Starting phenix.real_space_refine on Wed Feb 12 08:26:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6niy_9382/02_2025/6niy_9382.cif Found real_map, /net/cci-nas-00/data/ceres_data/6niy_9382/02_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_9382/02_2025/6niy_9382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6niy_9382/02_2025/6niy_9382.map" model { file = "/net/cci-nas-00/data/ceres_data/6niy_9382/02_2025/6niy_9382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6niy_9382/02_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-5592/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: 4.67, per 1000 atoms: 0.60 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: 1.81 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: 0.89 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: 2.38 Time building geometry restraints manager: 2.10 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: 0.250 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- 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 7889 Z= 0.542 Angle : 0.993 10.835 10671 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 *********************** 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 : 0.786 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: 0.2615 time to fit residues: 74.9669 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 : 0.854 ------------------------------------------------------------------------------- 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 = 0.118025 restraints weight = 11116.655| |-----------------------------------------------------------------------------| 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 7889 Z= 0.205 Angle : 0.615 7.726 10671 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 *********************** 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 : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.8230 (m) cc_final: 0.8022 (m) REVERT: A 358 TYR cc_start: 0.6513 (t80) cc_final: 0.6135 (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: 0.8404 (mtp85) cc_final: 0.8189 (mmm160) REVERT: N 34 MET cc_start: 0.8429 (mmp) cc_final: 0.8207 (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: 0.6280 (tp) REVERT: R 338 TYR cc_start: 0.5709 (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: 0.8446 (mt-10) cc_final: 0.8027 (mt-10) REVERT: B 217 MET cc_start: 0.8442 (ptp) cc_final: 0.7851 (tpt) REVERT: G 20 LYS cc_start: 0.8940 (pttm) cc_final: 0.8714 (pttm) outliers start: 18 outliers final: 8 residues processed: 205 average time/residue: 0.2074 time to fit residues: 56.9646 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 : 0.865 ------------------------------------------------------------------------------- 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: 0.5980 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 233 ASN ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.143909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114445 restraints weight = 11413.840| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.57 r_work: 0.3419 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7889 Z= 0.286 Angle : 0.604 7.406 10671 Z= 0.324 Chirality : 0.044 0.164 1198 Planarity : 0.004 0.036 1346 Dihedral : 5.011 52.161 1049 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.16 % Allowed : 16.15 % Favored : 79.69 % 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: -0.44 (0.26), residues: 937 helix: 1.15 (0.26), residues: 374 sheet: -0.25 (0.34), residues: 223 loop : -1.95 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.005 0.001 HIS R 377 PHE 0.019 0.002 PHE R 356 TYR 0.011 0.002 TYR R 372 ARG 0.005 0.000 ARG N 19 *********************** 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 200 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.985 Fit side-chains REVERT: A 40 THR cc_start: 0.8260 (m) cc_final: 0.8038 (m) REVERT: A 233 LYS cc_start: 0.8419 (mttt) cc_final: 0.8114 (mttt) REVERT: A 268 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7972 (pp20) REVERT: A 358 TYR cc_start: 0.6685 (t80) cc_final: 0.6143 (t80) REVERT: A 360 TYR cc_start: 0.9153 (m-80) cc_final: 0.8689 (m-80) REVERT: A 392 GLU cc_start: 0.7807 (mp0) cc_final: 0.7599 (mp0) REVERT: R 220 LYS cc_start: 0.5947 (mttt) cc_final: 0.5525 (mttm) REVERT: R 346 MET cc_start: 0.5426 (tmm) cc_final: 0.4352 (mmm) REVERT: R 351 LEU cc_start: 0.9054 (tt) cc_final: 0.8649 (tt) REVERT: R 393 PHE cc_start: 0.8029 (m-80) cc_final: 0.7525 (m-80) REVERT: B 23 LYS cc_start: 0.8508 (pptt) cc_final: 0.8269 (tppt) REVERT: G 20 LYS cc_start: 0.8980 (pttm) cc_final: 0.8740 (pttm) REVERT: G 62 ARG cc_start: 0.6948 (ttp80) cc_final: 0.5236 (ttp80) outliers start: 35 outliers final: 25 residues processed: 186 average time/residue: 0.1952 time to fit residues: 48.7803 Evaluate side-chains 181 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 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 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 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: 1.9990 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 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 ** 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 377 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 = 0.3932 r_free = 0.3932 target = 0.147183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117731 restraints weight = 11222.446| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.55 r_work: 0.3468 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7889 Z= 0.171 Angle : 0.547 7.363 10671 Z= 0.293 Chirality : 0.042 0.135 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.879 64.652 1049 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.04 % Allowed : 17.93 % Favored : 78.03 % 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: -0.20 (0.26), residues: 937 helix: 1.24 (0.26), residues: 377 sheet: -0.06 (0.33), residues: 221 loop : -1.75 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.005 0.001 HIS R 377 PHE 0.018 0.001 PHE R 356 TYR 0.013 0.001 TYR R 191 ARG 0.004 0.000 ARG A 389 *********************** 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 202 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LYS cc_start: 0.8462 (mttt) cc_final: 0.8151 (mtpt) REVERT: A 268 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7733 (pp20) REVERT: A 358 TYR cc_start: 0.6614 (t80) cc_final: 0.6197 (t80) REVERT: R 198 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7523 (mt) REVERT: R 220 LYS cc_start: 0.5736 (mttt) cc_final: 0.5332 (mttm) REVERT: R 329 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6752 (mm-30) REVERT: R 337 MET cc_start: 0.7214 (ppp) cc_final: 0.6583 (ptt) REVERT: R 346 MET cc_start: 0.5420 (tmm) cc_final: 0.4282 (mmm) REVERT: R 351 LEU cc_start: 0.9019 (tt) cc_final: 0.8700 (tt) REVERT: R 357 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7510 (t) REVERT: R 393 PHE cc_start: 0.7933 (m-80) cc_final: 0.7432 (m-80) REVERT: B 37 ILE cc_start: 0.7633 (pt) cc_final: 0.7317 (pt) REVERT: B 153 ASP cc_start: 0.8586 (p0) cc_final: 0.8124 (m-30) REVERT: B 217 MET cc_start: 0.8509 (ptp) cc_final: 0.7956 (tpt) REVERT: B 280 LYS cc_start: 0.8681 (tttt) cc_final: 0.8262 (ttpt) REVERT: G 19 LEU cc_start: 0.8422 (mm) cc_final: 0.8200 (mm) REVERT: G 20 LYS cc_start: 0.8957 (pttm) cc_final: 0.8721 (pttm) REVERT: P 11 LYS cc_start: 0.7892 (tttm) cc_final: 0.7346 (ttmm) outliers start: 34 outliers final: 21 residues processed: 188 average time/residue: 0.2028 time to fit residues: 51.8509 Evaluate side-chains 175 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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 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 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: 5.9990 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 0.0050 chunk 50 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 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 = 0.3873 r_free = 0.3873 target = 0.142070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112493 restraints weight = 11388.902| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.54 r_work: 0.3392 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7889 Z= 0.333 Angle : 0.627 7.605 10671 Z= 0.333 Chirality : 0.044 0.145 1198 Planarity : 0.004 0.039 1346 Dihedral : 5.200 73.274 1049 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 6.06 % Allowed : 18.05 % Favored : 75.89 % 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: -0.36 (0.26), residues: 937 helix: 1.13 (0.26), residues: 375 sheet: -0.40 (0.33), residues: 217 loop : -1.65 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 290 HIS 0.008 0.001 HIS R 377 PHE 0.021 0.002 PHE R 224 TYR 0.015 0.002 TYR R 191 ARG 0.004 0.000 ARG N 19 *********************** 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 208 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7799 (pp20) REVERT: A 358 TYR cc_start: 0.6751 (t80) cc_final: 0.6424 (t80) REVERT: R 187 MET cc_start: 0.7695 (tpt) cc_final: 0.7391 (tpt) REVERT: R 198 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7705 (mt) REVERT: R 337 MET cc_start: 0.7285 (ppp) cc_final: 0.6633 (ptt) REVERT: R 346 MET cc_start: 0.5437 (tmm) cc_final: 0.4204 (mmm) REVERT: R 351 LEU cc_start: 0.9109 (tt) cc_final: 0.8737 (tt) REVERT: R 357 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7593 (t) REVERT: R 367 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.4010 (mmm) REVERT: R 393 PHE cc_start: 0.7987 (m-80) cc_final: 0.7497 (m-80) REVERT: B 153 ASP cc_start: 0.8631 (p0) cc_final: 0.8262 (m-30) REVERT: B 334 SER cc_start: 0.9332 (OUTLIER) cc_final: 0.9080 (m) REVERT: G 11 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7278 (tm-30) REVERT: G 20 LYS cc_start: 0.8974 (pttm) cc_final: 0.8733 (pttm) REVERT: G 42 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7432 (pt0) REVERT: P 11 LYS cc_start: 0.7992 (tttm) cc_final: 0.7349 (ttmm) outliers start: 51 outliers final: 33 residues processed: 190 average time/residue: 0.1857 time to fit residues: 48.3247 Evaluate side-chains 189 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 71 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 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 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 186 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain P residue 3 ASN 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: 6.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN P 3 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.145314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116073 restraints weight = 11161.851| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.53 r_work: 0.3448 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7889 Z= 0.179 Angle : 0.553 7.395 10671 Z= 0.294 Chirality : 0.042 0.137 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.994 73.181 1049 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.75 % Allowed : 20.43 % Favored : 74.82 % 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: -0.03 (0.27), residues: 937 helix: 1.43 (0.26), residues: 371 sheet: -0.28 (0.33), residues: 218 loop : -1.43 (0.31), residues: 348 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 0.019 0.001 PHE R 359 TYR 0.013 0.001 TYR R 191 ARG 0.003 0.000 ARG N 19 *********************** 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 197 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7642 (pp20) REVERT: A 358 TYR cc_start: 0.6712 (t80) cc_final: 0.6457 (t80) REVERT: R 187 MET cc_start: 0.7700 (tpt) cc_final: 0.7342 (tpt) REVERT: R 198 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7681 (mt) REVERT: R 291 LEU cc_start: 0.6868 (tp) cc_final: 0.6532 (tp) REVERT: R 306 MET cc_start: 0.8210 (tpt) cc_final: 0.7985 (mmt) REVERT: R 337 MET cc_start: 0.7266 (ppp) cc_final: 0.6550 (ptt) REVERT: R 346 MET cc_start: 0.5448 (tmm) cc_final: 0.4443 (mmm) REVERT: R 351 LEU cc_start: 0.9155 (tt) cc_final: 0.8783 (tt) REVERT: R 357 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7601 (t) REVERT: R 367 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.4034 (mmm) REVERT: B 37 ILE cc_start: 0.7905 (pt) cc_final: 0.7526 (pt) REVERT: B 153 ASP cc_start: 0.8515 (p0) cc_final: 0.8263 (m-30) REVERT: B 217 MET cc_start: 0.8484 (ptp) cc_final: 0.7985 (tpt) REVERT: B 334 SER cc_start: 0.9331 (OUTLIER) cc_final: 0.9067 (m) REVERT: G 19 LEU cc_start: 0.8460 (mm) cc_final: 0.8245 (mm) REVERT: G 20 LYS cc_start: 0.8960 (pttm) cc_final: 0.8706 (pttm) REVERT: P 11 LYS cc_start: 0.7884 (tttm) cc_final: 0.7248 (ttmm) outliers start: 40 outliers final: 29 residues processed: 182 average time/residue: 0.1824 time to fit residues: 45.4613 Evaluate side-chains 181 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 85 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 0.0070 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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** B 155 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 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 = 0.3972 r_free = 0.3972 target = 0.150946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121656 restraints weight = 11008.120| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.49 r_work: 0.3509 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7889 Z= 0.158 Angle : 0.543 7.734 10671 Z= 0.289 Chirality : 0.041 0.136 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.821 70.740 1049 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.51 % Allowed : 21.97 % Favored : 73.52 % 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: 1.55 (0.27), residues: 371 sheet: -0.17 (0.33), residues: 219 loop : -1.41 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 236 HIS 0.005 0.001 HIS B 266 PHE 0.026 0.001 PHE R 224 TYR 0.013 0.001 TYR R 191 ARG 0.002 0.000 ARG N 19 *********************** 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 192 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: A 358 TYR cc_start: 0.6796 (t80) cc_final: 0.6536 (t80) REVERT: A 378 ASP cc_start: 0.8413 (m-30) cc_final: 0.8051 (m-30) REVERT: R 187 MET cc_start: 0.7778 (tpt) cc_final: 0.7411 (tpt) REVERT: R 198 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7708 (mt) REVERT: R 291 LEU cc_start: 0.6870 (tp) cc_final: 0.6528 (tp) REVERT: R 306 MET cc_start: 0.8265 (tpt) cc_final: 0.8045 (mmt) REVERT: R 337 MET cc_start: 0.7255 (ppp) cc_final: 0.6467 (ptt) REVERT: R 346 MET cc_start: 0.5557 (tmm) cc_final: 0.4503 (mmm) REVERT: R 351 LEU cc_start: 0.9178 (tt) cc_final: 0.8803 (tt) REVERT: R 357 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7663 (t) REVERT: R 367 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.4090 (mmm) REVERT: R 377 HIS cc_start: 0.7612 (m90) cc_final: 0.6881 (m90) REVERT: B 37 ILE cc_start: 0.7953 (pt) cc_final: 0.7615 (pt) REVERT: B 217 MET cc_start: 0.8628 (ptp) cc_final: 0.8045 (tpt) REVERT: B 334 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9075 (m) REVERT: G 19 LEU cc_start: 0.8495 (mm) cc_final: 0.8248 (mm) REVERT: G 20 LYS cc_start: 0.8969 (pttm) cc_final: 0.8713 (pttm) REVERT: G 42 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7356 (pt0) REVERT: P 11 LYS cc_start: 0.7936 (tttm) cc_final: 0.7230 (ttmm) outliers start: 38 outliers final: 24 residues processed: 175 average time/residue: 0.1809 time to fit residues: 43.2941 Evaluate side-chains 177 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 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 B 155 ASN B 266 HIS P 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.151601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.122322 restraints weight = 11091.281| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.51 r_work: 0.3519 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7889 Z= 0.165 Angle : 0.547 9.974 10671 Z= 0.289 Chirality : 0.041 0.137 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.660 66.862 1049 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.39 % Allowed : 22.33 % 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: 1.66 (0.27), residues: 371 sheet: -0.14 (0.33), residues: 221 loop : -1.32 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.005 0.001 HIS R 377 PHE 0.021 0.001 PHE R 359 TYR 0.010 0.001 TYR R 191 ARG 0.002 0.000 ARG N 19 *********************** 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 198 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7539 (pp20) REVERT: A 358 TYR cc_start: 0.6650 (t80) cc_final: 0.6397 (t80) REVERT: R 187 MET cc_start: 0.7714 (tpt) cc_final: 0.7329 (tpt) REVERT: R 198 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7691 (mt) REVERT: R 220 LYS cc_start: 0.5647 (mttt) cc_final: 0.5256 (mttm) REVERT: R 291 LEU cc_start: 0.6870 (tp) cc_final: 0.6485 (tp) REVERT: R 346 MET cc_start: 0.5434 (tmm) cc_final: 0.4384 (mmm) REVERT: R 351 LEU cc_start: 0.9185 (tt) cc_final: 0.8835 (tt) REVERT: R 357 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7563 (t) REVERT: R 367 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.4102 (mmm) REVERT: B 37 ILE cc_start: 0.7985 (pt) cc_final: 0.7666 (pt) REVERT: B 153 ASP cc_start: 0.8522 (p0) cc_final: 0.8191 (m-30) REVERT: B 165 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7360 (t) REVERT: B 215 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8374 (pt0) REVERT: G 19 LEU cc_start: 0.8486 (mm) cc_final: 0.8224 (mm) REVERT: G 20 LYS cc_start: 0.8941 (pttm) cc_final: 0.8679 (pttm) REVERT: G 32 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7462 (ptpp) REVERT: G 42 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7217 (pt0) REVERT: P 11 LYS cc_start: 0.7756 (tttm) cc_final: 0.7081 (ttmm) outliers start: 37 outliers final: 22 residues processed: 181 average time/residue: 0.1886 time to fit residues: 46.3210 Evaluate side-chains 183 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 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 331 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: 1.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.0070 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.151899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122634 restraints weight = 11153.240| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.51 r_work: 0.3523 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7889 Z= 0.172 Angle : 0.560 9.182 10671 Z= 0.296 Chirality : 0.041 0.163 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.623 64.517 1049 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: 0.25 (0.27), residues: 937 helix: 1.60 (0.27), residues: 377 sheet: -0.14 (0.34), residues: 223 loop : -1.24 (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 0.028 0.002 PHE R 224 TYR 0.011 0.001 TYR R 191 ARG 0.002 0.000 ARG N 19 *********************** 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 188 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7519 (pp20) REVERT: A 358 TYR cc_start: 0.6651 (t80) cc_final: 0.6312 (t80) REVERT: R 187 MET cc_start: 0.7691 (tpt) cc_final: 0.7281 (tpt) REVERT: R 198 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7688 (mt) REVERT: R 220 LYS cc_start: 0.5640 (mttt) cc_final: 0.5265 (mttm) REVERT: R 291 LEU cc_start: 0.6855 (tp) cc_final: 0.6451 (tp) REVERT: R 346 MET cc_start: 0.5421 (tmm) cc_final: 0.4359 (mmm) REVERT: R 351 LEU cc_start: 0.9189 (tt) cc_final: 0.8887 (tt) REVERT: R 357 VAL cc_start: 0.7835 (OUTLIER) cc_final: 0.7546 (t) REVERT: R 367 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.4112 (mmm) REVERT: R 397 GLU cc_start: 0.8242 (pm20) cc_final: 0.8021 (pm20) REVERT: B 37 ILE cc_start: 0.8025 (pt) cc_final: 0.7737 (pt) REVERT: B 101 MET cc_start: 0.8464 (mmm) cc_final: 0.8170 (mmm) REVERT: B 153 ASP cc_start: 0.8498 (p0) cc_final: 0.8209 (m-30) REVERT: B 165 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7376 (t) REVERT: B 217 MET cc_start: 0.8402 (ptp) cc_final: 0.7974 (tpt) REVERT: B 334 SER cc_start: 0.9391 (OUTLIER) cc_final: 0.9179 (m) REVERT: G 19 LEU cc_start: 0.8499 (mm) cc_final: 0.8239 (mm) REVERT: G 20 LYS cc_start: 0.8929 (pttm) cc_final: 0.8671 (pttm) REVERT: G 32 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7511 (ptpp) REVERT: G 42 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7556 (pt0) REVERT: P 11 LYS cc_start: 0.7818 (tttm) cc_final: 0.7119 (ttmm) outliers start: 33 outliers final: 24 residues processed: 175 average time/residue: 0.2057 time to fit residues: 49.3482 Evaluate side-chains 180 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 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: 7.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.0030 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 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 = 0.3960 r_free = 0.3960 target = 0.149898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120506 restraints weight = 11061.691| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.51 r_work: 0.3524 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7889 Z= 0.172 Angle : 0.552 8.966 10671 Z= 0.293 Chirality : 0.041 0.160 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.582 62.243 1049 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.80 % Allowed : 23.16 % Favored : 73.04 % 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 (0.27), residues: 937 helix: 1.66 (0.27), residues: 378 sheet: -0.10 (0.34), residues: 223 loop : -1.17 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.005 0.001 HIS B 266 PHE 0.025 0.001 PHE R 359 TYR 0.012 0.001 TYR R 191 ARG 0.002 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7562 (pp20) REVERT: A 358 TYR cc_start: 0.6675 (t80) cc_final: 0.6338 (t80) REVERT: R 187 MET cc_start: 0.7679 (tpt) cc_final: 0.7266 (tpt) REVERT: R 220 LYS cc_start: 0.5587 (mttt) cc_final: 0.5244 (mttm) REVERT: R 291 LEU cc_start: 0.6870 (tp) cc_final: 0.6446 (tp) REVERT: R 351 LEU cc_start: 0.9178 (tt) cc_final: 0.8951 (tt) REVERT: R 357 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7530 (t) REVERT: R 367 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.4193 (mmm) REVERT: B 37 ILE cc_start: 0.8087 (pt) cc_final: 0.7791 (pt) REVERT: B 101 MET cc_start: 0.8324 (mmm) cc_final: 0.8054 (mmm) REVERT: B 153 ASP cc_start: 0.8539 (p0) cc_final: 0.8269 (m-30) REVERT: B 165 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7369 (t) REVERT: B 215 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8438 (pt0) REVERT: B 217 MET cc_start: 0.8379 (ptp) cc_final: 0.7975 (tpt) REVERT: B 334 SER cc_start: 0.9380 (OUTLIER) cc_final: 0.9163 (m) REVERT: G 19 LEU cc_start: 0.8484 (mm) cc_final: 0.8220 (mm) REVERT: G 20 LYS cc_start: 0.8921 (pttm) cc_final: 0.8672 (pttm) REVERT: G 32 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7652 (ptpp) REVERT: G 42 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: P 11 LYS cc_start: 0.7846 (tttm) cc_final: 0.7044 (ttmm) outliers start: 32 outliers final: 23 residues processed: 172 average time/residue: 0.1970 time to fit residues: 46.0398 Evaluate side-chains 177 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 240 GLU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 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: 7.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 chunk 8 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.150631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.121352 restraints weight = 11104.149| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.50 r_work: 0.3538 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7889 Z= 0.165 Angle : 0.566 8.597 10671 Z= 0.300 Chirality : 0.041 0.203 1198 Planarity : 0.003 0.035 1346 Dihedral : 4.532 59.995 1049 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.68 % Allowed : 23.52 % Favored : 72.80 % 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: 0.41 (0.28), residues: 937 helix: 1.68 (0.27), residues: 378 sheet: -0.05 (0.34), residues: 223 loop : -1.11 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 236 HIS 0.004 0.001 HIS R 377 PHE 0.025 0.001 PHE R 359 TYR 0.012 0.001 TYR R 191 ARG 0.003 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3624.28 seconds wall clock time: 65 minutes 1.94 seconds (3901.94 seconds total)