Starting phenix.real_space_refine on Sat Aug 23 01:17:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0k_45087/08_2025/9c0k_45087.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0k_45087/08_2025/9c0k_45087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0k_45087/08_2025/9c0k_45087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0k_45087/08_2025/9c0k_45087.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0k_45087/08_2025/9c0k_45087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0k_45087/08_2025/9c0k_45087.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.134 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 54 5.16 5 C 5754 2.51 5 N 1555 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9019 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3095 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 14, 'TRANS': 359} Chain breaks: 3 Chain: "P" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 232 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "A" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1693 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain breaks: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.73, per 1000 atoms: 0.19 Number of scatterers: 9019 At special positions: 0 Unit cell: (73.87, 102.09, 169.32, 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 54 16.00 O 1656 8.00 N 1555 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 260.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 11 sheets defined 43.0% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 31 through 52 removed outlier: 3.543A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR R 42 " --> pdb=" O LYS R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 127 Processing helix chain 'R' and resid 138 through 169 removed outlier: 3.608A pdb=" N LEU R 142 " --> pdb=" O GLU R 138 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 174 through 211 removed outlier: 3.508A pdb=" N THR R 207 " --> pdb=" O TRP R 203 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA R 208 " --> pdb=" O MET R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 222 removed outlier: 3.580A pdb=" N ASP R 222 " --> pdb=" O LEU R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 256 removed outlier: 4.195A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 265 removed outlier: 3.582A pdb=" N ILE R 265 " --> pdb=" O GLU R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 274 Processing helix chain 'R' and resid 274 through 291 removed outlier: 4.014A pdb=" N LEU R 278 " --> pdb=" O TRP R 274 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 305 Processing helix chain 'R' and resid 306 through 336 Proline residue: R 312 - end of helix removed outlier: 3.817A pdb=" N ASN R 320 " --> pdb=" O ALA R 316 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER R 333 " --> pdb=" O CYS R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 355 Processing helix chain 'R' and resid 356 through 361 Processing helix chain 'R' and resid 362 through 370 Processing helix chain 'R' and resid 380 through 393 removed outlier: 3.516A pdb=" N SER R 389 " --> pdb=" O PHE R 385 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR R 391 " --> pdb=" O GLU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 402 Processing helix chain 'R' and resid 406 through 420 Processing helix chain 'P' and resid 3 through 28 removed outlier: 3.527A pdb=" N GLU P 17 " --> pdb=" O GLN P 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.670A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.849A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.108A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.970A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.514A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.567A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.562A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 79 through 84 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.235A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.440A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.517A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.780A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.628A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.460A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.608A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.703A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.577A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1624 1.32 - 1.45: 2512 1.45 - 1.57: 5014 1.57 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 9223 Sorted by residual: bond pdb=" CA SER R 352 " pdb=" CB SER R 352 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.58e-02 4.01e+03 1.59e+01 bond pdb=" N GLY A 355 " pdb=" CA GLY A 355 " ideal model delta sigma weight residual 1.444 1.478 -0.034 1.02e-02 9.61e+03 1.09e+01 bond pdb=" N VAL R 259 " pdb=" CA VAL R 259 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.27e-02 6.20e+03 8.81e+00 bond pdb=" CA SER R 261 " pdb=" CB SER R 261 " ideal model delta sigma weight residual 1.526 1.489 0.037 1.25e-02 6.40e+03 8.70e+00 bond pdb=" C ILE R 265 " pdb=" O ILE R 265 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.19e-02 7.06e+03 8.70e+00 ... (remaining 9218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 11887 1.74 - 3.48: 537 3.48 - 5.23: 56 5.23 - 6.97: 11 6.97 - 8.71: 5 Bond angle restraints: 12496 Sorted by residual: angle pdb=" N ARG R 267 " pdb=" CA ARG R 267 " pdb=" C ARG R 267 " ideal model delta sigma weight residual 114.31 106.61 7.70 1.29e+00 6.01e-01 3.57e+01 angle pdb=" N TYR R 269 " pdb=" CA TYR R 269 " pdb=" C TYR R 269 " ideal model delta sigma weight residual 113.12 105.85 7.27 1.25e+00 6.40e-01 3.38e+01 angle pdb=" N GLY P 2 " pdb=" CA GLY P 2 " pdb=" C GLY P 2 " ideal model delta sigma weight residual 114.67 108.77 5.90 1.10e+00 8.26e-01 2.88e+01 angle pdb=" N GLY P 4 " pdb=" CA GLY P 4 " pdb=" C GLY P 4 " ideal model delta sigma weight residual 113.24 106.29 6.95 1.31e+00 5.83e-01 2.81e+01 angle pdb=" N LEU R 268 " pdb=" CA LEU R 268 " pdb=" C LEU R 268 " ideal model delta sigma weight residual 113.17 106.70 6.47 1.26e+00 6.30e-01 2.64e+01 ... (remaining 12491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4947 17.97 - 35.93: 412 35.93 - 53.90: 69 53.90 - 71.87: 15 71.87 - 89.84: 8 Dihedral angle restraints: 5451 sinusoidal: 2180 harmonic: 3271 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -10.73 -75.27 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" SG CYS R 226 " pdb=" CB CYS R 296 " pdb=" SG CYS R 296 " pdb=" CA CYS R 296 " ideal model delta sinusoidal sigma weight residual 79.00 5.68 73.32 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA ILE R 265 " pdb=" C ILE R 265 " pdb=" N PHE R 266 " pdb=" CA PHE R 266 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 5448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1124 0.061 - 0.122: 205 0.122 - 0.183: 28 0.183 - 0.244: 14 0.244 - 0.305: 3 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA PHE R 413 " pdb=" N PHE R 413 " pdb=" C PHE R 413 " pdb=" CB PHE R 413 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA PHE R 260 " pdb=" N PHE R 260 " pdb=" C PHE R 260 " pdb=" CB PHE R 260 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA GLN B 75 " pdb=" N GLN B 75 " pdb=" C GLN B 75 " pdb=" CB GLN B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1371 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 142 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C LEU R 142 " -0.072 2.00e-02 2.50e+03 pdb=" O LEU R 142 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE R 143 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 266 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.70e+00 pdb=" C PHE R 266 " 0.054 2.00e-02 2.50e+03 pdb=" O PHE R 266 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG R 267 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 336 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C LYS R 336 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS R 336 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA R 337 " -0.016 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 547 2.73 - 3.27: 9106 3.27 - 3.82: 14913 3.82 - 4.36: 19545 4.36 - 4.90: 32226 Nonbonded interactions: 76337 Sorted by model distance: nonbonded pdb=" OD2 ASP A 354 " pdb=" NH1 ARG N 105 " model vdw 2.188 3.120 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.189 3.120 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.204 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.205 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.222 3.040 ... (remaining 76332 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: 2.080 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9229 Z= 0.328 Angle : 0.777 8.712 12508 Z= 0.523 Chirality : 0.054 0.305 1374 Planarity : 0.004 0.041 1588 Dihedral : 13.905 89.835 3315 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.10 % Allowed : 2.06 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.24), residues: 1097 helix: -0.98 (0.23), residues: 438 sheet: 0.11 (0.32), residues: 238 loop : -0.87 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.016 0.002 TYR R 269 PHE 0.028 0.002 PHE N 108 TRP 0.027 0.002 TRP R 91 HIS 0.007 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 9223) covalent geometry : angle 0.77629 (12496) SS BOND : bond 0.00230 ( 6) SS BOND : angle 1.31886 ( 12) hydrogen bonds : bond 0.26042 ( 450) hydrogen bonds : angle 9.04716 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 306 TRP cc_start: 0.7047 (t60) cc_final: 0.6573 (t-100) REVERT: A 314 GLU cc_start: 0.6509 (pm20) cc_final: 0.6309 (pm20) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.5953 time to fit residues: 77.5663 Evaluate side-chains 97 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 180 HIS A 35 GLN A 279 ASN A 357 HIS B 17 GLN B 237 ASN N 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.217753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150014 restraints weight = 8335.567| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.75 r_work: 0.3244 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9229 Z= 0.189 Angle : 0.635 8.052 12508 Z= 0.341 Chirality : 0.045 0.180 1374 Planarity : 0.005 0.040 1588 Dihedral : 4.877 27.118 1227 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.44 % Allowed : 8.63 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.25), residues: 1097 helix: 0.66 (0.24), residues: 434 sheet: 0.29 (0.34), residues: 226 loop : -1.00 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.017 0.002 TYR R 402 PHE 0.032 0.002 PHE N 108 TRP 0.015 0.002 TRP B 82 HIS 0.008 0.002 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 9223) covalent geometry : angle 0.63444 (12496) SS BOND : bond 0.00239 ( 6) SS BOND : angle 1.25858 ( 12) hydrogen bonds : bond 0.05329 ( 450) hydrogen bonds : angle 5.29237 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: R 306 TRP cc_start: 0.6873 (t60) cc_final: 0.5875 (t-100) REVERT: A 28 LYS cc_start: 0.7870 (mptt) cc_final: 0.7222 (mtpm) REVERT: A 209 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: A 373 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6906 (mmm160) REVERT: B 46 ARG cc_start: 0.8414 (mpt180) cc_final: 0.7583 (mmt180) REVERT: B 217 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8235 (pmm) REVERT: N 28 THR cc_start: 0.8436 (p) cc_final: 0.8230 (m) outliers start: 14 outliers final: 5 residues processed: 102 average time/residue: 0.5716 time to fit residues: 61.3614 Evaluate side-chains 100 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 99 HIS A 357 HIS B 17 GLN B 32 GLN B 237 ASN B 239 ASN B 268 ASN N 123 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.218928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.153383 restraints weight = 8298.446| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.65 r_work: 0.3302 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9229 Z= 0.138 Angle : 0.535 7.363 12508 Z= 0.289 Chirality : 0.042 0.147 1374 Planarity : 0.004 0.033 1588 Dihedral : 4.521 25.946 1227 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.95 % Allowed : 10.69 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.25), residues: 1097 helix: 1.29 (0.24), residues: 437 sheet: 0.50 (0.35), residues: 205 loop : -0.98 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.017 0.001 TYR R 402 PHE 0.022 0.002 PHE N 108 TRP 0.015 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9223) covalent geometry : angle 0.53448 (12496) SS BOND : bond 0.00167 ( 6) SS BOND : angle 1.01561 ( 12) hydrogen bonds : bond 0.04446 ( 450) hydrogen bonds : angle 4.69243 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.220 Fit side-chains REVERT: R 303 MET cc_start: 0.5445 (tpp) cc_final: 0.4129 (ppp) REVERT: R 306 TRP cc_start: 0.7003 (t60) cc_final: 0.5763 (t-100) REVERT: R 397 MET cc_start: 0.7607 (ptp) cc_final: 0.7167 (ptt) REVERT: P 16 GLU cc_start: 0.3253 (OUTLIER) cc_final: 0.3046 (mp0) REVERT: A 28 LYS cc_start: 0.7924 (mptt) cc_final: 0.7249 (mtpm) REVERT: A 209 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: A 314 GLU cc_start: 0.7168 (pm20) cc_final: 0.6954 (pm20) REVERT: A 373 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7046 (mmm160) REVERT: B 217 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8155 (pmm) REVERT: N 5 GLN cc_start: 0.7807 (tp40) cc_final: 0.7129 (mt0) outliers start: 19 outliers final: 8 residues processed: 107 average time/residue: 0.5935 time to fit residues: 66.9871 Evaluate side-chains 102 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 357 HIS B 17 GLN B 32 GLN B 237 ASN N 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.214911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155287 restraints weight = 8340.874| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.61 r_work: 0.3214 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 9229 Z= 0.236 Angle : 0.636 7.628 12508 Z= 0.339 Chirality : 0.046 0.220 1374 Planarity : 0.004 0.037 1588 Dihedral : 4.879 25.713 1225 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.88 % Allowed : 11.82 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.25), residues: 1097 helix: 1.43 (0.25), residues: 437 sheet: 0.43 (0.34), residues: 219 loop : -1.02 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 19 TYR 0.021 0.002 TYR R 402 PHE 0.040 0.002 PHE N 108 TRP 0.020 0.002 TRP A 234 HIS 0.009 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 9223) covalent geometry : angle 0.63529 (12496) SS BOND : bond 0.00431 ( 6) SS BOND : angle 1.11122 ( 12) hydrogen bonds : bond 0.04855 ( 450) hydrogen bonds : angle 4.79165 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.257 Fit side-chains REVERT: R 233 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6105 (tpt) REVERT: R 297 TRP cc_start: 0.7696 (OUTLIER) cc_final: 0.7431 (m-10) REVERT: R 303 MET cc_start: 0.5527 (tpp) cc_final: 0.4734 (tpp) REVERT: R 306 TRP cc_start: 0.7118 (t60) cc_final: 0.5996 (t-100) REVERT: R 369 PHE cc_start: 0.4497 (m-80) cc_final: 0.3749 (p90) REVERT: R 397 MET cc_start: 0.7681 (ptp) cc_final: 0.7256 (ptt) REVERT: A 17 LYS cc_start: 0.7432 (ttpt) cc_final: 0.7138 (tptp) REVERT: A 28 LYS cc_start: 0.7980 (mptt) cc_final: 0.7390 (mtpp) REVERT: A 209 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: A 373 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7203 (mmm160) REVERT: B 217 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8356 (pmm) REVERT: N 5 GLN cc_start: 0.7812 (tp40) cc_final: 0.7281 (mt0) outliers start: 28 outliers final: 9 residues processed: 113 average time/residue: 0.5601 time to fit residues: 66.8443 Evaluate side-chains 103 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 363 HIS A 213 GLN A 357 HIS B 17 GLN B 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.218277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168361 restraints weight = 8389.761| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.03 r_work: 0.3315 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9229 Z= 0.129 Angle : 0.520 6.222 12508 Z= 0.280 Chirality : 0.041 0.141 1374 Planarity : 0.004 0.034 1588 Dihedral : 4.480 24.165 1225 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.06 % Allowed : 14.18 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1097 helix: 1.78 (0.25), residues: 437 sheet: 0.38 (0.35), residues: 206 loop : -0.94 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.019 0.001 TYR R 402 PHE 0.018 0.002 PHE N 108 TRP 0.016 0.001 TRP A 234 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9223) covalent geometry : angle 0.51911 (12496) SS BOND : bond 0.00191 ( 6) SS BOND : angle 0.86965 ( 12) hydrogen bonds : bond 0.03940 ( 450) hydrogen bonds : angle 4.46391 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.329 Fit side-chains REVERT: R 233 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6018 (tpt) REVERT: R 297 TRP cc_start: 0.7532 (OUTLIER) cc_final: 0.7225 (m-10) REVERT: R 303 MET cc_start: 0.5448 (tpp) cc_final: 0.4824 (tpp) REVERT: R 306 TRP cc_start: 0.7176 (t60) cc_final: 0.6124 (t-100) REVERT: R 369 PHE cc_start: 0.4448 (m-80) cc_final: 0.3884 (OUTLIER) REVERT: R 387 GLU cc_start: 0.6556 (tp30) cc_final: 0.5943 (tp30) REVERT: R 397 MET cc_start: 0.7752 (ptp) cc_final: 0.7383 (ptt) REVERT: R 412 GLU cc_start: 0.6199 (tp30) cc_final: 0.5956 (tp30) REVERT: P 16 GLU cc_start: 0.3002 (OUTLIER) cc_final: 0.2707 (mp0) REVERT: A 17 LYS cc_start: 0.7339 (ttpt) cc_final: 0.7100 (tptp) REVERT: A 28 LYS cc_start: 0.7966 (mptt) cc_final: 0.7392 (mtpp) REVERT: A 209 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 373 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7021 (mmm160) REVERT: B 59 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: B 217 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8335 (pmm) REVERT: N 5 GLN cc_start: 0.7896 (tp40) cc_final: 0.7403 (mt0) REVERT: N 122 THR cc_start: 0.8631 (p) cc_final: 0.8273 (t) outliers start: 20 outliers final: 11 residues processed: 114 average time/residue: 0.6362 time to fit residues: 76.3286 Evaluate side-chains 115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 40.0000 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.0040 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 357 HIS B 17 GLN B 32 GLN N 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.218472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168460 restraints weight = 8355.647| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.93 r_work: 0.3310 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9229 Z= 0.122 Angle : 0.522 9.986 12508 Z= 0.277 Chirality : 0.041 0.141 1374 Planarity : 0.003 0.033 1588 Dihedral : 4.346 22.804 1225 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.06 % Allowed : 15.01 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.26), residues: 1097 helix: 1.96 (0.25), residues: 437 sheet: 0.38 (0.35), residues: 206 loop : -0.90 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.017 0.001 TYR R 402 PHE 0.021 0.001 PHE N 108 TRP 0.015 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9223) covalent geometry : angle 0.52155 (12496) SS BOND : bond 0.00157 ( 6) SS BOND : angle 0.84250 ( 12) hydrogen bonds : bond 0.03775 ( 450) hydrogen bonds : angle 4.33860 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.226 Fit side-chains REVERT: R 233 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.5994 (tpt) REVERT: R 297 TRP cc_start: 0.7552 (OUTLIER) cc_final: 0.7254 (m-10) REVERT: R 306 TRP cc_start: 0.7152 (t60) cc_final: 0.6110 (t-100) REVERT: R 369 PHE cc_start: 0.4252 (m-80) cc_final: 0.3862 (OUTLIER) REVERT: R 387 GLU cc_start: 0.6573 (tp30) cc_final: 0.5931 (tp30) REVERT: R 397 MET cc_start: 0.7715 (ptp) cc_final: 0.7354 (ptt) REVERT: A 17 LYS cc_start: 0.7337 (ttpt) cc_final: 0.7100 (tptp) REVERT: A 209 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: A 373 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7033 (mmm160) REVERT: B 46 ARG cc_start: 0.8433 (mpt180) cc_final: 0.7817 (mmt-90) REVERT: B 59 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: B 217 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8379 (pmm) REVERT: N 5 GLN cc_start: 0.7913 (tp40) cc_final: 0.7413 (OUTLIER) outliers start: 20 outliers final: 14 residues processed: 118 average time/residue: 0.5843 time to fit residues: 72.7395 Evaluate side-chains 121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 357 HIS B 17 GLN B 32 GLN B 237 ASN N 84 ASN N 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.214416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168914 restraints weight = 8329.052| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.91 r_work: 0.3321 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9229 Z= 0.228 Angle : 0.630 10.349 12508 Z= 0.333 Chirality : 0.045 0.213 1374 Planarity : 0.004 0.041 1588 Dihedral : 4.756 22.760 1225 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.88 % Allowed : 14.90 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1097 helix: 1.77 (0.25), residues: 437 sheet: 0.39 (0.35), residues: 218 loop : -0.97 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.019 0.002 TYR R 242 PHE 0.040 0.002 PHE N 108 TRP 0.025 0.002 TRP R 420 HIS 0.008 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 9223) covalent geometry : angle 0.62950 (12496) SS BOND : bond 0.00199 ( 6) SS BOND : angle 1.01000 ( 12) hydrogen bonds : bond 0.04518 ( 450) hydrogen bonds : angle 4.57358 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.251 Fit side-chains REVERT: R 233 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6077 (tpt) REVERT: R 297 TRP cc_start: 0.7495 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: R 303 MET cc_start: 0.5539 (tpp) cc_final: 0.4145 (ppp) REVERT: R 306 TRP cc_start: 0.7246 (t60) cc_final: 0.6014 (t-100) REVERT: R 397 MET cc_start: 0.7756 (ptp) cc_final: 0.7385 (ptt) REVERT: P 16 GLU cc_start: 0.2838 (OUTLIER) cc_final: 0.2567 (mp0) REVERT: A 17 LYS cc_start: 0.7522 (ttpt) cc_final: 0.7241 (tptp) REVERT: A 28 LYS cc_start: 0.8020 (mptt) cc_final: 0.7427 (mtpp) REVERT: A 209 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: A 373 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7197 (mmm160) REVERT: B 46 ARG cc_start: 0.8441 (mpt180) cc_final: 0.7716 (mmt-90) REVERT: B 55 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8077 (mp) REVERT: B 59 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8529 (m-80) REVERT: B 76 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7965 (p0) REVERT: B 214 ARG cc_start: 0.8247 (mpt180) cc_final: 0.8037 (mpt180) REVERT: B 217 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8430 (pmm) REVERT: N 5 GLN cc_start: 0.7883 (tp40) cc_final: 0.7383 (mt0) outliers start: 28 outliers final: 10 residues processed: 112 average time/residue: 0.6007 time to fit residues: 71.3749 Evaluate side-chains 109 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 357 HIS B 17 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.217561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.165657 restraints weight = 8319.884| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.01 r_work: 0.3294 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9229 Z= 0.134 Angle : 0.536 9.068 12508 Z= 0.285 Chirality : 0.041 0.140 1374 Planarity : 0.004 0.033 1588 Dihedral : 4.437 21.815 1225 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.06 % Allowed : 16.24 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.26), residues: 1097 helix: 1.97 (0.25), residues: 437 sheet: 0.28 (0.35), residues: 207 loop : -0.91 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.019 0.001 TYR R 402 PHE 0.021 0.002 PHE N 108 TRP 0.021 0.001 TRP R 420 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9223) covalent geometry : angle 0.53613 (12496) SS BOND : bond 0.00169 ( 6) SS BOND : angle 0.81522 ( 12) hydrogen bonds : bond 0.03833 ( 450) hydrogen bonds : angle 4.34166 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.362 Fit side-chains REVERT: R 233 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6166 (tpt) REVERT: R 297 TRP cc_start: 0.7637 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: R 303 MET cc_start: 0.5482 (tpp) cc_final: 0.3991 (ppp) REVERT: R 306 TRP cc_start: 0.7190 (t60) cc_final: 0.5885 (t-100) REVERT: R 397 MET cc_start: 0.7809 (ptp) cc_final: 0.7456 (ptt) REVERT: P 16 GLU cc_start: 0.2741 (OUTLIER) cc_final: 0.2524 (mp0) REVERT: A 17 LYS cc_start: 0.7391 (ttpt) cc_final: 0.7089 (tptp) REVERT: A 209 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: A 373 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7191 (mmm160) REVERT: B 46 ARG cc_start: 0.8548 (mpt180) cc_final: 0.7882 (mmt-90) REVERT: B 59 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8528 (m-80) REVERT: B 76 ASP cc_start: 0.8386 (p0) cc_final: 0.8169 (p0) REVERT: B 214 ARG cc_start: 0.8391 (mpt180) cc_final: 0.8182 (mpt180) REVERT: B 217 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8432 (pmm) REVERT: N 5 GLN cc_start: 0.8030 (tp40) cc_final: 0.7442 (OUTLIER) outliers start: 20 outliers final: 10 residues processed: 113 average time/residue: 0.6485 time to fit residues: 77.4509 Evaluate side-chains 110 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 20.0000 chunk 73 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 79 optimal weight: 0.0170 chunk 9 optimal weight: 30.0000 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 30.0000 chunk 6 optimal weight: 40.0000 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 357 HIS B 17 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.219493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.152290 restraints weight = 8303.350| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.83 r_work: 0.3341 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9229 Z= 0.108 Angle : 0.503 8.225 12508 Z= 0.267 Chirality : 0.040 0.137 1374 Planarity : 0.003 0.036 1588 Dihedral : 4.186 21.278 1225 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.16 % Allowed : 15.83 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.26), residues: 1097 helix: 2.15 (0.25), residues: 438 sheet: 0.23 (0.35), residues: 208 loop : -0.83 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.017 0.001 TYR N 80 PHE 0.016 0.001 PHE A 212 TRP 0.020 0.001 TRP R 420 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9223) covalent geometry : angle 0.50312 (12496) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.78262 ( 12) hydrogen bonds : bond 0.03503 ( 450) hydrogen bonds : angle 4.14625 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.373 Fit side-chains REVERT: R 233 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.5665 (tpp) REVERT: R 297 TRP cc_start: 0.7745 (OUTLIER) cc_final: 0.7541 (m-10) REVERT: R 303 MET cc_start: 0.5345 (tpp) cc_final: 0.3863 (ppp) REVERT: R 306 TRP cc_start: 0.7016 (t60) cc_final: 0.5608 (t-100) REVERT: R 397 MET cc_start: 0.7619 (ptp) cc_final: 0.7224 (ptt) REVERT: A 17 LYS cc_start: 0.7169 (ttpt) cc_final: 0.6807 (tptp) REVERT: A 209 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 373 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7011 (mmm160) REVERT: A 392 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7753 (mt-10) REVERT: B 46 ARG cc_start: 0.8557 (mpt180) cc_final: 0.7745 (mmt-90) REVERT: B 59 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: B 76 ASP cc_start: 0.8290 (p0) cc_final: 0.8029 (p0) REVERT: B 217 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8229 (pmm) REVERT: B 219 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7873 (mmt-90) REVERT: B 268 ASN cc_start: 0.7524 (m110) cc_final: 0.7312 (m-40) REVERT: N 5 GLN cc_start: 0.7929 (tp40) cc_final: 0.7243 (mt0) outliers start: 21 outliers final: 9 residues processed: 113 average time/residue: 0.6206 time to fit residues: 74.3032 Evaluate side-chains 107 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 30.0000 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 357 HIS B 17 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.217942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.152496 restraints weight = 8292.899| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.51 r_work: 0.3315 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9229 Z= 0.134 Angle : 0.531 6.699 12508 Z= 0.283 Chirality : 0.042 0.150 1374 Planarity : 0.004 0.040 1588 Dihedral : 4.298 21.586 1225 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.64 % Allowed : 16.75 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.26), residues: 1097 helix: 2.15 (0.25), residues: 438 sheet: 0.32 (0.36), residues: 207 loop : -0.86 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.017 0.001 TYR R 402 PHE 0.023 0.002 PHE N 108 TRP 0.019 0.001 TRP R 420 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9223) covalent geometry : angle 0.53066 (12496) SS BOND : bond 0.00156 ( 6) SS BOND : angle 0.82453 ( 12) hydrogen bonds : bond 0.03773 ( 450) hydrogen bonds : angle 4.22117 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.231 Fit side-chains REVERT: R 233 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.5739 (tpp) REVERT: R 297 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.7494 (m-10) REVERT: R 303 MET cc_start: 0.5434 (tpp) cc_final: 0.3952 (ppp) REVERT: R 306 TRP cc_start: 0.7053 (t60) cc_final: 0.5744 (t-100) REVERT: R 397 MET cc_start: 0.7667 (ptp) cc_final: 0.7273 (ptt) REVERT: A 17 LYS cc_start: 0.7286 (ttpt) cc_final: 0.6929 (tptp) REVERT: A 209 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: A 373 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7089 (mmm160) REVERT: A 392 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7796 (mt-10) REVERT: B 46 ARG cc_start: 0.8548 (mpt180) cc_final: 0.7736 (mmt-90) REVERT: B 59 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: B 76 ASP cc_start: 0.8325 (p0) cc_final: 0.8071 (p0) REVERT: B 214 ARG cc_start: 0.8324 (mpt180) cc_final: 0.7993 (mpt180) REVERT: B 217 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8273 (pmm) REVERT: B 268 ASN cc_start: 0.7535 (m110) cc_final: 0.7276 (m-40) REVERT: N 5 GLN cc_start: 0.7962 (tp40) cc_final: 0.7242 (mt0) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.6053 time to fit residues: 70.2381 Evaluate side-chains 110 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 0.0470 chunk 78 optimal weight: 0.9980 chunk 107 optimal weight: 0.0470 chunk 98 optimal weight: 5.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 357 HIS B 17 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.232981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.178052 restraints weight = 8734.613| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.69 r_work: 0.3773 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9229 Z= 0.107 Angle : 0.497 6.680 12508 Z= 0.265 Chirality : 0.040 0.139 1374 Planarity : 0.003 0.041 1588 Dihedral : 4.142 21.106 1225 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.85 % Allowed : 16.24 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.26), residues: 1097 helix: 2.23 (0.25), residues: 439 sheet: 0.28 (0.36), residues: 208 loop : -0.82 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.016 0.001 TYR R 402 PHE 0.017 0.001 PHE A 212 TRP 0.018 0.001 TRP R 420 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9223) covalent geometry : angle 0.49717 (12496) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.76338 ( 12) hydrogen bonds : bond 0.03491 ( 450) hydrogen bonds : angle 4.10074 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3128.97 seconds wall clock time: 53 minutes 55.03 seconds (3235.03 seconds total)