Starting phenix.real_space_refine on Sun Jul 27 00:04:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0k_45087/07_2025/9c0k_45087.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0k_45087/07_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_45087/07_2025/9c0k_45087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0k_45087/07_2025/9c0k_45087.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0k_45087/07_2025/9c0k_45087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0k_45087/07_2025/9c0k_45087.cif" } resolution = 2.72 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= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.99, per 1000 atoms: 0.78 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.11 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: 2.65 Time building geometry restraints manager: 2.96 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: 2.270 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.780 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.027 0.002 TRP R 91 HIS 0.007 0.001 HIS B 62 PHE 0.028 0.002 PHE N 108 TYR 0.016 0.002 TYR R 269 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.26042 ( 450) hydrogen bonds : angle 9.04716 ( 1275) SS BOND : bond 0.00230 ( 6) SS BOND : angle 1.31886 ( 12) covalent geometry : bond 0.00516 ( 9223) covalent geometry : angle 0.77629 (12496) *********************** 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 : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 306 TRP cc_start: 0.7047 (t60) cc_final: 0.6574 (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: 1.6297 time to fit residues: 213.2284 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 : 1.103 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 357 HIS B 17 GLN B 220 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 = 0.4350 r_free = 0.4350 target = 0.218428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.171735 restraints weight = 8223.322| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.69 r_work: 0.3316 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9229 Z= 0.179 Angle : 0.621 8.050 12508 Z= 0.335 Chirality : 0.044 0.166 1374 Planarity : 0.005 0.040 1588 Dihedral : 4.814 26.837 1227 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.34 % Allowed : 8.53 % Favored : 90.13 % 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: -0.17 (0.25), residues: 1097 helix: 0.59 (0.24), residues: 440 sheet: 0.37 (0.34), residues: 212 loop : -0.98 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.007 0.002 HIS B 62 PHE 0.029 0.002 PHE N 108 TYR 0.017 0.002 TYR R 402 ARG 0.004 0.001 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.05588 ( 450) hydrogen bonds : angle 5.36564 ( 1275) SS BOND : bond 0.00244 ( 6) SS BOND : angle 1.22357 ( 12) covalent geometry : bond 0.00399 ( 9223) covalent geometry : angle 0.61964 (12496) *********************** 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: 13 poor density : 98 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: R 306 TRP cc_start: 0.6991 (t60) cc_final: 0.6155 (t-100) REVERT: A 28 LYS cc_start: 0.7995 (mptt) cc_final: 0.7470 (mtpm) REVERT: A 209 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: A 373 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7035 (mmm160) REVERT: B 46 ARG cc_start: 0.8369 (mpt180) cc_final: 0.7758 (mmt180) REVERT: B 217 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8314 (pmm) REVERT: N 28 THR cc_start: 0.8544 (p) cc_final: 0.8258 (m) outliers start: 13 outliers final: 4 residues processed: 102 average time/residue: 1.6112 time to fit residues: 173.5661 Evaluate side-chains 96 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN 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 = 0.4338 r_free = 0.4338 target = 0.217469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168734 restraints weight = 8422.810| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.02 r_work: 0.3346 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1940 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= 0.136 Angle : 0.537 7.401 12508 Z= 0.290 Chirality : 0.042 0.146 1374 Planarity : 0.004 0.033 1588 Dihedral : 4.541 25.872 1227 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.95 % Allowed : 9.87 % Favored : 88.18 % 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: 0.37 (0.25), residues: 1097 helix: 1.35 (0.25), residues: 437 sheet: 0.49 (0.35), residues: 205 loop : -0.96 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.009 0.001 HIS A 220 PHE 0.023 0.002 PHE N 108 TYR 0.017 0.001 TYR R 402 ARG 0.008 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 450) hydrogen bonds : angle 4.70887 ( 1275) SS BOND : bond 0.00172 ( 6) SS BOND : angle 1.02987 ( 12) covalent geometry : bond 0.00298 ( 9223) covalent geometry : angle 0.53675 (12496) *********************** 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 : 1.041 Fit side-chains REVERT: R 233 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.5984 (tpt) REVERT: R 303 MET cc_start: 0.5420 (tpp) cc_final: 0.4178 (ppp) REVERT: R 306 TRP cc_start: 0.7014 (t60) cc_final: 0.5923 (t-100) REVERT: R 397 MET cc_start: 0.7689 (ptp) cc_final: 0.7302 (ptt) REVERT: P 16 GLU cc_start: 0.3347 (OUTLIER) cc_final: 0.3111 (mp0) REVERT: A 28 LYS cc_start: 0.7926 (mptt) cc_final: 0.7411 (mtpp) REVERT: A 209 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: A 373 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7040 (mmm160) REVERT: B 217 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8251 (pmm) REVERT: N 5 GLN cc_start: 0.7782 (tp40) cc_final: 0.7342 (mt0) outliers start: 19 outliers final: 6 residues processed: 108 average time/residue: 1.4565 time to fit residues: 166.6728 Evaluate side-chains 100 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 MET 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 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 217 MET Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 14 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 99 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.217714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159832 restraints weight = 8356.090| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.35 r_work: 0.3271 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9229 Z= 0.130 Angle : 0.514 6.622 12508 Z= 0.278 Chirality : 0.041 0.144 1374 Planarity : 0.004 0.034 1588 Dihedral : 4.401 24.566 1227 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.75 % Allowed : 12.44 % Favored : 85.82 % 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: 0.61 (0.25), residues: 1097 helix: 1.73 (0.25), residues: 438 sheet: 0.42 (0.35), residues: 205 loop : -0.92 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.008 0.001 HIS A 220 PHE 0.023 0.002 PHE N 108 TYR 0.017 0.001 TYR R 402 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 450) hydrogen bonds : angle 4.44876 ( 1275) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.91463 ( 12) covalent geometry : bond 0.00287 ( 9223) covalent geometry : angle 0.51366 (12496) *********************** 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 111 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.994 Fit side-chains REVERT: R 306 TRP cc_start: 0.7044 (t60) cc_final: 0.6021 (t-100) REVERT: R 397 MET cc_start: 0.7770 (ptp) cc_final: 0.7369 (ptt) REVERT: P 16 GLU cc_start: 0.3343 (OUTLIER) cc_final: 0.3127 (mp0) REVERT: A 17 LYS cc_start: 0.7264 (ttpt) cc_final: 0.7057 (tptp) REVERT: A 373 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7058 (mmm160) REVERT: B 217 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8352 (pmm) REVERT: N 5 GLN cc_start: 0.7879 (tp40) cc_final: 0.7346 (mt0) outliers start: 17 outliers final: 8 residues processed: 105 average time/residue: 1.5265 time to fit residues: 169.4655 Evaluate side-chains 100 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain A residue 216 LYS 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 70 LEU 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 87 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.0770 chunk 4 optimal weight: 10.0000 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4352 r_free = 0.4352 target = 0.218683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.170228 restraints weight = 8299.042| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.97 r_work: 0.3327 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2402 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= 0.133 Angle : 0.523 10.464 12508 Z= 0.279 Chirality : 0.041 0.143 1374 Planarity : 0.004 0.033 1588 Dihedral : 4.357 23.436 1225 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.26 % Allowed : 13.05 % Favored : 84.69 % 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: 0.69 (0.26), residues: 1097 helix: 1.87 (0.25), residues: 443 sheet: 0.37 (0.35), residues: 206 loop : -0.96 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS B 62 PHE 0.024 0.002 PHE N 108 TYR 0.018 0.001 TYR N 80 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 450) hydrogen bonds : angle 4.35229 ( 1275) SS BOND : bond 0.00158 ( 6) SS BOND : angle 0.89528 ( 12) covalent geometry : bond 0.00299 ( 9223) covalent geometry : angle 0.52218 (12496) *********************** 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 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.222 Fit side-chains REVERT: R 233 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6046 (tpt) REVERT: R 297 TRP cc_start: 0.7380 (OUTLIER) cc_final: 0.7078 (m-10) REVERT: R 303 MET cc_start: 0.4848 (tpt) cc_final: 0.4378 (ppp) REVERT: R 306 TRP cc_start: 0.6777 (t60) cc_final: 0.5634 (t-100) REVERT: R 387 GLU cc_start: 0.6672 (tp30) cc_final: 0.6088 (tp30) REVERT: R 397 MET cc_start: 0.7794 (ptp) cc_final: 0.7403 (ptt) REVERT: A 17 LYS cc_start: 0.7305 (ttpt) cc_final: 0.7102 (tptp) REVERT: A 373 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7074 (mmm160) REVERT: B 46 ARG cc_start: 0.8427 (mpt180) cc_final: 0.7738 (mmp80) REVERT: B 217 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8358 (pmm) REVERT: N 5 GLN cc_start: 0.7895 (tp40) cc_final: 0.7363 (mt0) outliers start: 22 outliers final: 8 residues processed: 114 average time/residue: 1.5966 time to fit residues: 192.3598 Evaluate side-chains 107 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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 217 MET Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.217444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.167977 restraints weight = 8270.951| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.93 r_work: 0.3327 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9229 Z= 0.145 Angle : 0.536 8.911 12508 Z= 0.286 Chirality : 0.042 0.152 1374 Planarity : 0.004 0.033 1588 Dihedral : 4.395 22.916 1225 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.16 % Allowed : 14.08 % 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 (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: 0.71 (0.25), residues: 1097 helix: 1.87 (0.25), residues: 444 sheet: 0.39 (0.35), residues: 206 loop : -0.93 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS B 62 PHE 0.027 0.002 PHE N 108 TYR 0.016 0.001 TYR R 402 ARG 0.008 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 450) hydrogen bonds : angle 4.35115 ( 1275) SS BOND : bond 0.00156 ( 6) SS BOND : angle 0.88934 ( 12) covalent geometry : bond 0.00332 ( 9223) covalent geometry : angle 0.53537 (12496) *********************** 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 121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.988 Fit side-chains REVERT: R 233 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6039 (tpt) REVERT: R 297 TRP cc_start: 0.7417 (OUTLIER) cc_final: 0.7100 (m-10) REVERT: R 303 MET cc_start: 0.4946 (tpt) cc_final: 0.4355 (ppp) REVERT: R 306 TRP cc_start: 0.6871 (t60) cc_final: 0.5716 (t-100) REVERT: R 369 PHE cc_start: 0.4265 (m-80) cc_final: 0.3864 (p90) REVERT: R 387 GLU cc_start: 0.6553 (tp30) cc_final: 0.5933 (tp30) REVERT: R 397 MET cc_start: 0.7790 (ptp) cc_final: 0.7443 (ptt) REVERT: A 17 LYS cc_start: 0.7307 (ttpt) cc_final: 0.7085 (tptp) REVERT: A 28 LYS cc_start: 0.7948 (mptt) cc_final: 0.7401 (mtpp) REVERT: A 373 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7098 (mmm160) REVERT: B 59 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: B 217 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8370 (pmm) REVERT: N 5 GLN cc_start: 0.7883 (tp40) cc_final: 0.7353 (OUTLIER) outliers start: 21 outliers final: 11 residues processed: 113 average time/residue: 1.5471 time to fit residues: 184.6962 Evaluate side-chains 110 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 216 LYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 105 optimal weight: 0.1980 chunk 7 optimal weight: 50.0000 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 40.0000 chunk 61 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.218961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.170745 restraints weight = 8398.316| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.77 r_work: 0.3366 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9229 Z= 0.116 Angle : 0.505 8.191 12508 Z= 0.269 Chirality : 0.041 0.139 1374 Planarity : 0.003 0.033 1588 Dihedral : 4.233 21.502 1225 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.95 % Allowed : 14.80 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1097 helix: 2.03 (0.25), residues: 443 sheet: 0.33 (0.35), residues: 208 loop : -0.85 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.007 0.001 HIS A 220 PHE 0.019 0.001 PHE A 212 TYR 0.016 0.001 TYR R 402 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 450) hydrogen bonds : angle 4.22387 ( 1275) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.80664 ( 12) covalent geometry : bond 0.00257 ( 9223) covalent geometry : angle 0.50510 (12496) *********************** 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 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: R 233 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6079 (tpt) REVERT: R 297 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: R 306 TRP cc_start: 0.6962 (t60) cc_final: 0.5900 (t-100) REVERT: R 364 GLU cc_start: 0.7664 (mp0) cc_final: 0.6373 (tp30) REVERT: R 369 PHE cc_start: 0.4273 (m-80) cc_final: 0.3861 (p90) REVERT: R 387 GLU cc_start: 0.6682 (tp30) cc_final: 0.6078 (tp30) REVERT: R 397 MET cc_start: 0.7863 (ptp) cc_final: 0.7529 (ptt) REVERT: A 17 LYS cc_start: 0.7331 (ttpt) cc_final: 0.7098 (tptp) REVERT: A 373 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7115 (mmm160) REVERT: A 386 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8015 (ttm) REVERT: A 392 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7942 (mt-10) REVERT: B 46 ARG cc_start: 0.8522 (mpt180) cc_final: 0.7831 (mmp80) REVERT: B 59 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: B 76 ASP cc_start: 0.8322 (p0) cc_final: 0.8097 (p0) REVERT: B 217 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8468 (pmm) REVERT: N 5 GLN cc_start: 0.8033 (tp40) cc_final: 0.7424 (mt0) outliers start: 19 outliers final: 9 residues processed: 114 average time/residue: 1.4973 time to fit residues: 180.7839 Evaluate side-chains 115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 216 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 N 84 ASN N 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.218497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.152318 restraints weight = 8379.643| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.55 r_work: 0.3356 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2780 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= 0.130 Angle : 0.520 8.398 12508 Z= 0.277 Chirality : 0.041 0.142 1374 Planarity : 0.004 0.034 1588 Dihedral : 4.275 21.348 1225 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.95 % Allowed : 15.52 % Favored : 82.53 % 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: 0.88 (0.26), residues: 1097 helix: 2.03 (0.25), residues: 444 sheet: 0.42 (0.36), residues: 206 loop : -0.83 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.025 0.002 PHE N 108 TYR 0.016 0.001 TYR R 402 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 450) hydrogen bonds : angle 4.23405 ( 1275) SS BOND : bond 0.00137 ( 6) SS BOND : angle 0.83818 ( 12) covalent geometry : bond 0.00296 ( 9223) covalent geometry : angle 0.51919 (12496) *********************** 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 113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.971 Fit side-chains REVERT: R 233 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6005 (tpt) REVERT: R 297 TRP cc_start: 0.7658 (OUTLIER) cc_final: 0.7412 (m-10) REVERT: R 303 MET cc_start: 0.5148 (tpt) cc_final: 0.4335 (ppp) REVERT: R 306 TRP cc_start: 0.6905 (t60) cc_final: 0.5698 (t-100) REVERT: R 397 MET cc_start: 0.7712 (ptp) cc_final: 0.7342 (ptt) REVERT: A 17 LYS cc_start: 0.7340 (ttpt) cc_final: 0.6981 (tptp) REVERT: A 28 LYS cc_start: 0.7888 (mptt) cc_final: 0.7294 (mtpm) REVERT: A 373 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7117 (mmm160) REVERT: A 386 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7951 (ttm) REVERT: A 392 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7859 (mt-10) REVERT: B 46 ARG cc_start: 0.8589 (mpt180) cc_final: 0.7742 (mmp80) REVERT: B 59 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: B 76 ASP cc_start: 0.8308 (p0) cc_final: 0.8035 (p0) REVERT: B 214 ARG cc_start: 0.8300 (mpt180) cc_final: 0.8038 (mpt180) REVERT: B 217 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8379 (pmm) REVERT: N 5 GLN cc_start: 0.7923 (tp40) cc_final: 0.7227 (mt0) outliers start: 19 outliers final: 10 residues processed: 106 average time/residue: 1.5203 time to fit residues: 171.0294 Evaluate side-chains 105 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 216 LYS 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 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 17 optimal weight: 0.0470 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.234845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.179827 restraints weight = 8901.318| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.10 r_work: 0.3821 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9229 Z= 0.098 Angle : 0.482 11.816 12508 Z= 0.255 Chirality : 0.040 0.135 1374 Planarity : 0.003 0.036 1588 Dihedral : 4.015 20.372 1225 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.64 % Allowed : 16.24 % Favored : 82.12 % 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: 1.06 (0.26), residues: 1097 helix: 2.22 (0.25), residues: 444 sheet: 0.43 (0.36), residues: 206 loop : -0.73 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.015 0.001 TYR R 402 ARG 0.008 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 450) hydrogen bonds : angle 4.03256 ( 1275) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.73738 ( 12) covalent geometry : bond 0.00210 ( 9223) covalent geometry : angle 0.48192 (12496) *********************** 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 116 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.035 Fit side-chains REVERT: R 233 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.5958 (tpt) REVERT: R 297 TRP cc_start: 0.7614 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: R 303 MET cc_start: 0.4963 (tpt) cc_final: 0.4311 (ppp) REVERT: R 306 TRP cc_start: 0.6947 (t60) cc_final: 0.5783 (t-100) REVERT: R 397 MET cc_start: 0.7671 (ptp) cc_final: 0.7314 (ptt) REVERT: A 17 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6894 (tptp) REVERT: A 28 LYS cc_start: 0.7883 (mptt) cc_final: 0.7408 (mtpm) REVERT: A 373 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7019 (mmm160) REVERT: A 386 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7953 (ttm) REVERT: A 392 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7830 (mt-10) REVERT: B 46 ARG cc_start: 0.8531 (mpt180) cc_final: 0.7874 (mmp80) REVERT: B 59 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: B 76 ASP cc_start: 0.8322 (p0) cc_final: 0.8113 (p0) REVERT: N 5 GLN cc_start: 0.7971 (tp40) cc_final: 0.7352 (mp10) outliers start: 16 outliers final: 6 residues processed: 110 average time/residue: 1.4519 time to fit residues: 169.4049 Evaluate side-chains 99 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 224 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 59 TYR Chi-restraints excluded: chain B residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 237 ASN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.232113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.174515 restraints weight = 8721.522| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.14 r_work: 0.3784 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9229 Z= 0.118 Angle : 0.510 10.651 12508 Z= 0.270 Chirality : 0.041 0.141 1374 Planarity : 0.003 0.039 1588 Dihedral : 4.122 21.220 1225 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.34 % Allowed : 16.65 % 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 (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: 1.00 (0.26), residues: 1097 helix: 2.19 (0.25), residues: 445 sheet: 0.40 (0.36), residues: 208 loop : -0.79 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 PHE 0.022 0.001 PHE N 108 TYR 0.014 0.001 TYR R 402 ARG 0.010 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 450) hydrogen bonds : angle 4.09003 ( 1275) SS BOND : bond 0.00137 ( 6) SS BOND : angle 0.79427 ( 12) covalent geometry : bond 0.00265 ( 9223) covalent geometry : angle 0.50962 (12496) ********************** 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 109 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.937 Fit side-chains REVERT: R 233 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6150 (tpt) REVERT: R 297 TRP cc_start: 0.7597 (OUTLIER) cc_final: 0.7284 (m-10) REVERT: R 303 MET cc_start: 0.5077 (tpt) cc_final: 0.4385 (ppp) REVERT: R 306 TRP cc_start: 0.6929 (t60) cc_final: 0.5788 (t-100) REVERT: R 397 MET cc_start: 0.7658 (ptp) cc_final: 0.7300 (ptt) REVERT: A 17 LYS cc_start: 0.7314 (ttpt) cc_final: 0.7003 (tptp) REVERT: A 28 LYS cc_start: 0.7907 (mptt) cc_final: 0.7416 (mtpp) REVERT: A 373 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7060 (mmm160) REVERT: A 386 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8000 (ttm) REVERT: A 392 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7840 (mt-10) REVERT: B 46 ARG cc_start: 0.8582 (mpt180) cc_final: 0.7945 (mmt-90) REVERT: B 59 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: B 196 THR cc_start: 0.7963 (p) cc_final: 0.7532 (p) REVERT: N 5 GLN cc_start: 0.7972 (tp40) cc_final: 0.7275 (mp10) outliers start: 13 outliers final: 6 residues processed: 107 average time/residue: 1.5071 time to fit residues: 171.0399 Evaluate side-chains 104 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 224 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 0.1980 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.232307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.172690 restraints weight = 8775.741| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.01 r_work: 0.3753 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9229 Z= 0.115 Angle : 0.505 10.143 12508 Z= 0.268 Chirality : 0.041 0.140 1374 Planarity : 0.003 0.042 1588 Dihedral : 4.126 21.126 1225 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.34 % Allowed : 16.96 % 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 (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: 1.05 (0.26), residues: 1097 helix: 2.23 (0.25), residues: 444 sheet: 0.43 (0.35), residues: 213 loop : -0.78 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.008 0.001 HIS A 220 PHE 0.019 0.001 PHE N 108 TYR 0.016 0.001 TYR N 80 ARG 0.010 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 450) hydrogen bonds : angle 4.06694 ( 1275) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.74784 ( 12) covalent geometry : bond 0.00257 ( 9223) covalent geometry : angle 0.50422 (12496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7557.44 seconds wall clock time: 130 minutes 44.70 seconds (7844.70 seconds total)