Starting phenix.real_space_refine on Tue Mar 3 17:32:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6niy_9382/03_2026/6niy_9382.cif Found real_map, /net/cci-nas-00/data/ceres_data/6niy_9382/03_2026/6niy_9382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6niy_9382/03_2026/6niy_9382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6niy_9382/03_2026/6niy_9382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6niy_9382/03_2026/6niy_9382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6niy_9382/03_2026/6niy_9382.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 4925 2.51 5 N 1355 2.21 5 O 1391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7727 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1445 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2173 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain breaks: 2 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2570 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "P" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 142 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Time building chain proxies: 1.74, per 1000 atoms: 0.23 Number of scatterers: 7727 At special positions: 0 Unit cell: (119.78, 110.24, 82.68, 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 56 16.00 O 1391 8.00 N 1355 7.00 C 4925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.02 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: 0.67 Conformation dependent library (CDL) restraints added in 368.7 milliseconds 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 41.9% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.528A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.504A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.726A pdb=" N LEU A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.775A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.924A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.706A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 173 removed outlier: 3.544A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.513A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU R 204 " --> pdb=" O ILE R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 249 Processing helix chain 'R' and resid 258 through 267 removed outlier: 3.566A pdb=" N TYR R 262 " --> pdb=" O ARG R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 285 removed outlier: 3.530A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix removed outlier: 3.580A pdb=" N THR R 325 " --> pdb=" O ARG R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.559A pdb=" N ILE R 371 " --> pdb=" O MET R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 393 removed outlier: 3.642A pdb=" N ILE R 390 " --> pdb=" O PHE R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 412 removed outlier: 3.557A pdb=" N ILE R 411 " --> pdb=" O ALA R 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 27 removed outlier: 3.839A pdb=" N ASP B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.926A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.846A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 removed outlier: 3.557A pdb=" N LYS P 11 " --> pdb=" O CYS P 7 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 3.514A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.715A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.533A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.750A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.587A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.477A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.612A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192 removed outlier: 7.146A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.347A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.657A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1116 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: 1.17 Time building geometry restraints manager: 0.90 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: 2501 1.34 - 1.47: 1990 1.47 - 1.59: 3318 1.59 - 1.72: 0 1.72 - 1.84: 80 Bond restraints: 7889 Sorted by residual: bond pdb=" CB ASP B 205 " pdb=" CG ASP B 205 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.23e+00 bond pdb=" CB ASN P 3 " pdb=" CG ASN P 3 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.10e+00 bond pdb=" CB TRP B 211 " pdb=" CG TRP B 211 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.00e+00 bond pdb=" CG LEU B 146 " pdb=" CD2 LEU B 146 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CA SER B 72 " pdb=" CB SER B 72 " ideal model delta sigma weight residual 1.534 1.493 0.041 2.47e-02 1.64e+03 2.76e+00 ... (remaining 7884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 10233 2.17 - 4.33: 372 4.33 - 6.50: 49 6.50 - 8.67: 12 8.67 - 10.83: 5 Bond angle restraints: 10671 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 130.00 -8.46 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C SER P 2 " pdb=" N ASN P 3 " pdb=" CA ASN P 3 " ideal model delta sigma weight residual 122.07 127.85 -5.78 1.43e+00 4.89e-01 1.63e+01 angle pdb=" CA VAL R 272 " pdb=" CB VAL R 272 " pdb=" CG1 VAL R 272 " ideal model delta sigma weight residual 110.40 116.97 -6.57 1.70e+00 3.46e-01 1.49e+01 angle pdb=" CA PRO R 273 " pdb=" N PRO R 273 " pdb=" CD PRO R 273 " ideal model delta sigma weight residual 112.00 106.91 5.09 1.40e+00 5.10e-01 1.32e+01 ... (remaining 10666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 4128 15.88 - 31.76: 429 31.76 - 47.64: 97 47.64 - 63.52: 16 63.52 - 79.40: 7 Dihedral angle restraints: 4677 sinusoidal: 1866 harmonic: 2811 Sorted by residual: dihedral pdb=" C VAL R 272 " pdb=" N VAL R 272 " pdb=" CA VAL R 272 " pdb=" CB VAL R 272 " ideal model delta harmonic sigma weight residual -122.00 -133.58 11.58 0 2.50e+00 1.60e-01 2.14e+01 dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual -86.00 -121.79 35.79 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CA ARG N 38 " pdb=" C ARG N 38 " pdb=" N GLN N 39 " pdb=" CA GLN N 39 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 4674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 842 0.060 - 0.119: 275 0.119 - 0.179: 67 0.179 - 0.238: 8 0.238 - 0.298: 6 Chirality restraints: 1198 Sorted by residual: chirality pdb=" CA VAL R 272 " pdb=" N VAL R 272 " pdb=" C VAL R 272 " pdb=" CB VAL R 272 " both_signs ideal model delta sigma weight residual False 2.44 2.14 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL R 272 " pdb=" CA VAL R 272 " pdb=" CG1 VAL R 272 " pdb=" CG2 VAL R 272 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1195 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " 0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO R 304 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 17 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C GLN B 17 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN B 17 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE B 18 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 236 " 0.026 2.00e-02 2.50e+03 1.29e-02 4.16e+00 pdb=" CG TRP R 236 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP R 236 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP R 236 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 236 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 236 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 236 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 236 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 236 " -0.003 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2181 2.81 - 3.33: 6867 3.33 - 3.85: 12661 3.85 - 4.38: 14463 4.38 - 4.90: 25663 Nonbonded interactions: 61835 Sorted by model distance: nonbonded pdb=" O PHE R 359 " pdb=" OG SER P 5 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.297 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.299 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.304 3.040 ... (remaining 61830 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.610 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 : 0.008 0.070 7893 Z= 0.362 Angle : 0.994 10.835 10679 Z= 0.557 Chirality : 0.064 0.298 1198 Planarity : 0.007 0.084 1346 Dihedral : 13.736 79.397 2841 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.06 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.26), residues: 937 helix: 0.94 (0.25), residues: 370 sheet: -0.69 (0.34), residues: 221 loop : -2.30 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.017 0.002 TYR B 59 PHE 0.024 0.003 PHE B 253 TRP 0.026 0.003 TRP R 236 HIS 0.010 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00833 ( 7889) covalent geometry : angle 0.99290 (10671) SS BOND : bond 0.00963 ( 4) SS BOND : angle 1.85562 ( 8) hydrogen bonds : bond 0.25817 ( 389) hydrogen bonds : angle 8.36355 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.8070 (m) cc_final: 0.7843 (m) REVERT: A 233 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7200 (mtpp) REVERT: A 333 ARG cc_start: 0.6793 (mtt180) cc_final: 0.5734 (ttt180) REVERT: A 334 VAL cc_start: 0.5547 (m) cc_final: 0.5298 (p) REVERT: A 358 TYR cc_start: 0.6297 (t80) cc_final: 0.5782 (t80) REVERT: A 360 TYR cc_start: 0.8788 (m-80) cc_final: 0.8291 (m-80) REVERT: A 378 ASP cc_start: 0.8536 (m-30) cc_final: 0.8027 (m-30) REVERT: A 381 ASP cc_start: 0.8654 (t70) cc_final: 0.8302 (t0) REVERT: A 392 GLU cc_start: 0.7621 (mp0) cc_final: 0.6773 (mp0) REVERT: A 394 LEU cc_start: 0.7576 (tp) cc_final: 0.7369 (tp) REVERT: N 34 MET cc_start: 0.8467 (mmp) cc_final: 0.8170 (mmm) REVERT: R 153 ILE cc_start: 0.7475 (mt) cc_final: 0.7190 (pt) REVERT: R 220 LYS cc_start: 0.5803 (mttt) cc_final: 0.5524 (mttm) REVERT: R 321 ARG cc_start: 0.7682 (ttt180) cc_final: 0.7399 (ptt180) REVERT: R 338 TYR cc_start: 0.5826 (m-10) cc_final: 0.5289 (m-80) REVERT: R 351 LEU cc_start: 0.8948 (tt) cc_final: 0.8573 (tt) REVERT: B 215 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8048 (mt-10) REVERT: G 22 GLU cc_start: 0.7382 (pt0) cc_final: 0.6774 (mt-10) REVERT: G 32 LYS cc_start: 0.8271 (mtmm) cc_final: 0.8041 (mtmm) outliers start: 1 outliers final: 1 residues processed: 227 average time/residue: 0.1177 time to fit residues: 33.9586 Evaluate side-chains 161 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 5 GLN R 179 GLN R 227 GLN R 233 ASN R 395 ASN B 32 GLN G 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118201 restraints weight = 11187.915| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.55 r_work: 0.3470 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7893 Z= 0.146 Angle : 0.610 7.658 10679 Z= 0.330 Chirality : 0.044 0.167 1198 Planarity : 0.004 0.043 1346 Dihedral : 5.286 50.016 1051 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.38 % Allowed : 13.18 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.26), residues: 937 helix: 1.23 (0.26), residues: 373 sheet: -0.23 (0.34), residues: 222 loop : -2.01 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 389 TYR 0.012 0.001 TYR R 372 PHE 0.022 0.002 PHE R 356 TRP 0.019 0.002 TRP B 211 HIS 0.007 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7889) covalent geometry : angle 0.60977 (10671) SS BOND : bond 0.00293 ( 4) SS BOND : angle 1.05628 ( 8) hydrogen bonds : bond 0.04796 ( 389) hydrogen bonds : angle 5.20340 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.8219 (m) cc_final: 0.8004 (m) REVERT: A 233 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7862 (mtpt) REVERT: A 358 TYR cc_start: 0.6521 (t80) cc_final: 0.6064 (t80) REVERT: A 360 TYR cc_start: 0.9118 (m-80) cc_final: 0.8849 (m-80) REVERT: A 378 ASP cc_start: 0.8654 (m-30) cc_final: 0.8139 (m-30) REVERT: A 389 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8201 (mmm160) REVERT: N 34 MET cc_start: 0.8436 (mmp) cc_final: 0.8222 (mmm) REVERT: R 220 LYS cc_start: 0.5803 (mttt) cc_final: 0.5493 (mttm) REVERT: R 291 LEU cc_start: 0.6694 (tp) cc_final: 0.6449 (tp) REVERT: R 338 TYR cc_start: 0.5725 (m-10) cc_final: 0.5320 (m-80) REVERT: R 351 LEU cc_start: 0.9074 (tt) cc_final: 0.8751 (tt) REVERT: B 23 LYS cc_start: 0.8473 (pptt) cc_final: 0.8169 (tppt) REVERT: B 215 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8051 (mt-10) REVERT: B 217 MET cc_start: 0.8455 (ptp) cc_final: 0.7865 (tpt) REVERT: G 20 LYS cc_start: 0.8941 (pttm) cc_final: 0.8719 (pttm) outliers start: 20 outliers final: 11 residues processed: 202 average time/residue: 0.0926 time to fit residues: 25.2093 Evaluate side-chains 172 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 0.0370 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 227 GLN R 277 HIS R 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.147236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117938 restraints weight = 11128.436| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.56 r_work: 0.3471 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7893 Z= 0.128 Angle : 0.555 7.777 10679 Z= 0.297 Chirality : 0.042 0.164 1198 Planarity : 0.003 0.037 1346 Dihedral : 4.748 47.780 1049 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.80 % Allowed : 16.03 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.29 (0.26), residues: 937 helix: 1.23 (0.26), residues: 377 sheet: -0.18 (0.33), residues: 229 loop : -1.87 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.009 0.001 TYR R 191 PHE 0.020 0.001 PHE R 356 TRP 0.016 0.001 TRP B 211 HIS 0.005 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7889) covalent geometry : angle 0.55500 (10671) SS BOND : bond 0.00138 ( 4) SS BOND : angle 0.85024 ( 8) hydrogen bonds : bond 0.03952 ( 389) hydrogen bonds : angle 4.69880 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7888 (pp20) REVERT: A 358 TYR cc_start: 0.6561 (t80) cc_final: 0.6157 (t80) REVERT: A 378 ASP cc_start: 0.8626 (m-30) cc_final: 0.8371 (m-30) REVERT: A 389 ARG cc_start: 0.8467 (mtp85) cc_final: 0.8228 (mmm160) REVERT: R 220 LYS cc_start: 0.5791 (mttt) cc_final: 0.5375 (mttm) REVERT: R 306 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7858 (mmt) REVERT: R 346 MET cc_start: 0.5411 (tmm) cc_final: 0.4311 (mmm) REVERT: R 351 LEU cc_start: 0.9039 (tt) cc_final: 0.8693 (tt) REVERT: R 393 PHE cc_start: 0.8046 (m-80) cc_final: 0.7553 (m-80) REVERT: B 23 LYS cc_start: 0.8486 (pptt) cc_final: 0.8281 (tppt) REVERT: B 215 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8319 (mt-10) REVERT: G 19 LEU cc_start: 0.8488 (mm) cc_final: 0.8252 (mm) REVERT: G 20 LYS cc_start: 0.8964 (pttm) cc_final: 0.8727 (pttm) REVERT: G 32 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7934 (mttp) REVERT: P 11 LYS cc_start: 0.7879 (tttm) cc_final: 0.7388 (ttmm) outliers start: 32 outliers final: 24 residues processed: 185 average time/residue: 0.0872 time to fit residues: 22.1847 Evaluate side-chains 180 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 81 optimal weight: 0.0870 overall best weight: 1.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 233 ASN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117159 restraints weight = 11345.572| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.59 r_work: 0.3464 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7893 Z= 0.133 Angle : 0.549 7.430 10679 Z= 0.294 Chirality : 0.042 0.135 1198 Planarity : 0.003 0.039 1346 Dihedral : 4.632 47.038 1049 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.80 % Allowed : 17.22 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 937 helix: 1.29 (0.26), residues: 377 sheet: -0.03 (0.34), residues: 223 loop : -1.74 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.013 0.001 TYR R 191 PHE 0.021 0.002 PHE R 356 TRP 0.015 0.001 TRP B 211 HIS 0.005 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7889) covalent geometry : angle 0.54845 (10671) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.75713 ( 8) hydrogen bonds : bond 0.03616 ( 389) hydrogen bonds : angle 4.58109 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 LYS cc_start: 0.8350 (mttt) cc_final: 0.8051 (mtmt) REVERT: A 268 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7767 (pp20) REVERT: A 358 TYR cc_start: 0.6558 (t80) cc_final: 0.6290 (t80) REVERT: R 187 MET cc_start: 0.7693 (tpt) cc_final: 0.7193 (tpt) REVERT: R 220 LYS cc_start: 0.5685 (mttt) cc_final: 0.5276 (mttm) REVERT: R 337 MET cc_start: 0.7314 (ppp) cc_final: 0.6696 (ptt) REVERT: R 346 MET cc_start: 0.5404 (tmm) cc_final: 0.4261 (mmm) REVERT: R 351 LEU cc_start: 0.9076 (tt) cc_final: 0.8714 (tt) REVERT: R 357 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7515 (t) REVERT: B 23 LYS cc_start: 0.8477 (pptt) cc_final: 0.8220 (tppt) REVERT: B 37 ILE cc_start: 0.7633 (pt) cc_final: 0.7306 (pt) REVERT: B 153 ASP cc_start: 0.8620 (p0) cc_final: 0.8200 (m-30) REVERT: B 215 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8321 (mt-10) REVERT: G 20 LYS cc_start: 0.8951 (pttm) cc_final: 0.8706 (pttm) REVERT: G 32 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7857 (mtmm) REVERT: P 11 LYS cc_start: 0.7897 (tttm) cc_final: 0.7298 (ttmm) outliers start: 32 outliers final: 23 residues processed: 177 average time/residue: 0.0790 time to fit residues: 19.0843 Evaluate side-chains 174 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 395 ASN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.141971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112104 restraints weight = 11555.638| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.56 r_work: 0.3393 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7893 Z= 0.230 Angle : 0.625 7.597 10679 Z= 0.334 Chirality : 0.044 0.148 1198 Planarity : 0.004 0.036 1346 Dihedral : 4.995 57.733 1049 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.82 % Allowed : 16.75 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.26), residues: 937 helix: 1.21 (0.26), residues: 374 sheet: -0.31 (0.33), residues: 224 loop : -1.66 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.014 0.002 TYR R 372 PHE 0.019 0.002 PHE R 235 TRP 0.016 0.002 TRP R 290 HIS 0.009 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 7889) covalent geometry : angle 0.62494 (10671) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.89228 ( 8) hydrogen bonds : bond 0.03986 ( 389) hydrogen bonds : angle 4.71977 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7807 (pp20) REVERT: A 358 TYR cc_start: 0.6711 (t80) cc_final: 0.6398 (t80) REVERT: R 187 MET cc_start: 0.7823 (tpt) cc_final: 0.7407 (tpt) REVERT: R 198 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7712 (mt) REVERT: R 337 MET cc_start: 0.7300 (ppp) cc_final: 0.6627 (ptt) REVERT: R 346 MET cc_start: 0.5476 (tmm) cc_final: 0.4280 (mmm) REVERT: R 351 LEU cc_start: 0.9110 (tt) cc_final: 0.8753 (tt) REVERT: R 357 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7603 (t) REVERT: R 367 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.4036 (mmm) REVERT: R 373 ASP cc_start: 0.6721 (t0) cc_final: 0.6312 (t0) REVERT: R 377 HIS cc_start: 0.7629 (m90) cc_final: 0.7075 (m90) REVERT: R 393 PHE cc_start: 0.8081 (m-80) cc_final: 0.7591 (m-80) REVERT: B 23 LYS cc_start: 0.8490 (pptt) cc_final: 0.8198 (tppt) REVERT: B 153 ASP cc_start: 0.8622 (p0) cc_final: 0.8237 (m-30) REVERT: B 215 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 334 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.9099 (m) REVERT: G 11 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7318 (tm-30) REVERT: G 19 LEU cc_start: 0.8585 (mm) cc_final: 0.8360 (mm) REVERT: G 20 LYS cc_start: 0.8975 (pttm) cc_final: 0.8727 (pttm) REVERT: G 32 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7925 (mtmm) REVERT: G 42 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7463 (pt0) REVERT: P 11 LYS cc_start: 0.8010 (tttm) cc_final: 0.7350 (ttmm) outliers start: 49 outliers final: 32 residues processed: 186 average time/residue: 0.0744 time to fit residues: 19.3090 Evaluate side-chains 186 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 412 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.146626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117138 restraints weight = 11196.628| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.55 r_work: 0.3462 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7893 Z= 0.114 Angle : 0.544 7.422 10679 Z= 0.289 Chirality : 0.041 0.132 1198 Planarity : 0.003 0.033 1346 Dihedral : 4.774 62.342 1049 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.68 % Allowed : 20.31 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.01 (0.27), residues: 937 helix: 1.39 (0.26), residues: 378 sheet: -0.19 (0.33), residues: 224 loop : -1.48 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 19 TYR 0.013 0.001 TYR R 191 PHE 0.019 0.001 PHE R 359 TRP 0.014 0.001 TRP R 236 HIS 0.004 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7889) covalent geometry : angle 0.54356 (10671) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.76603 ( 8) hydrogen bonds : bond 0.03319 ( 389) hydrogen bonds : angle 4.45911 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7608 (pp20) REVERT: A 358 TYR cc_start: 0.6638 (t80) cc_final: 0.6391 (t80) REVERT: A 378 ASP cc_start: 0.8344 (m-30) cc_final: 0.7928 (m-30) REVERT: R 187 MET cc_start: 0.7922 (tpt) cc_final: 0.7481 (tpt) REVERT: R 198 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7629 (mt) REVERT: R 291 LEU cc_start: 0.6815 (tp) cc_final: 0.6505 (tp) REVERT: R 306 MET cc_start: 0.8210 (tpt) cc_final: 0.8007 (mmt) REVERT: R 337 MET cc_start: 0.7193 (ppp) cc_final: 0.6475 (ptt) REVERT: R 346 MET cc_start: 0.5423 (tmm) cc_final: 0.4413 (mmm) REVERT: R 351 LEU cc_start: 0.9145 (tt) cc_final: 0.8780 (tt) REVERT: R 357 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7637 (t) REVERT: R 367 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.4087 (mmm) REVERT: B 23 LYS cc_start: 0.8440 (pptt) cc_final: 0.8176 (tppt) REVERT: B 37 ILE cc_start: 0.7902 (pt) cc_final: 0.7528 (pt) REVERT: B 57 LYS cc_start: 0.8766 (pttp) cc_final: 0.8524 (ptpp) REVERT: B 101 MET cc_start: 0.8229 (mmm) cc_final: 0.7940 (mmm) REVERT: B 215 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8260 (mt-10) REVERT: G 19 LEU cc_start: 0.8527 (mm) cc_final: 0.8272 (mm) REVERT: G 20 LYS cc_start: 0.8952 (pttm) cc_final: 0.8698 (pttm) REVERT: P 11 LYS cc_start: 0.7896 (tttm) cc_final: 0.7226 (ttmm) outliers start: 31 outliers final: 23 residues processed: 183 average time/residue: 0.0825 time to fit residues: 20.8134 Evaluate side-chains 172 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 0.0060 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.150222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.120798 restraints weight = 11112.859| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.48 r_work: 0.3504 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7893 Z= 0.127 Angle : 0.552 7.529 10679 Z= 0.294 Chirality : 0.041 0.133 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.733 64.137 1049 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.51 % Allowed : 21.26 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 937 helix: 1.53 (0.27), residues: 372 sheet: -0.28 (0.33), residues: 223 loop : -1.34 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.012 0.001 TYR R 191 PHE 0.018 0.001 PHE R 359 TRP 0.013 0.001 TRP R 236 HIS 0.005 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7889) covalent geometry : angle 0.55194 (10671) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.66327 ( 8) hydrogen bonds : bond 0.03326 ( 389) hydrogen bonds : angle 4.39311 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7723 (pp20) REVERT: A 358 TYR cc_start: 0.6818 (t80) cc_final: 0.6558 (t80) REVERT: A 378 ASP cc_start: 0.8492 (m-30) cc_final: 0.8080 (m-30) REVERT: R 187 MET cc_start: 0.7990 (tpt) cc_final: 0.7568 (tpt) REVERT: R 198 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7677 (mt) REVERT: R 220 LYS cc_start: 0.5620 (mttt) cc_final: 0.5214 (mttm) REVERT: R 291 LEU cc_start: 0.6879 (tp) cc_final: 0.6545 (tp) REVERT: R 337 MET cc_start: 0.7226 (ppp) cc_final: 0.6462 (ptt) REVERT: R 346 MET cc_start: 0.5559 (tmm) cc_final: 0.4480 (mmm) REVERT: R 351 LEU cc_start: 0.9181 (tt) cc_final: 0.8812 (tt) REVERT: R 357 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7706 (t) REVERT: R 367 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.4170 (mmm) REVERT: B 23 LYS cc_start: 0.8428 (pptt) cc_final: 0.8143 (tppt) REVERT: B 37 ILE cc_start: 0.7871 (pt) cc_final: 0.7537 (pt) REVERT: B 101 MET cc_start: 0.8585 (mmm) cc_final: 0.8112 (mmm) REVERT: B 153 ASP cc_start: 0.8750 (p0) cc_final: 0.8247 (m-30) REVERT: B 217 MET cc_start: 0.8515 (ptp) cc_final: 0.7975 (tpt) REVERT: B 334 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.9096 (m) REVERT: G 19 LEU cc_start: 0.8516 (mm) cc_final: 0.8268 (mm) REVERT: G 20 LYS cc_start: 0.8981 (pttm) cc_final: 0.8728 (pttm) REVERT: G 42 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: P 11 LYS cc_start: 0.7855 (tttm) cc_final: 0.7195 (ttmm) outliers start: 38 outliers final: 25 residues processed: 174 average time/residue: 0.0816 time to fit residues: 19.6893 Evaluate side-chains 175 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.144484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115184 restraints weight = 11336.740| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.48 r_work: 0.3455 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7893 Z= 0.176 Angle : 0.590 8.620 10679 Z= 0.314 Chirality : 0.043 0.138 1198 Planarity : 0.003 0.034 1346 Dihedral : 4.863 67.389 1049 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.87 % Allowed : 20.78 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.27), residues: 937 helix: 1.33 (0.26), residues: 378 sheet: -0.39 (0.33), residues: 224 loop : -1.43 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.013 0.001 TYR R 191 PHE 0.025 0.002 PHE R 224 TRP 0.015 0.002 TRP R 236 HIS 0.005 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7889) covalent geometry : angle 0.58946 (10671) SS BOND : bond 0.00076 ( 4) SS BOND : angle 0.73761 ( 8) hydrogen bonds : bond 0.03568 ( 389) hydrogen bonds : angle 4.46475 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7593 (pp20) REVERT: A 358 TYR cc_start: 0.6720 (t80) cc_final: 0.6401 (t80) REVERT: R 187 MET cc_start: 0.7946 (tpt) cc_final: 0.7510 (tpt) REVERT: R 198 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7711 (mt) REVERT: R 291 LEU cc_start: 0.6628 (tp) cc_final: 0.6283 (tp) REVERT: R 351 LEU cc_start: 0.9203 (tt) cc_final: 0.8877 (tt) REVERT: R 357 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7673 (t) REVERT: R 367 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.4276 (mmm) REVERT: B 23 LYS cc_start: 0.8437 (pptt) cc_final: 0.8161 (tppt) REVERT: B 37 ILE cc_start: 0.8028 (pt) cc_final: 0.7706 (pt) REVERT: B 57 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8232 (ptpp) REVERT: B 153 ASP cc_start: 0.8606 (p0) cc_final: 0.8157 (m-30) REVERT: B 215 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7983 (mt-10) REVERT: B 217 MET cc_start: 0.8347 (ptp) cc_final: 0.7870 (tpt) REVERT: B 334 SER cc_start: 0.9374 (OUTLIER) cc_final: 0.9127 (m) REVERT: G 20 LYS cc_start: 0.8985 (pttm) cc_final: 0.8739 (pttm) REVERT: G 42 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: P 11 LYS cc_start: 0.7778 (tttm) cc_final: 0.7105 (ttmm) outliers start: 41 outliers final: 27 residues processed: 176 average time/residue: 0.0833 time to fit residues: 20.3882 Evaluate side-chains 183 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 0.0030 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN R 277 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.151904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.125196 restraints weight = 10907.521| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.16 r_work: 0.3578 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7893 Z= 0.118 Angle : 0.562 8.152 10679 Z= 0.297 Chirality : 0.041 0.133 1198 Planarity : 0.003 0.034 1346 Dihedral : 4.700 65.502 1049 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.04 % Allowed : 21.50 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 937 helix: 1.46 (0.27), residues: 377 sheet: -0.21 (0.34), residues: 221 loop : -1.35 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 13 TYR 0.012 0.001 TYR R 191 PHE 0.021 0.001 PHE R 359 TRP 0.015 0.001 TRP R 236 HIS 0.005 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7889) covalent geometry : angle 0.56152 (10671) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.64028 ( 8) hydrogen bonds : bond 0.03252 ( 389) hydrogen bonds : angle 4.37700 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7671 (pp20) REVERT: A 358 TYR cc_start: 0.6855 (t80) cc_final: 0.6581 (t80) REVERT: R 187 MET cc_start: 0.8019 (tpt) cc_final: 0.7664 (tpt) REVERT: R 198 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7815 (mt) REVERT: R 220 LYS cc_start: 0.5735 (mttt) cc_final: 0.5332 (mttm) REVERT: R 291 LEU cc_start: 0.6633 (tp) cc_final: 0.6267 (tp) REVERT: R 351 LEU cc_start: 0.9234 (tt) cc_final: 0.8880 (tt) REVERT: R 357 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7616 (t) REVERT: R 367 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.4296 (mmm) REVERT: B 23 LYS cc_start: 0.8474 (pptt) cc_final: 0.8241 (tppt) REVERT: B 37 ILE cc_start: 0.7981 (pt) cc_final: 0.7657 (pt) REVERT: B 57 LYS cc_start: 0.8757 (ptpp) cc_final: 0.8251 (ptpp) REVERT: B 101 MET cc_start: 0.8533 (mmm) cc_final: 0.8228 (mmm) REVERT: B 153 ASP cc_start: 0.8632 (p0) cc_final: 0.8291 (m-30) REVERT: B 172 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7734 (mp0) REVERT: B 215 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8175 (mt-10) REVERT: B 334 SER cc_start: 0.9428 (OUTLIER) cc_final: 0.9181 (m) REVERT: G 19 LEU cc_start: 0.8590 (mm) cc_final: 0.8387 (mm) REVERT: G 32 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7644 (ptpp) REVERT: G 42 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: P 11 LYS cc_start: 0.7877 (tttm) cc_final: 0.7174 (ttmm) outliers start: 34 outliers final: 24 residues processed: 172 average time/residue: 0.0808 time to fit residues: 19.3174 Evaluate side-chains 180 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 69 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.150215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120508 restraints weight = 11116.539| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.50 r_work: 0.3526 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7893 Z= 0.114 Angle : 0.567 8.117 10679 Z= 0.302 Chirality : 0.041 0.131 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.577 62.498 1049 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.33 % Allowed : 22.45 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.27), residues: 937 helix: 1.46 (0.27), residues: 378 sheet: -0.12 (0.34), residues: 221 loop : -1.22 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.012 0.001 TYR R 191 PHE 0.025 0.001 PHE R 359 TRP 0.015 0.001 TRP R 236 HIS 0.004 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7889) covalent geometry : angle 0.56711 (10671) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.57595 ( 8) hydrogen bonds : bond 0.03153 ( 389) hydrogen bonds : angle 4.33452 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: A 358 TYR cc_start: 0.6668 (t80) cc_final: 0.6342 (t80) REVERT: R 187 MET cc_start: 0.7921 (tpt) cc_final: 0.7476 (tpt) REVERT: R 198 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7666 (mt) REVERT: R 220 LYS cc_start: 0.5613 (mttt) cc_final: 0.5248 (mttm) REVERT: R 291 LEU cc_start: 0.6578 (tp) cc_final: 0.6222 (tp) REVERT: R 351 LEU cc_start: 0.9167 (tt) cc_final: 0.8923 (tt) REVERT: R 357 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7564 (t) REVERT: R 367 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.4214 (mmm) REVERT: B 23 LYS cc_start: 0.8462 (pptt) cc_final: 0.8164 (tppt) REVERT: B 37 ILE cc_start: 0.8100 (pt) cc_final: 0.7815 (pt) REVERT: B 57 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8225 (ptpp) REVERT: B 153 ASP cc_start: 0.8476 (p0) cc_final: 0.8130 (m-30) REVERT: B 165 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7338 (t) REVERT: B 172 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7743 (mp0) REVERT: B 215 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8035 (mt-10) REVERT: B 217 MET cc_start: 0.8323 (pmm) cc_final: 0.7670 (tpt) REVERT: B 334 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.9078 (m) REVERT: G 32 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7417 (ptpp) REVERT: G 42 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: P 11 LYS cc_start: 0.7781 (tttm) cc_final: 0.7046 (ttmm) outliers start: 28 outliers final: 19 residues processed: 171 average time/residue: 0.0841 time to fit residues: 20.0199 Evaluate side-chains 177 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.149338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119762 restraints weight = 11071.483| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.47 r_work: 0.3484 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7893 Z= 0.159 Angle : 0.615 8.047 10679 Z= 0.327 Chirality : 0.043 0.157 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.743 63.702 1049 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.92 % Allowed : 22.21 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.27), residues: 937 helix: 1.31 (0.27), residues: 378 sheet: -0.21 (0.34), residues: 221 loop : -1.25 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.014 0.001 TYR R 191 PHE 0.024 0.002 PHE R 359 TRP 0.017 0.001 TRP R 236 HIS 0.005 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7889) covalent geometry : angle 0.61491 (10671) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.60972 ( 8) hydrogen bonds : bond 0.03392 ( 389) hydrogen bonds : angle 4.43000 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1913.42 seconds wall clock time: 33 minutes 27.80 seconds (2007.80 seconds total)