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10809 Z= 0.128 Angle : 0.709 13.769 14659 Z= 0.356 Chirality : 0.043 0.196 1635 Planarity : 0.004 0.096 1857 Dihedral : 5.755 87.870 1477 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.49 % Allowed : 25.73 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.23), residues: 1333 helix: 0.27 (0.24), residues: 451 sheet: -0.35 (0.32), residues: 266 loop : -2.34 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 25 TYR 0.018 0.001 TYR A 69 PHE 0.023 0.001 PHE H 32 TRP 0.053 0.002 TRP H 50 HIS 0.005 0.001 HIS R 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10806) covalent geometry : angle 0.70897 / 0.36 (14653) SS BOND : bond 0.00169 / 0.09 ( 3) SS BOND : angle 0.68131 / 0.36 ( 6) hydrogen bonds : bond 0.03634 / 2.51 ( 442) hydrogen bonds : angle 4.77429 / 3.50 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8204 (m) cc_final: 0.7928 (p) REVERT: R 218 GLN cc_start: 0.8437 (mt0) cc_final: 0.7849 (mp10) REVERT: R 228 GLN cc_start: 0.9372 (mt0) cc_final: 0.9058 (tp40) REVERT: R 257 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7767 (mmt180) REVERT: R 301 MET cc_start: 0.7407 (pmm) cc_final: 0.6605 (pmm) REVERT: R 433 HIS cc_start: 0.6278 (OUTLIER) cc_final: 0.5739 (p-80) REVERT: R 447 GLU cc_start: 0.8070 (tp30) cc_final: 0.7549 (tm-30) REVERT: R 485 ARG cc_start: 0.6667 (ttt180) cc_final: 0.5651 (tpp80) REVERT: R 491 GLN cc_start: 0.7763 (tp40) cc_final: 0.7396 (tp40) REVERT: A 18 MET cc_start: 0.7282 (mmm) cc_final: 0.6704 (tpp) REVERT: A 74 TYR cc_start: 0.8178 (m-10) cc_final: 0.7904 (m-80) REVERT: A 232 LEU cc_start: 0.8694 (mp) cc_final: 0.8048 (tp) REVERT: A 283 LEU cc_start: 0.8388 (tt) cc_final: 0.8139 (tp) REVERT: B 127 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8779 (mtmt) REVERT: B 136 SER cc_start: 0.8661 (m) cc_final: 0.8447 (t) REVERT: B 289 TYR cc_start: 0.8740 (m-80) cc_final: 0.8225 (m-80) REVERT: B 301 LYS cc_start: 0.7502 (mtmt) cc_final: 0.6826 (mmtt) REVERT: B 325 MET cc_start: 0.7182 (ttm) cc_final: 0.6870 (ttm) REVERT: B 333 ASP cc_start: 0.8657 (p0) cc_final: 0.8273 (p0) REVERT: L 59 VAL cc_start: 0.9296 (t) cc_final: 0.9001 (p) REVERT: H 86 MET cc_start: 0.8378 (mpp) cc_final: 0.7879 (mpp) REVERT: H 120 TYR cc_start: 0.8323 (m-10) cc_final: 0.7953 (m-10) outliers start: 51 outliers final: 47 residues processed: 294 average time/residue: 0.0906 time to fit residues: 39.2295 Evaluate side-chains 298 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 73 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 340 HIS ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 = 0.3751 r_free = 0.3751 target = 0.105532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.086813 restraints weight = 35558.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089286 restraints weight = 20194.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090928 restraints weight = 13618.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092094 restraints weight = 10294.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092896 restraints weight = 8403.593| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10809 Z= 0.155 Angle : 0.722 13.861 14659 Z= 0.366 Chirality : 0.044 0.189 1635 Planarity : 0.005 0.095 1857 Dihedral : 5.842 87.655 1477 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.49 % Allowed : 26.26 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.23), residues: 1333 helix: 0.26 (0.24), residues: 453 sheet: -0.36 (0.32), residues: 266 loop : -2.38 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.021 0.001 TYR H 112 PHE 0.024 0.001 PHE R 484 TRP 0.065 0.003 TRP R 339 HIS 0.006 0.001 HIS R 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (10806) covalent geometry : angle 0.72205 / 0.37 (14653) SS BOND : bond 0.00212 / 0.11 ( 3) SS BOND : angle 0.87638 / 0.47 ( 6) hydrogen bonds : bond 0.03768 / 2.58 ( 442) hydrogen bonds : angle 4.89008 / 3.58 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 253 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8125 (m) cc_final: 0.7851 (p) REVERT: R 218 GLN cc_start: 0.8497 (mt0) cc_final: 0.7929 (mp10) REVERT: R 228 GLN cc_start: 0.9379 (mt0) cc_final: 0.9070 (tp40) REVERT: R 257 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7788 (mmt180) REVERT: R 301 MET cc_start: 0.7515 (pmm) cc_final: 0.6767 (pmm) REVERT: R 433 HIS cc_start: 0.6321 (OUTLIER) cc_final: 0.5714 (p-80) REVERT: R 447 GLU cc_start: 0.8294 (tp30) cc_final: 0.7823 (tm-30) REVERT: R 449 MET cc_start: 0.8932 (ttt) cc_final: 0.8468 (tpp) REVERT: R 485 ARG cc_start: 0.6722 (ttt180) cc_final: 0.5683 (tpp80) REVERT: R 491 GLN cc_start: 0.7824 (tp40) cc_final: 0.7472 (tp40) REVERT: A 74 TYR cc_start: 0.8169 (m-10) cc_final: 0.7917 (m-80) REVERT: B 46 ARG cc_start: 0.7961 (tpt170) cc_final: 0.6896 (tpp80) REVERT: B 57 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8686 (mtpt) REVERT: B 127 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8793 (mtmt) REVERT: B 136 SER cc_start: 0.8794 (m) cc_final: 0.8564 (t) REVERT: B 176 GLN cc_start: 0.9124 (pt0) cc_final: 0.8376 (pp30) REVERT: B 289 TYR cc_start: 0.8734 (m-80) cc_final: 0.8239 (m-80) REVERT: B 325 MET cc_start: 0.7391 (ttm) cc_final: 0.7064 (ttm) REVERT: B 333 ASP cc_start: 0.8685 (p0) cc_final: 0.8309 (p0) REVERT: L 59 VAL cc_start: 0.9313 (t) cc_final: 0.9019 (p) REVERT: H 86 MET cc_start: 0.8363 (mpp) cc_final: 0.7904 (mpp) REVERT: H 120 TYR cc_start: 0.8354 (m-10) cc_final: 0.7977 (m-10) outliers start: 51 outliers final: 49 residues processed: 283 average time/residue: 0.0857 time to fit residues: 36.1962 Evaluate side-chains 302 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 = 0.3733 r_free = 0.3733 target = 0.104430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085728 restraints weight = 35783.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.088172 restraints weight = 20330.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089844 restraints weight = 13738.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090956 restraints weight = 10384.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.091760 restraints weight = 8508.907| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10809 Z= 0.172 Angle : 0.732 14.660 14659 Z= 0.373 Chirality : 0.044 0.189 1635 Planarity : 0.005 0.096 1857 Dihedral : 5.963 88.170 1477 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.76 % Allowed : 26.26 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.23), residues: 1333 helix: 0.22 (0.24), residues: 453 sheet: -0.59 (0.32), residues: 263 loop : -2.38 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 25 TYR 0.043 0.002 TYR H 34 PHE 0.021 0.002 PHE H 32 TRP 0.068 0.003 TRP R 339 HIS 0.005 0.001 HIS R 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (10806) covalent geometry : angle 0.73163 / 0.37 (14653) SS BOND : bond 0.00238 / 0.12 ( 3) SS BOND : angle 0.92146 / 0.49 ( 6) hydrogen bonds : bond 0.03843 / 2.62 ( 442) hydrogen bonds : angle 4.94604 / 3.62 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.79 seconds wall clock time: 38 minutes 4.17 seconds (2284.17 seconds total)