Starting phenix.real_space_refine on Mon Apr 28 13:17:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6niy_9382/04_2025/6niy_9382.cif Found real_map, /net/cci-nas-00/data/ceres_data/6niy_9382/04_2025/6niy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6niy_9382/04_2025/6niy_9382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6niy_9382/04_2025/6niy_9382.map" model { file = "/net/cci-nas-00/data/ceres_data/6niy_9382/04_2025/6niy_9382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6niy_9382/04_2025/6niy_9382.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.54, per 1000 atoms: 0.59 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: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.05 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: 2.16 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.980 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.710 ------------------------------------------------------------------------------- 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 : 5.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.026 0.003 TRP R 236 HIS 0.010 0.002 HIS A 357 PHE 0.024 0.003 PHE B 253 TYR 0.017 0.002 TYR B 59 ARG 0.006 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.25817 ( 389) hydrogen bonds : angle 8.36355 ( 1116) SS BOND : bond 0.00963 ( 4) SS BOND : angle 1.85562 ( 8) covalent geometry : bond 0.00833 ( 7889) covalent geometry : angle 0.99290 (10671) *********************** 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 : 0.947 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: 0.7199 (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: 0.7368 (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: 0.2565 time to fit residues: 73.5536 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 : 0.906 ------------------------------------------------------------------------------- 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 78 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 233 ASN R 395 ASN B 32 GLN G 44 HIS P 3 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.147311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118024 restraints weight = 11116.595| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.53 r_work: 0.3472 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7893 Z= 0.148 Angle : 0.616 7.726 10679 Z= 0.334 Chirality : 0.044 0.169 1198 Planarity : 0.004 0.044 1346 Dihedral : 5.297 50.323 1051 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.14 % Allowed : 13.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 937 helix: 1.32 (0.26), residues: 367 sheet: -0.20 (0.34), residues: 222 loop : -1.98 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.005 0.001 HIS R 277 PHE 0.023 0.002 PHE R 356 TYR 0.012 0.001 TYR R 372 ARG 0.006 0.001 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05165 ( 389) hydrogen bonds : angle 5.24863 ( 1116) SS BOND : bond 0.00380 ( 4) SS BOND : angle 1.43080 ( 8) covalent geometry : bond 0.00310 ( 7889) covalent geometry : angle 0.61517 (10671) *********************** 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: 18 poor density : 195 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.8232 (m) cc_final: 0.8024 (m) REVERT: A 358 TYR cc_start: 0.6512 (t80) cc_final: 0.6134 (t80) REVERT: A 360 TYR cc_start: 0.9116 (m-80) cc_final: 0.8829 (m-80) REVERT: A 378 ASP cc_start: 0.8641 (m-30) cc_final: 0.8080 (m-30) REVERT: A 389 ARG cc_start: 0.8405 (mtp85) cc_final: 0.8190 (mmm160) REVERT: N 34 MET cc_start: 0.8429 (mmp) cc_final: 0.8205 (mmm) REVERT: R 220 LYS cc_start: 0.5827 (mttt) cc_final: 0.5515 (mttm) REVERT: R 291 LEU cc_start: 0.6518 (tp) cc_final: 0.6281 (tp) REVERT: R 338 TYR cc_start: 0.5710 (m-10) cc_final: 0.5319 (m-80) REVERT: R 351 LEU cc_start: 0.9071 (tt) cc_final: 0.8745 (tt) REVERT: B 23 LYS cc_start: 0.8493 (pptt) cc_final: 0.8167 (tppt) REVERT: B 215 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 217 MET cc_start: 0.8443 (ptp) cc_final: 0.7851 (tpt) REVERT: G 20 LYS cc_start: 0.8940 (pttm) cc_final: 0.8715 (pttm) outliers start: 18 outliers final: 8 residues processed: 205 average time/residue: 0.1929 time to fit residues: 52.9149 Evaluate side-chains 168 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 284 TYR Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 277 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 67 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 395 ASN P 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115761 restraints weight = 11351.364| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.57 r_work: 0.3442 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7893 Z= 0.159 Angle : 0.577 7.437 10679 Z= 0.310 Chirality : 0.043 0.163 1198 Planarity : 0.004 0.036 1346 Dihedral : 4.913 50.742 1049 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.16 % Allowed : 15.91 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 937 helix: 1.23 (0.26), residues: 374 sheet: -0.18 (0.34), residues: 223 loop : -1.92 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS R 377 PHE 0.020 0.002 PHE R 356 TYR 0.010 0.001 TYR R 372 ARG 0.004 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 389) hydrogen bonds : angle 4.83421 ( 1116) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.97089 ( 8) covalent geometry : bond 0.00356 ( 7889) covalent geometry : angle 0.57669 (10671) *********************** 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 202 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.853 Fit side-chains REVERT: A 40 THR cc_start: 0.8245 (m) cc_final: 0.8024 (m) REVERT: A 268 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7961 (pp20) REVERT: A 358 TYR cc_start: 0.6661 (t80) cc_final: 0.6275 (t80) REVERT: A 378 ASP cc_start: 0.8652 (m-30) cc_final: 0.8408 (m-30) REVERT: A 392 GLU cc_start: 0.7691 (mp0) cc_final: 0.7476 (mp0) REVERT: R 198 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7532 (mt) REVERT: R 220 LYS cc_start: 0.5897 (mttt) cc_final: 0.5486 (mttm) REVERT: R 346 MET cc_start: 0.5425 (tmm) cc_final: 0.4373 (mmm) REVERT: R 351 LEU cc_start: 0.9052 (tt) cc_final: 0.8666 (tt) REVERT: R 393 PHE cc_start: 0.8020 (m-80) cc_final: 0.7527 (m-80) REVERT: B 23 LYS cc_start: 0.8515 (pptt) cc_final: 0.8286 (tppt) REVERT: B 215 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8270 (mt-10) REVERT: G 11 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7451 (tm-30) REVERT: G 19 LEU cc_start: 0.8551 (mm) cc_final: 0.8339 (mm) REVERT: G 20 LYS cc_start: 0.8974 (pttm) cc_final: 0.8738 (pttm) REVERT: G 62 ARG cc_start: 0.6945 (ttp80) cc_final: 0.5227 (ttp80) outliers start: 35 outliers final: 25 residues processed: 186 average time/residue: 0.1914 time to fit residues: 48.1998 Evaluate side-chains 181 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 198 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 29 THR 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 15 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 7 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 227 GLN R 233 ASN R 277 HIS ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.148327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.118852 restraints weight = 11192.232| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.56 r_work: 0.3482 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7893 Z= 0.114 Angle : 0.540 7.473 10679 Z= 0.288 Chirality : 0.041 0.133 1198 Planarity : 0.003 0.034 1346 Dihedral : 4.765 60.078 1049 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.80 % Allowed : 18.29 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 937 helix: 1.25 (0.26), residues: 380 sheet: -0.01 (0.34), residues: 223 loop : -1.72 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 377 PHE 0.019 0.001 PHE R 359 TYR 0.013 0.001 TYR R 191 ARG 0.005 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 389) hydrogen bonds : angle 4.56324 ( 1116) SS BOND : bond 0.00069 ( 4) SS BOND : angle 0.74923 ( 8) covalent geometry : bond 0.00244 ( 7889) covalent geometry : angle 0.53987 (10671) *********************** 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 199 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7734 (pp20) REVERT: A 358 TYR cc_start: 0.6577 (t80) cc_final: 0.6293 (t80) REVERT: A 378 ASP cc_start: 0.8564 (m-30) cc_final: 0.8314 (m-30) REVERT: R 220 LYS cc_start: 0.5656 (mttt) cc_final: 0.5259 (mttm) REVERT: R 337 MET cc_start: 0.7230 (ppp) cc_final: 0.6624 (ptt) REVERT: R 346 MET cc_start: 0.5532 (tmm) cc_final: 0.4383 (mmm) REVERT: R 351 LEU cc_start: 0.9026 (tt) cc_final: 0.8692 (tt) REVERT: R 357 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7453 (t) REVERT: B 23 LYS cc_start: 0.8448 (pptt) cc_final: 0.8204 (tppt) REVERT: B 37 ILE cc_start: 0.7595 (pt) cc_final: 0.7278 (pt) REVERT: B 153 ASP cc_start: 0.8571 (p0) cc_final: 0.8135 (m-30) REVERT: B 215 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8294 (mt-10) REVERT: B 280 LYS cc_start: 0.8671 (tttt) cc_final: 0.8252 (ttpt) REVERT: G 20 LYS cc_start: 0.8946 (pttm) cc_final: 0.8704 (pttm) REVERT: P 11 LYS cc_start: 0.7859 (tttm) cc_final: 0.7313 (ttmm) outliers start: 32 outliers final: 20 residues processed: 187 average time/residue: 0.2037 time to fit residues: 52.0868 Evaluate side-chains 172 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 395 ASN B 155 ASN P 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.144478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114870 restraints weight = 11274.368| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.54 r_work: 0.3431 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3174 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= 0.177 Angle : 0.587 7.512 10679 Z= 0.312 Chirality : 0.043 0.141 1198 Planarity : 0.004 0.041 1346 Dihedral : 4.949 68.540 1049 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.11 % Allowed : 18.65 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.27), residues: 937 helix: 1.24 (0.26), residues: 378 sheet: -0.11 (0.34), residues: 216 loop : -1.62 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.008 0.001 HIS R 377 PHE 0.022 0.002 PHE R 224 TYR 0.014 0.002 TYR R 191 ARG 0.004 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 389) hydrogen bonds : angle 4.59343 ( 1116) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.79413 ( 8) covalent geometry : bond 0.00403 ( 7889) covalent geometry : angle 0.58642 (10671) *********************** 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 200 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7791 (pp20) REVERT: A 358 TYR cc_start: 0.6706 (t80) cc_final: 0.6370 (t80) REVERT: A 378 ASP cc_start: 0.8512 (m-30) cc_final: 0.8034 (m-30) REVERT: R 187 MET cc_start: 0.7641 (tpt) cc_final: 0.7233 (tpt) REVERT: R 220 LYS cc_start: 0.5795 (mttt) cc_final: 0.5384 (mttm) REVERT: R 337 MET cc_start: 0.7296 (ppp) cc_final: 0.6594 (ptt) REVERT: R 346 MET cc_start: 0.5457 (tmm) cc_final: 0.4195 (mmm) REVERT: R 351 LEU cc_start: 0.9098 (tt) cc_final: 0.8737 (tt) REVERT: R 357 VAL cc_start: 0.7825 (OUTLIER) cc_final: 0.7560 (t) REVERT: R 367 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.3947 (mmm) REVERT: R 393 PHE cc_start: 0.7905 (m-80) cc_final: 0.7403 (m-80) REVERT: B 23 LYS cc_start: 0.8481 (pptt) cc_final: 0.8214 (tppt) REVERT: B 37 ILE cc_start: 0.7836 (pt) cc_final: 0.7484 (pt) REVERT: B 153 ASP cc_start: 0.8555 (p0) cc_final: 0.8184 (m-30) REVERT: B 217 MET cc_start: 0.8442 (ptp) cc_final: 0.7974 (tpt) REVERT: B 334 SER cc_start: 0.9330 (OUTLIER) cc_final: 0.9077 (m) REVERT: G 19 LEU cc_start: 0.8526 (mm) cc_final: 0.8299 (mm) REVERT: G 20 LYS cc_start: 0.8960 (pttm) cc_final: 0.8708 (pttm) REVERT: P 11 LYS cc_start: 0.7986 (tttm) cc_final: 0.7322 (ttmm) outliers start: 43 outliers final: 25 residues processed: 187 average time/residue: 0.1906 time to fit residues: 48.5079 Evaluate side-chains 183 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 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 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP 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 334 SER Chi-restraints excluded: chain B residue 336 LEU 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 88 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 227 GLN R 277 HIS R 412 GLN B 266 HIS B 340 ASN P 3 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.152034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122613 restraints weight = 10972.370| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.51 r_work: 0.3522 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7893 Z= 0.113 Angle : 0.540 7.743 10679 Z= 0.287 Chirality : 0.041 0.132 1198 Planarity : 0.003 0.037 1346 Dihedral : 4.788 69.229 1049 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.51 % Allowed : 19.83 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 937 helix: 1.44 (0.26), residues: 375 sheet: -0.07 (0.34), residues: 219 loop : -1.39 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS R 377 PHE 0.020 0.001 PHE R 359 TYR 0.012 0.001 TYR R 191 ARG 0.002 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 389) hydrogen bonds : angle 4.39973 ( 1116) SS BOND : bond 0.00092 ( 4) SS BOND : angle 0.74303 ( 8) covalent geometry : bond 0.00245 ( 7889) covalent geometry : angle 0.53933 (10671) *********************** 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: 38 poor density : 160 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7508 (pp20) REVERT: A 358 TYR cc_start: 0.6667 (t80) cc_final: 0.6428 (t80) REVERT: A 378 ASP cc_start: 0.8528 (m-30) cc_final: 0.8291 (m-30) REVERT: R 187 MET cc_start: 0.7752 (tpt) cc_final: 0.7430 (tpt) REVERT: R 220 LYS cc_start: 0.5572 (mttt) cc_final: 0.5162 (mttm) REVERT: R 291 LEU cc_start: 0.6797 (tp) cc_final: 0.6480 (tp) REVERT: R 337 MET cc_start: 0.7267 (ppp) cc_final: 0.6540 (ptt) REVERT: R 346 MET cc_start: 0.5467 (tmm) cc_final: 0.4184 (mmm) REVERT: R 351 LEU cc_start: 0.9154 (tt) cc_final: 0.8790 (tt) REVERT: R 357 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7508 (t) REVERT: R 367 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.3948 (mmm) REVERT: B 23 LYS cc_start: 0.8431 (pptt) cc_final: 0.8198 (tppt) REVERT: B 37 ILE cc_start: 0.7857 (pt) cc_final: 0.7489 (pt) REVERT: B 57 LYS cc_start: 0.8676 (pttp) cc_final: 0.8473 (ptpp) REVERT: B 75 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6755 (pt0) REVERT: B 153 ASP cc_start: 0.8447 (p0) cc_final: 0.8243 (m-30) REVERT: B 215 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 280 LYS cc_start: 0.8667 (tttt) cc_final: 0.8298 (ttpt) REVERT: B 334 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.9071 (m) REVERT: G 19 LEU cc_start: 0.8511 (mm) cc_final: 0.8275 (mm) REVERT: G 20 LYS cc_start: 0.8950 (pttm) cc_final: 0.8701 (pttm) REVERT: G 42 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7286 (pt0) REVERT: P 11 LYS cc_start: 0.7940 (tttm) cc_final: 0.7242 (ttmm) outliers start: 38 outliers final: 23 residues processed: 182 average time/residue: 0.1833 time to fit residues: 45.4069 Evaluate side-chains 178 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 75 GLN 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 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 85 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN P 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.151645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.122266 restraints weight = 11061.262| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.49 r_work: 0.3521 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7893 Z= 0.114 Angle : 0.537 8.063 10679 Z= 0.286 Chirality : 0.041 0.138 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.866 77.506 1049 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.87 % Allowed : 20.43 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 937 helix: 1.53 (0.27), residues: 371 sheet: -0.17 (0.33), residues: 223 loop : -1.29 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 236 HIS 0.005 0.001 HIS R 377 PHE 0.020 0.001 PHE R 359 TYR 0.012 0.001 TYR R 191 ARG 0.002 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 389) hydrogen bonds : angle 4.33914 ( 1116) SS BOND : bond 0.00108 ( 4) SS BOND : angle 0.61840 ( 8) covalent geometry : bond 0.00249 ( 7889) covalent geometry : angle 0.53737 (10671) *********************** 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 199 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7507 (pp20) REVERT: A 358 TYR cc_start: 0.6637 (t80) cc_final: 0.6317 (t80) REVERT: A 378 ASP cc_start: 0.8483 (m-30) cc_final: 0.8236 (m-30) REVERT: R 187 MET cc_start: 0.7818 (tpt) cc_final: 0.7445 (tpt) REVERT: R 198 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7650 (mt) REVERT: R 220 LYS cc_start: 0.5557 (mttt) cc_final: 0.5191 (mttm) REVERT: R 291 LEU cc_start: 0.6809 (tp) cc_final: 0.6471 (tp) REVERT: R 337 MET cc_start: 0.7226 (ppp) cc_final: 0.6416 (ptt) REVERT: R 346 MET cc_start: 0.5442 (tmm) cc_final: 0.4219 (mmm) REVERT: R 351 LEU cc_start: 0.9162 (tt) cc_final: 0.8800 (tt) REVERT: R 357 VAL cc_start: 0.7787 (OUTLIER) cc_final: 0.7512 (t) REVERT: R 367 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.4054 (mmm) REVERT: B 23 LYS cc_start: 0.8401 (pptt) cc_final: 0.8165 (tppt) REVERT: B 37 ILE cc_start: 0.7929 (pt) cc_final: 0.7588 (pt) REVERT: B 75 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6633 (pt0) REVERT: B 101 MET cc_start: 0.8157 (mmm) cc_final: 0.7831 (mmm) REVERT: B 165 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7288 (t) REVERT: B 215 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8088 (mt-10) REVERT: B 217 MET cc_start: 0.8305 (pmm) cc_final: 0.7736 (tpt) REVERT: B 280 LYS cc_start: 0.8640 (tttt) cc_final: 0.8422 (ttpt) REVERT: G 19 LEU cc_start: 0.8503 (mm) cc_final: 0.8241 (mm) REVERT: G 20 LYS cc_start: 0.8944 (pttm) cc_final: 0.8688 (pttm) REVERT: G 42 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7297 (pt0) REVERT: P 11 LYS cc_start: 0.7964 (tttm) cc_final: 0.7246 (ttmm) outliers start: 41 outliers final: 23 residues processed: 182 average time/residue: 0.1889 time to fit residues: 47.0627 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 : 0.822 ------------------------------------------------------------------------------- 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 37 VAL 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 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 10 GLU 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 G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.151702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.122364 restraints weight = 11117.616| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.49 r_work: 0.3523 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7893 Z= 0.124 Angle : 0.555 8.448 10679 Z= 0.297 Chirality : 0.041 0.139 1198 Planarity : 0.003 0.033 1346 Dihedral : 5.027 89.012 1049 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.16 % Allowed : 21.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 937 helix: 1.42 (0.27), residues: 377 sheet: -0.10 (0.34), residues: 223 loop : -1.26 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.004 0.001 HIS R 377 PHE 0.023 0.002 PHE R 359 TYR 0.011 0.001 TYR R 191 ARG 0.002 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 389) hydrogen bonds : angle 4.30875 ( 1116) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.61625 ( 8) covalent geometry : bond 0.00278 ( 7889) covalent geometry : angle 0.55515 (10671) *********************** 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 189 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7543 (pp20) REVERT: A 358 TYR cc_start: 0.6653 (t80) cc_final: 0.6340 (t80) REVERT: A 378 ASP cc_start: 0.8484 (m-30) cc_final: 0.8234 (m-30) REVERT: R 187 MET cc_start: 0.7876 (tpt) cc_final: 0.7474 (tpt) REVERT: R 198 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7649 (mt) REVERT: R 220 LYS cc_start: 0.5556 (mttt) cc_final: 0.5194 (mttm) REVERT: R 291 LEU cc_start: 0.6833 (tp) cc_final: 0.6481 (tp) REVERT: R 346 MET cc_start: 0.5424 (tmm) cc_final: 0.4193 (mmm) REVERT: R 351 LEU cc_start: 0.9191 (tt) cc_final: 0.8845 (tt) REVERT: R 357 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7568 (t) REVERT: R 367 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.4081 (mmm) REVERT: R 397 GLU cc_start: 0.8115 (pm20) cc_final: 0.7888 (pm20) REVERT: B 23 LYS cc_start: 0.8476 (pptt) cc_final: 0.8216 (tppt) REVERT: B 37 ILE cc_start: 0.8025 (pt) cc_final: 0.7726 (pt) REVERT: B 59 TYR cc_start: 0.8966 (m-80) cc_final: 0.8686 (m-80) REVERT: B 75 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6658 (pt0) REVERT: B 101 MET cc_start: 0.8216 (mmm) cc_final: 0.7829 (mmm) REVERT: B 165 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7339 (t) REVERT: B 215 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 217 MET cc_start: 0.8239 (pmm) cc_final: 0.7655 (tpt) REVERT: B 280 LYS cc_start: 0.8685 (tttt) cc_final: 0.8482 (ttpt) REVERT: G 19 LEU cc_start: 0.8595 (mm) cc_final: 0.8370 (mm) REVERT: G 20 LYS cc_start: 0.8944 (pttm) cc_final: 0.8694 (pttm) REVERT: G 32 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7418 (ptpp) REVERT: G 42 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7321 (pt0) REVERT: P 11 LYS cc_start: 0.7833 (tttm) cc_final: 0.7116 (ttmm) outliers start: 35 outliers final: 20 residues processed: 173 average time/residue: 0.1900 time to fit residues: 44.7004 Evaluate side-chains 175 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 37 VAL 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 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 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 G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122274 restraints weight = 11187.189| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.51 r_work: 0.3519 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7893 Z= 0.122 Angle : 0.554 7.946 10679 Z= 0.293 Chirality : 0.041 0.140 1198 Planarity : 0.003 0.034 1346 Dihedral : 4.848 80.149 1049 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.16 % Allowed : 21.85 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 937 helix: 1.47 (0.27), residues: 378 sheet: -0.08 (0.34), residues: 223 loop : -1.16 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 332 HIS 0.005 0.001 HIS B 266 PHE 0.023 0.001 PHE R 359 TYR 0.012 0.001 TYR R 191 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 389) hydrogen bonds : angle 4.28767 ( 1116) SS BOND : bond 0.00119 ( 4) SS BOND : angle 0.60127 ( 8) covalent geometry : bond 0.00273 ( 7889) covalent geometry : angle 0.55369 (10671) *********************** 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 186 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7916 (ptpt) REVERT: A 268 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7551 (pp20) REVERT: A 358 TYR cc_start: 0.6655 (t80) cc_final: 0.6332 (t80) REVERT: A 378 ASP cc_start: 0.8465 (m-30) cc_final: 0.8008 (m-30) REVERT: R 187 MET cc_start: 0.7893 (tpt) cc_final: 0.7473 (tpt) REVERT: R 198 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7648 (mt) REVERT: R 220 LYS cc_start: 0.5597 (mttt) cc_final: 0.5245 (mttm) REVERT: R 291 LEU cc_start: 0.6784 (tp) cc_final: 0.6435 (tp) REVERT: R 306 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7899 (mmt) REVERT: R 346 MET cc_start: 0.5430 (tmm) cc_final: 0.4383 (mmm) REVERT: R 351 LEU cc_start: 0.9191 (tt) cc_final: 0.8909 (tt) REVERT: R 357 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7555 (t) REVERT: R 367 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.4110 (mmm) REVERT: B 23 LYS cc_start: 0.8471 (pptt) cc_final: 0.8206 (tppt) REVERT: B 37 ILE cc_start: 0.8099 (pt) cc_final: 0.7804 (pt) REVERT: B 101 MET cc_start: 0.8262 (mmm) cc_final: 0.7844 (mmm) REVERT: B 165 THR cc_start: 0.7573 (OUTLIER) cc_final: 0.7331 (t) REVERT: B 215 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 217 MET cc_start: 0.8259 (pmm) cc_final: 0.7595 (tpt) REVERT: B 334 SER cc_start: 0.9380 (OUTLIER) cc_final: 0.9136 (m) REVERT: G 19 LEU cc_start: 0.8589 (mm) cc_final: 0.8364 (mm) REVERT: G 20 LYS cc_start: 0.8947 (pttm) cc_final: 0.8689 (pttm) REVERT: G 32 LYS cc_start: 0.7818 (mtmm) cc_final: 0.7439 (ptpp) REVERT: G 42 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7322 (pt0) REVERT: P 11 LYS cc_start: 0.7841 (tttm) cc_final: 0.7067 (ttmm) outliers start: 35 outliers final: 23 residues processed: 172 average time/residue: 0.1906 time to fit residues: 44.8633 Evaluate side-chains 179 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 37 VAL 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 301 ILE Chi-restraints excluded: chain R residue 306 MET 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 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 54 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN P 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113900 restraints weight = 11292.354| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.50 r_work: 0.3413 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3679 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= 0.196 Angle : 0.627 7.988 10679 Z= 0.335 Chirality : 0.044 0.164 1198 Planarity : 0.004 0.040 1346 Dihedral : 5.157 81.621 1049 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.39 % Allowed : 21.97 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.27), residues: 937 helix: 1.28 (0.26), residues: 379 sheet: -0.27 (0.34), residues: 219 loop : -1.21 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 332 HIS 0.006 0.001 HIS R 377 PHE 0.026 0.002 PHE R 359 TYR 0.015 0.002 TYR R 191 ARG 0.003 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 389) hydrogen bonds : angle 4.51464 ( 1116) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.69339 ( 8) covalent geometry : bond 0.00450 ( 7889) covalent geometry : angle 0.62670 (10671) ********************** 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 193 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7635 (pp20) REVERT: A 358 TYR cc_start: 0.6800 (t80) cc_final: 0.6475 (t80) REVERT: N 53 GLN cc_start: 0.8302 (mp10) cc_final: 0.8049 (pt0) REVERT: R 187 MET cc_start: 0.7860 (tpt) cc_final: 0.7401 (tpt) REVERT: R 198 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7657 (mt) REVERT: R 220 LYS cc_start: 0.5719 (mttt) cc_final: 0.5339 (mttm) REVERT: R 291 LEU cc_start: 0.6856 (tp) cc_final: 0.6504 (tp) REVERT: R 306 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7934 (mmt) REVERT: R 351 LEU cc_start: 0.9191 (tt) cc_final: 0.8874 (tt) REVERT: R 357 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7650 (t) REVERT: B 23 LYS cc_start: 0.8451 (pptt) cc_final: 0.8155 (tppt) REVERT: B 37 ILE cc_start: 0.8102 (pt) cc_final: 0.7786 (pt) REVERT: B 57 LYS cc_start: 0.8718 (ptpp) cc_final: 0.8406 (ptpp) REVERT: B 215 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8070 (mt-10) REVERT: B 217 MET cc_start: 0.8345 (pmm) cc_final: 0.7663 (tpt) REVERT: B 334 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.9156 (m) REVERT: G 20 LYS cc_start: 0.8966 (pttm) cc_final: 0.8705 (pttm) REVERT: G 32 LYS cc_start: 0.7928 (mtmm) cc_final: 0.7656 (ptpp) REVERT: G 42 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: P 11 LYS cc_start: 0.7762 (tttm) cc_final: 0.7009 (ttmm) outliers start: 37 outliers final: 24 residues processed: 178 average time/residue: 0.1965 time to fit residues: 48.1230 Evaluate side-chains 181 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 A residue 394 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 64 VAL 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 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 301 ILE Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 357 VAL 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 17 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 B 340 ASN P 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.148686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119082 restraints weight = 11191.240| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.52 r_work: 0.3502 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7893 Z= 0.122 Angle : 0.585 8.998 10679 Z= 0.311 Chirality : 0.042 0.207 1198 Planarity : 0.003 0.034 1346 Dihedral : 4.995 80.389 1049 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.92 % Allowed : 22.80 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.27), residues: 937 helix: 1.46 (0.27), residues: 377 sheet: -0.19 (0.34), residues: 224 loop : -1.08 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 332 HIS 0.004 0.001 HIS R 377 PHE 0.025 0.001 PHE R 359 TYR 0.013 0.001 TYR R 191 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 389) hydrogen bonds : angle 4.41254 ( 1116) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.58266 ( 8) covalent geometry : bond 0.00272 ( 7889) covalent geometry : angle 0.58491 (10671) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3682.63 seconds wall clock time: 64 minutes 9.45 seconds (3849.45 seconds total)