Starting phenix.real_space_refine on Fri Oct 23 10:30:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v4p_21044/10_2026/6v4p_21044.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v4p_21044/10_2026/6v4p_21044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v4p_21044/10_2026/6v4p_21044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v4p_21044/10_2026/6v4p_21044.map" model { file = "/net/cci-nas-00/data/ceres_data/6v4p_21044/10_2026/6v4p_21044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v4p_21044/10_2026/6v4p_21044.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6v4p_21044/10_2026/6v4p_21044.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v4p_21044/10_2026/6v4p_21044.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 41 5.16 5 C 6131 2.51 5 N 1636 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9717 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3467 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 27, 'TRANS': 424} Chain: "B" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2927 Classifications: {'peptide': 375} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 356} Chain: "C" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1665 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "D" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1651 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 6, 'TRANS': 203} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.78, per 1000 atoms: 0.18 Number of scatterers: 9717 At special positions: 0 Unit cell: (99, 150, 76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 41 16.00 Mg 1 11.99 O 1902 8.00 N 1636 7.00 C 6131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " 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: 0.79 Conformation dependent library (CDL) restraints added in 325.7 milliseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 24 sheets defined 12.5% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.763A pdb=" N SER B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.665A pdb=" N LEU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 4.311A pdb=" N ASP B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.765A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 291 through 302 Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.501A pdb=" N LYS C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.505A pdb=" N SER C 91 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.936A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 189 removed outlier: 4.083A pdb=" N HIS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 8.111A pdb=" N GLY A 63 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 10 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLN A 7 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG A 449 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP A 434 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 424 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 420 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 removed outlier: 4.338A pdb=" N VAL A 53 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.583A pdb=" N GLN A 82 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 5.748A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.521A pdb=" N GLY A 398 " --> pdb=" O GLN A 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 65 removed outlier: 6.503A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AB4, first strand: chain 'B' and resid 190 through 197 removed outlier: 6.161A pdb=" N PHE B 153 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR B 195 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE B 151 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR B 197 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 149 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS B 244 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 307 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 246 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 309 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE B 248 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR B 311 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR B 250 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B 333 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL B 310 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.351A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AB8, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.593A pdb=" N LYS C 148 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR C 181 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.593A pdb=" N LYS C 148 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR C 181 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 174 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 155 through 159 removed outlier: 4.480A pdb=" N TYR C 199 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.824A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU D 33 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.824A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 114 through 118 removed outlier: 4.928A pdb=" N SER D 131 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU D 181 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU D 179 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU D 135 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N SER D 177 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN D 137 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D 175 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 147 through 150 347 hydrogen bonds defined for protein. 888 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: 1.29 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: 1.19 - 1.32: 1634 1.32 - 1.44: 2738 1.44 - 1.57: 5507 1.57 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 9938 Sorted by residual: bond pdb=" N LEU B 375 " pdb=" CA LEU B 375 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.32e-02 5.74e+03 1.23e+01 bond pdb=" CA ASN D 32 " pdb=" C ASN D 32 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.34e-02 5.57e+03 1.12e+01 bond pdb=" C ILE D 29 " pdb=" O ILE D 29 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" C SER D 30 " pdb=" O SER D 30 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.26e-02 6.30e+03 8.11e+00 bond pdb=" C ASN D 32 " pdb=" O ASN D 32 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.26e-02 6.30e+03 7.78e+00 ... (remaining 9933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 13420 2.70 - 5.41: 88 5.41 - 8.11: 5 8.11 - 10.81: 0 10.81 - 13.52: 1 Bond angle restraints: 13514 Sorted by residual: angle pdb=" C LEU B 375 " pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " ideal model delta sigma weight residual 109.61 117.10 -7.49 1.58e+00 4.01e-01 2.25e+01 angle pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " pdb=" CG LEU B 375 " ideal model delta sigma weight residual 116.30 102.78 13.52 3.50e+00 8.16e-02 1.49e+01 angle pdb=" C CYS B 374 " pdb=" N LEU B 375 " pdb=" CA LEU B 375 " ideal model delta sigma weight residual 121.31 126.33 -5.02 1.49e+00 4.50e-01 1.13e+01 angle pdb=" N SER D 30 " pdb=" CA SER D 30 " pdb=" C SER D 30 " ideal model delta sigma weight residual 110.80 117.64 -6.84 2.13e+00 2.20e-01 1.03e+01 angle pdb=" C ILE D 29 " pdb=" N SER D 30 " pdb=" CA SER D 30 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.34e+00 ... (remaining 13509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 5514 16.69 - 33.39: 297 33.39 - 50.08: 77 50.08 - 66.77: 25 66.77 - 83.47: 9 Dihedral angle restraints: 5922 sinusoidal: 2300 harmonic: 3622 Sorted by residual: dihedral pdb=" CA LEU B 375 " pdb=" C LEU B 375 " pdb=" N ASN B 376 " pdb=" CA ASN B 376 " ideal model delta harmonic sigma weight residual -180.00 -151.79 -28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA THR D 39 " pdb=" C THR D 39 " pdb=" N SER D 40 " pdb=" CA SER D 40 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C LEU B 375 " pdb=" N LEU B 375 " pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " ideal model delta harmonic sigma weight residual -122.60 -133.94 11.34 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 5919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1328 0.073 - 0.146: 162 0.146 - 0.218: 2 0.218 - 0.291: 2 0.291 - 0.364: 2 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA LEU B 375 " pdb=" N LEU B 375 " pdb=" C LEU B 375 " pdb=" CB LEU B 375 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU B 375 " pdb=" CB LEU B 375 " pdb=" CD1 LEU B 375 " pdb=" CD2 LEU B 375 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA SER D 30 " pdb=" N SER D 30 " pdb=" C SER D 30 " pdb=" CB SER D 30 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 1493 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 375 " 0.019 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C LEU B 375 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU B 375 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 376 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 29 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ILE D 29 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE D 29 " -0.015 2.00e-02 2.50e+03 pdb=" N SER D 30 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 153 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO C 154 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 154 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 154 " -0.021 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 209 2.65 - 3.21: 8814 3.21 - 3.77: 15823 3.77 - 4.34: 23593 4.34 - 4.90: 38440 Nonbonded interactions: 86879 Sorted by model distance: nonbonded pdb=" OE2 GLU B 220 " pdb="MG MG B 701 " model vdw 2.084 2.170 nonbonded pdb=" OH TYR A 288 " pdb=" OD1 ASP B 259 " model vdw 2.197 3.040 nonbonded pdb=" NZ LYS B 417 " pdb=" O PHE B 421 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR B 178 " pdb=" OD2 ASP C 57 " model vdw 2.233 3.040 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.241 3.040 ... (remaining 86874 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.090 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 0.046 9948 Z= 0.223 Angle : 0.601 13.516 13534 Z= 0.336 Chirality : 0.047 0.364 1496 Planarity : 0.004 0.042 1758 Dihedral : 12.282 83.466 3584 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.07 % Favored : 95.69 % Rotamer: Outliers : 3.16 % Allowed : 7.72 % Favored : 89.12 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.21), residues: 1254 helix: -2.93 (0.33), residues: 116 sheet: -1.38 (0.22), residues: 448 loop : -1.87 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 352 TYR 0.014 0.002 TYR D 50 PHE 0.017 0.002 PHE A 19 TRP 0.017 0.002 TRP C 33 HIS 0.005 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 ( 9938) covalent geometry : angle 0.60047 / 0.34 (13514) SS BOND : bond 0.00271 / 0.17 ( 10) SS BOND : angle 0.96227 / 0.49 ( 20) hydrogen bonds : bond 0.20625 / 14.10 ( 329) hydrogen bonds : angle 9.87975 / 6.90 ( 888) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.369 Fit side-chains REVERT: A 23 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8841 (pp) REVERT: A 77 ARG cc_start: 0.7045 (mpt180) cc_final: 0.6137 (ttt-90) REVERT: A 120 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 125 THR cc_start: 0.9011 (p) cc_final: 0.8534 (p) REVERT: A 166 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: A 208 ARG cc_start: 0.7988 (mpt180) cc_final: 0.7667 (mmt180) REVERT: A 386 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7845 (mtm180) REVERT: A 401 SER cc_start: 0.8835 (p) cc_final: 0.8554 (m) REVERT: B 93 ARG cc_start: 0.7249 (ptm160) cc_final: 0.6320 (ttt180) REVERT: B 108 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7484 (pt0) REVERT: B 137 LYS cc_start: 0.8387 (mttt) cc_final: 0.7989 (mtmt) REVERT: B 187 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.7806 (tmm) REVERT: B 277 SER cc_start: 0.8844 (p) cc_final: 0.8592 (m) REVERT: B 323 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7710 (mt-10) REVERT: B 365 GLU cc_start: 0.8079 (mp0) cc_final: 0.7709 (pm20) REVERT: B 387 MET cc_start: 0.7990 (mtm) cc_final: 0.7682 (mtm) REVERT: B 400 GLU cc_start: 0.7933 (tt0) cc_final: 0.7546 (tt0) REVERT: B 402 LYS cc_start: 0.6772 (mtpt) cc_final: 0.6169 (mptt) REVERT: B 426 ILE cc_start: 0.9085 (mt) cc_final: 0.8833 (mm) REVERT: B 428 GLN cc_start: 0.8446 (mt0) cc_final: 0.8242 (mt0) REVERT: C 3 GLN cc_start: 0.7627 (tt0) cc_final: 0.7057 (mm-40) REVERT: C 32 TYR cc_start: 0.7811 (m-80) cc_final: 0.7391 (m-80) REVERT: C 100 ASP cc_start: 0.8450 (p0) cc_final: 0.8171 (p0) REVERT: C 122 LYS cc_start: 0.7556 (tttt) cc_final: 0.7218 (tttm) REVERT: D 70 ASP cc_start: 0.8047 (t70) cc_final: 0.7825 (t70) REVERT: D 103 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7978 (ttpp) REVERT: D 105 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7111 (mt-10) outliers start: 34 outliers final: 10 residues processed: 209 average time/residue: 0.5286 time to fit residues: 118.8423 Evaluate side-chains 159 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 451 GLN B 267 GLN B 280 HIS C 3 GLN D 124 GLN D 137 ASN D 147 GLN D 155 GLN D 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.148786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.102945 restraints weight = 9740.298| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.82 r_work: 0.2709 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9948 Z= 0.153 Angle : 0.566 8.577 13534 Z= 0.302 Chirality : 0.045 0.150 1496 Planarity : 0.004 0.040 1758 Dihedral : 7.415 58.044 1396 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 3.72 % Allowed : 12.19 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.22), residues: 1254 helix: -1.81 (0.40), residues: 122 sheet: -0.92 (0.23), residues: 446 loop : -1.18 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 91 TYR 0.011 0.001 TYR D 50 PHE 0.013 0.002 PHE A 331 TRP 0.014 0.002 TRP C 33 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9938) covalent geometry : angle 0.56347 / 0.30 (13514) SS BOND : bond 0.00820 / 0.40 ( 10) SS BOND : angle 1.59152 / 0.68 ( 20) hydrogen bonds : bond 0.03892 / 2.61 ( 329) hydrogen bonds : angle 6.92685 / 4.97 ( 888) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.392 Fit side-chains REVERT: A 23 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8752 (pp) REVERT: A 77 ARG cc_start: 0.7698 (mpt180) cc_final: 0.6815 (ttt-90) REVERT: A 120 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7195 (mt-10) REVERT: A 125 THR cc_start: 0.9012 (p) cc_final: 0.8599 (p) REVERT: A 159 ASP cc_start: 0.8254 (m-30) cc_final: 0.8054 (m-30) REVERT: A 166 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: A 208 ARG cc_start: 0.8464 (mpt180) cc_final: 0.8146 (mmt-90) REVERT: A 355 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8810 (mtt180) REVERT: A 400 ARG cc_start: 0.8294 (mmt180) cc_final: 0.7691 (mmt90) REVERT: A 401 SER cc_start: 0.8868 (p) cc_final: 0.8640 (m) REVERT: B 93 ARG cc_start: 0.7399 (ptm160) cc_final: 0.6448 (ttt180) REVERT: B 108 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7904 (mt-10) REVERT: B 137 LYS cc_start: 0.8594 (mttt) cc_final: 0.8106 (mtmt) REVERT: B 187 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8150 (tmm) REVERT: B 277 SER cc_start: 0.8968 (p) cc_final: 0.8666 (m) REVERT: B 312 GLU cc_start: 0.8100 (tp30) cc_final: 0.7887 (mm-30) REVERT: B 323 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8106 (mt-10) REVERT: B 365 GLU cc_start: 0.8341 (mp0) cc_final: 0.8034 (pm20) REVERT: B 387 MET cc_start: 0.8807 (mtm) cc_final: 0.8351 (mtm) REVERT: B 400 GLU cc_start: 0.8341 (tt0) cc_final: 0.7961 (tt0) REVERT: B 402 LYS cc_start: 0.7295 (mtpt) cc_final: 0.7033 (tttm) REVERT: C 3 GLN cc_start: 0.7836 (tt0) cc_final: 0.7315 (mm-40) REVERT: C 32 TYR cc_start: 0.8213 (m-80) cc_final: 0.7864 (m-80) REVERT: C 122 LYS cc_start: 0.7585 (tttt) cc_final: 0.7220 (tttm) REVERT: D 55 MET cc_start: 0.8872 (mmm) cc_final: 0.8501 (mmm) REVERT: D 79 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: D 81 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: D 175 LEU cc_start: 0.7460 (tt) cc_final: 0.7222 (tt) outliers start: 40 outliers final: 22 residues processed: 185 average time/residue: 0.5373 time to fit residues: 106.8828 Evaluate side-chains 172 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [100, 24, 120, 25, 121, 68, 47, 110, 10, 67, 31] chunk 100 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 134 GLN B 274 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.147548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.102003 restraints weight = 9687.210| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.09 r_work: 0.2680 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9948 Z= 0.203 Angle : 0.573 8.034 13534 Z= 0.304 Chirality : 0.046 0.148 1496 Planarity : 0.004 0.040 1758 Dihedral : 7.202 59.765 1392 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 4.37 % Allowed : 13.12 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.23), residues: 1254 helix: -1.31 (0.42), residues: 122 sheet: -0.67 (0.24), residues: 446 loop : -0.89 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 91 TYR 0.023 0.002 TYR C 150 PHE 0.016 0.002 PHE A 19 TRP 0.019 0.002 TRP C 33 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 9938) covalent geometry : angle 0.57029 / 0.30 (13514) SS BOND : bond 0.00558 / 0.28 ( 10) SS BOND : angle 1.66010 / 0.73 ( 20) hydrogen bonds : bond 0.03955 / 2.66 ( 329) hydrogen bonds : angle 6.55969 / 4.72 ( 888) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.395 Fit side-chains REVERT: A 77 ARG cc_start: 0.7614 (mpt180) cc_final: 0.6764 (ttt-90) REVERT: A 120 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 125 THR cc_start: 0.8995 (p) cc_final: 0.8543 (p) REVERT: A 134 GLN cc_start: 0.8563 (mt0) cc_final: 0.8316 (mt0) REVERT: A 166 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: A 197 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8376 (pp30) REVERT: A 208 ARG cc_start: 0.8468 (mpt180) cc_final: 0.8089 (mmt-90) REVERT: A 355 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8777 (mtt180) REVERT: A 386 ARG cc_start: 0.8600 (mtm180) cc_final: 0.8343 (mtp-110) REVERT: A 401 SER cc_start: 0.8904 (p) cc_final: 0.8666 (m) REVERT: B 93 ARG cc_start: 0.7275 (ptm160) cc_final: 0.6211 (ttt180) REVERT: B 108 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7940 (mt-10) REVERT: B 137 LYS cc_start: 0.8531 (mttt) cc_final: 0.8061 (mtmt) REVERT: B 187 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8221 (tmm) REVERT: B 277 SER cc_start: 0.8993 (p) cc_final: 0.8686 (m) REVERT: B 278 ASP cc_start: 0.8177 (p0) cc_final: 0.7968 (p0) REVERT: B 323 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8098 (mt-10) REVERT: B 365 GLU cc_start: 0.8313 (mp0) cc_final: 0.8008 (pm20) REVERT: B 387 MET cc_start: 0.8841 (mtm) cc_final: 0.8296 (mtm) REVERT: B 400 GLU cc_start: 0.8368 (tt0) cc_final: 0.7927 (tt0) REVERT: B 402 LYS cc_start: 0.6981 (mtpt) cc_final: 0.6774 (tmtm) REVERT: C 3 GLN cc_start: 0.7852 (tt0) cc_final: 0.7306 (mm-40) REVERT: C 19 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8983 (ttpp) REVERT: C 32 TYR cc_start: 0.8200 (m-80) cc_final: 0.7862 (m-80) REVERT: C 122 LYS cc_start: 0.7618 (tttt) cc_final: 0.7299 (tttm) REVERT: D 81 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: D 103 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8089 (ttpp) outliers start: 47 outliers final: 22 residues processed: 171 average time/residue: 0.5801 time to fit residues: 106.2844 Evaluate side-chains 166 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [83, 29, 105, 0, 39, 24, 89, 40, 43, 63, 101] chunk 83 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.148948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.104387 restraints weight = 9759.858| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.17 r_work: 0.2718 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9948 Z= 0.164 Angle : 0.543 8.160 13534 Z= 0.286 Chirality : 0.045 0.143 1496 Planarity : 0.004 0.038 1758 Dihedral : 6.877 58.614 1388 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 4.09 % Allowed : 13.95 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.23), residues: 1254 helix: -0.93 (0.44), residues: 122 sheet: -0.52 (0.24), residues: 457 loop : -0.75 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 91 TYR 0.013 0.001 TYR D 50 PHE 0.014 0.002 PHE A 19 TRP 0.016 0.002 TRP C 33 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 9938) covalent geometry : angle 0.54002 / 0.28 (13514) SS BOND : bond 0.00551 / 0.28 ( 10) SS BOND : angle 1.52798 / 0.68 ( 20) hydrogen bonds : bond 0.03477 / 2.33 ( 329) hydrogen bonds : angle 6.25877 / 4.52 ( 888) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.347 Fit side-chains REVERT: A 75 GLU cc_start: 0.8511 (mp0) cc_final: 0.8306 (mt-10) REVERT: A 77 ARG cc_start: 0.7638 (mpt180) cc_final: 0.6855 (ttt-90) REVERT: A 125 THR cc_start: 0.8920 (p) cc_final: 0.8468 (p) REVERT: A 166 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: A 208 ARG cc_start: 0.8476 (mpt180) cc_final: 0.8242 (mmp80) REVERT: A 401 SER cc_start: 0.8887 (p) cc_final: 0.8657 (m) REVERT: B 62 ARG cc_start: 0.7926 (mtp-110) cc_final: 0.7617 (mtm110) REVERT: B 93 ARG cc_start: 0.7310 (ptm160) cc_final: 0.6264 (ttt180) REVERT: B 137 LYS cc_start: 0.8559 (mttt) cc_final: 0.8093 (mtmt) REVERT: B 187 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8133 (tmm) REVERT: B 234 GLU cc_start: 0.7709 (pm20) cc_final: 0.7346 (pm20) REVERT: B 277 SER cc_start: 0.9015 (p) cc_final: 0.8663 (m) REVERT: B 278 ASP cc_start: 0.8325 (p0) cc_final: 0.8107 (p0) REVERT: B 312 GLU cc_start: 0.8095 (tp30) cc_final: 0.7886 (mm-30) REVERT: B 323 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8083 (mt-10) REVERT: B 365 GLU cc_start: 0.8338 (mp0) cc_final: 0.8044 (pm20) REVERT: B 387 MET cc_start: 0.8808 (mtm) cc_final: 0.8276 (mtm) REVERT: B 400 GLU cc_start: 0.8288 (tt0) cc_final: 0.7887 (tt0) REVERT: B 402 LYS cc_start: 0.7090 (mtpt) cc_final: 0.6862 (tptp) REVERT: C 3 GLN cc_start: 0.7837 (tt0) cc_final: 0.7342 (mm-40) REVERT: C 32 TYR cc_start: 0.8182 (m-80) cc_final: 0.7862 (m-80) REVERT: C 67 LYS cc_start: 0.8478 (tppt) cc_final: 0.8274 (tppt) REVERT: C 122 LYS cc_start: 0.7544 (tttt) cc_final: 0.7308 (tttp) REVERT: D 55 MET cc_start: 0.8867 (mmm) cc_final: 0.8586 (mmm) REVERT: D 81 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: D 103 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8136 (ttpp) outliers start: 44 outliers final: 23 residues processed: 175 average time/residue: 0.5465 time to fit residues: 102.7736 Evaluate side-chains 169 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [121, 93, 53, 35, 91, 37, 106, 19, 18, 48, 12] chunk 121 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.148201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.102265 restraints weight = 9782.860| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.92 r_work: 0.2697 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9948 Z= 0.168 Angle : 0.545 11.005 13534 Z= 0.287 Chirality : 0.045 0.143 1496 Planarity : 0.004 0.038 1758 Dihedral : 6.632 58.309 1386 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 4.37 % Allowed : 14.70 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.23), residues: 1254 helix: -0.75 (0.45), residues: 122 sheet: -0.45 (0.24), residues: 458 loop : -0.62 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 91 TYR 0.027 0.002 TYR C 150 PHE 0.014 0.002 PHE A 19 TRP 0.016 0.002 TRP C 33 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 9938) covalent geometry : angle 0.54151 / 0.29 (13514) SS BOND : bond 0.00640 / 0.32 ( 10) SS BOND : angle 1.59589 / 0.71 ( 20) hydrogen bonds : bond 0.03435 / 2.31 ( 329) hydrogen bonds : angle 6.13767 / 4.44 ( 888) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7694 (mpt180) cc_final: 0.6856 (ttt-90) REVERT: A 125 THR cc_start: 0.8959 (p) cc_final: 0.8502 (p) REVERT: A 166 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: A 180 GLU cc_start: 0.8388 (mp0) cc_final: 0.8179 (mp0) REVERT: A 192 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8489 (mp) REVERT: A 208 ARG cc_start: 0.8503 (mpt180) cc_final: 0.8274 (mmp80) REVERT: A 401 SER cc_start: 0.8922 (p) cc_final: 0.8698 (m) REVERT: B 62 ARG cc_start: 0.7891 (mtp-110) cc_final: 0.7598 (mtm110) REVERT: B 93 ARG cc_start: 0.7318 (ptm160) cc_final: 0.6201 (ttt180) REVERT: B 137 LYS cc_start: 0.8572 (mttt) cc_final: 0.8102 (mtmt) REVERT: B 187 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8171 (tmm) REVERT: B 234 GLU cc_start: 0.7781 (pm20) cc_final: 0.7411 (pm20) REVERT: B 277 SER cc_start: 0.9016 (p) cc_final: 0.8668 (m) REVERT: B 278 ASP cc_start: 0.8340 (p0) cc_final: 0.8090 (p0) REVERT: B 312 GLU cc_start: 0.8110 (tp30) cc_final: 0.7907 (mm-30) REVERT: B 323 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8109 (mt-10) REVERT: B 365 GLU cc_start: 0.8350 (mp0) cc_final: 0.8058 (pm20) REVERT: B 387 MET cc_start: 0.8828 (mtm) cc_final: 0.8307 (mtm) REVERT: B 400 GLU cc_start: 0.8287 (tt0) cc_final: 0.7899 (tt0) REVERT: B 402 LYS cc_start: 0.7086 (mtpt) cc_final: 0.6844 (tptp) REVERT: C 3 GLN cc_start: 0.7829 (tt0) cc_final: 0.7381 (mm-40) REVERT: C 32 TYR cc_start: 0.8196 (m-80) cc_final: 0.7857 (m-80) REVERT: C 69 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8166 (tttt) REVERT: C 122 LYS cc_start: 0.7504 (tttt) cc_final: 0.7246 (tttp) REVERT: D 81 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: D 103 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8192 (ttpp) outliers start: 47 outliers final: 25 residues processed: 184 average time/residue: 0.5675 time to fit residues: 112.1150 Evaluate side-chains 172 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [95, 39, 51, 49, 54, 114, 16, 65, 99, 60, 13] chunk 95 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 16 optimal weight: 0.0060 chunk 65 optimal weight: 0.0670 chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.150323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.105534 restraints weight = 9807.932| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.02 r_work: 0.2757 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9948 Z= 0.122 Angle : 0.512 8.909 13534 Z= 0.268 Chirality : 0.044 0.142 1496 Planarity : 0.004 0.039 1758 Dihedral : 6.469 59.292 1386 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 4.19 % Allowed : 15.07 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.23), residues: 1254 helix: -0.46 (0.46), residues: 122 sheet: -0.24 (0.24), residues: 441 loop : -0.55 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 91 TYR 0.011 0.001 TYR D 50 PHE 0.012 0.001 PHE A 191 TRP 0.014 0.001 TRP A 235 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9938) covalent geometry : angle 0.50976 / 0.27 (13514) SS BOND : bond 0.00659 / 0.33 ( 10) SS BOND : angle 1.26373 / 0.57 ( 20) hydrogen bonds : bond 0.03072 / 2.06 ( 329) hydrogen bonds : angle 5.90814 / 4.28 ( 888) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7619 (mpt180) cc_final: 0.6764 (ttt-90) REVERT: A 125 THR cc_start: 0.8977 (p) cc_final: 0.8745 (p) REVERT: A 192 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8434 (mp) REVERT: A 208 ARG cc_start: 0.8390 (mpt180) cc_final: 0.8145 (mmp80) REVERT: A 248 LEU cc_start: 0.8885 (mp) cc_final: 0.8671 (mt) REVERT: A 400 ARG cc_start: 0.8381 (mmt180) cc_final: 0.7790 (mmt90) REVERT: B 62 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.7578 (mtm110) REVERT: B 72 LYS cc_start: 0.8110 (ptmm) cc_final: 0.7881 (tptt) REVERT: B 93 ARG cc_start: 0.7228 (ptm160) cc_final: 0.6053 (ttt180) REVERT: B 137 LYS cc_start: 0.8459 (mttt) cc_final: 0.8014 (mtmt) REVERT: B 187 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8209 (tmm) REVERT: B 234 GLU cc_start: 0.7796 (pm20) cc_final: 0.7373 (pm20) REVERT: B 277 SER cc_start: 0.8995 (p) cc_final: 0.8664 (m) REVERT: B 323 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8079 (mt-10) REVERT: B 365 GLU cc_start: 0.8300 (mp0) cc_final: 0.8031 (pm20) REVERT: B 387 MET cc_start: 0.8789 (mtm) cc_final: 0.8258 (mtm) REVERT: B 400 GLU cc_start: 0.8229 (tt0) cc_final: 0.7940 (tt0) REVERT: B 402 LYS cc_start: 0.7012 (mtpt) cc_final: 0.6784 (mptt) REVERT: C 3 GLN cc_start: 0.7841 (tt0) cc_final: 0.7381 (mm-40) REVERT: C 32 TYR cc_start: 0.8161 (m-80) cc_final: 0.7829 (m-80) REVERT: C 69 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8138 (tttt) REVERT: D 55 MET cc_start: 0.8752 (mmm) cc_final: 0.8394 (mmm) REVERT: D 103 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8084 (ttpp) outliers start: 45 outliers final: 24 residues processed: 185 average time/residue: 0.5120 time to fit residues: 101.9872 Evaluate side-chains 173 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [119, 29, 81, 117, 92, 64, 97, 14, 46, 63, 44] chunk 119 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.146988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.090746 restraints weight = 9732.354| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.51 r_work: 0.2690 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 9948 Z= 0.262 Angle : 0.600 12.437 13534 Z= 0.315 Chirality : 0.047 0.155 1496 Planarity : 0.004 0.046 1758 Dihedral : 6.746 59.947 1386 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.28 % Allowed : 15.26 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1254 helix: -0.65 (0.45), residues: 122 sheet: -0.41 (0.24), residues: 452 loop : -0.49 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 91 TYR 0.017 0.002 TYR D 50 PHE 0.019 0.002 PHE A 19 TRP 0.021 0.002 TRP C 33 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 ( 9938) covalent geometry : angle 0.59645 / 0.31 (13514) SS BOND : bond 0.00695 / 0.34 ( 10) SS BOND : angle 1.78235 / 0.78 ( 20) hydrogen bonds : bond 0.03818 / 2.59 ( 329) hydrogen bonds : angle 6.17971 / 4.47 ( 888) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.458 Fit side-chains REVERT: A 77 ARG cc_start: 0.7672 (mpt180) cc_final: 0.6851 (ttt-90) REVERT: A 134 GLN cc_start: 0.8506 (mt0) cc_final: 0.8288 (mt0) REVERT: A 166 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: A 192 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 208 ARG cc_start: 0.8486 (mpt180) cc_final: 0.8262 (mmp80) REVERT: A 355 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8757 (mtt180) REVERT: A 400 ARG cc_start: 0.8356 (mmt180) cc_final: 0.7768 (mmt90) REVERT: B 62 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7579 (mtm110) REVERT: B 93 ARG cc_start: 0.7329 (ptm160) cc_final: 0.6139 (ttt180) REVERT: B 137 LYS cc_start: 0.8570 (mttt) cc_final: 0.8111 (mtmt) REVERT: B 187 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8087 (tmm) REVERT: B 234 GLU cc_start: 0.7764 (pm20) cc_final: 0.7303 (pm20) REVERT: B 323 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8131 (mt-10) REVERT: B 387 MET cc_start: 0.8761 (mtm) cc_final: 0.8204 (mtm) REVERT: B 400 GLU cc_start: 0.8254 (tt0) cc_final: 0.7935 (tt0) REVERT: B 402 LYS cc_start: 0.7041 (mtpt) cc_final: 0.6779 (mptt) REVERT: C 3 GLN cc_start: 0.7809 (tt0) cc_final: 0.7382 (mm-40) REVERT: C 32 TYR cc_start: 0.8154 (m-80) cc_final: 0.7806 (m-80) REVERT: C 51 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8708 (tp) REVERT: C 67 LYS cc_start: 0.8322 (tppt) cc_final: 0.8072 (tppt) REVERT: C 69 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8170 (tttt) REVERT: D 103 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8201 (ttpp) REVERT: D 205 VAL cc_start: 0.6026 (OUTLIER) cc_final: 0.5675 (p) outliers start: 46 outliers final: 27 residues processed: 174 average time/residue: 0.5261 time to fit residues: 98.8294 Evaluate side-chains 173 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [17, 46, 32, 60, 108, 57, 21, 71, 28, 48, 4] chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 57 optimal weight: 0.0570 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 chunk 4 optimal weight: 0.0270 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 32 ASN D 92 ASN D 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.151416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.107098 restraints weight = 9833.231| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.07 r_work: 0.2778 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9948 Z= 0.110 Angle : 0.509 9.449 13534 Z= 0.267 Chirality : 0.043 0.142 1496 Planarity : 0.004 0.045 1758 Dihedral : 6.410 57.813 1386 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.16 % Allowed : 17.21 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.23), residues: 1254 helix: -0.28 (0.46), residues: 122 sheet: -0.20 (0.24), residues: 437 loop : -0.43 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 91 TYR 0.017 0.001 TYR C 150 PHE 0.012 0.001 PHE A 191 TRP 0.012 0.001 TRP A 235 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9938) covalent geometry : angle 0.50711 / 0.27 (13514) SS BOND : bond 0.00542 / 0.27 ( 10) SS BOND : angle 1.27137 / 0.56 ( 20) hydrogen bonds : bond 0.02959 / 1.98 ( 329) hydrogen bonds : angle 5.82813 / 4.22 ( 888) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.402 Fit side-chains REVERT: A 77 ARG cc_start: 0.7582 (mpt180) cc_final: 0.6765 (ttt-90) REVERT: A 125 THR cc_start: 0.8999 (p) cc_final: 0.8794 (p) REVERT: A 192 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 208 ARG cc_start: 0.8363 (mpt180) cc_final: 0.8129 (mmp80) REVERT: A 355 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8767 (mtt90) REVERT: A 400 ARG cc_start: 0.8346 (mmt180) cc_final: 0.7790 (mmt90) REVERT: B 62 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.7443 (mtm110) REVERT: B 72 LYS cc_start: 0.8027 (ptmm) cc_final: 0.7745 (ttpt) REVERT: B 93 ARG cc_start: 0.7214 (ptm160) cc_final: 0.5974 (ttt180) REVERT: B 137 LYS cc_start: 0.8503 (mttt) cc_final: 0.8052 (mtmt) REVERT: B 233 ASP cc_start: 0.8493 (p0) cc_final: 0.8290 (p0) REVERT: B 234 GLU cc_start: 0.7779 (pm20) cc_final: 0.7280 (pm20) REVERT: B 277 SER cc_start: 0.8884 (p) cc_final: 0.8603 (m) REVERT: B 323 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8114 (mt-10) REVERT: B 365 GLU cc_start: 0.8246 (mp0) cc_final: 0.8000 (pm20) REVERT: B 387 MET cc_start: 0.8780 (mtm) cc_final: 0.8227 (mtm) REVERT: B 400 GLU cc_start: 0.8230 (tt0) cc_final: 0.7900 (tt0) REVERT: B 402 LYS cc_start: 0.7026 (mtpt) cc_final: 0.6809 (mptt) REVERT: C 3 GLN cc_start: 0.7792 (tt0) cc_final: 0.7365 (mm-40) REVERT: C 32 TYR cc_start: 0.8174 (m-80) cc_final: 0.7793 (m-80) REVERT: D 103 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8073 (ttpp) REVERT: D 205 VAL cc_start: 0.6038 (OUTLIER) cc_final: 0.5689 (p) outliers start: 34 outliers final: 17 residues processed: 173 average time/residue: 0.5634 time to fit residues: 104.6601 Evaluate side-chains 164 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [41, 60, 10, 21, 57, 77, 95, 109, 86, 35, 28] chunk 41 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 95 optimal weight: 30.0000 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.149160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.104165 restraints weight = 9711.397| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.89 r_work: 0.2708 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9948 Z= 0.172 Angle : 0.546 11.927 13534 Z= 0.286 Chirality : 0.045 0.148 1496 Planarity : 0.004 0.046 1758 Dihedral : 6.431 58.709 1383 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.79 % Allowed : 17.58 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1254 helix: -0.33 (0.46), residues: 122 sheet: -0.30 (0.24), residues: 452 loop : -0.40 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 91 TYR 0.014 0.001 TYR D 50 PHE 0.015 0.002 PHE A 19 TRP 0.016 0.002 TRP C 33 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 9938) covalent geometry : angle 0.54274 / 0.28 (13514) SS BOND : bond 0.00631 / 0.31 ( 10) SS BOND : angle 1.53186 / 0.67 ( 20) hydrogen bonds : bond 0.03343 / 2.26 ( 329) hydrogen bonds : angle 5.94242 / 4.30 ( 888) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.398 Fit side-chains REVERT: A 77 ARG cc_start: 0.7694 (mpt180) cc_final: 0.6774 (ttt-90) REVERT: A 120 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7364 (mt-10) REVERT: A 125 THR cc_start: 0.8963 (p) cc_final: 0.8516 (p) REVERT: A 166 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: A 192 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 208 ARG cc_start: 0.8461 (mpt180) cc_final: 0.8219 (mmp80) REVERT: A 400 ARG cc_start: 0.8370 (mmt180) cc_final: 0.7763 (mmt90) REVERT: B 72 LYS cc_start: 0.8028 (ptmm) cc_final: 0.7737 (ttpt) REVERT: B 93 ARG cc_start: 0.7248 (ptm160) cc_final: 0.5996 (ttt180) REVERT: B 108 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7738 (mt-10) REVERT: B 137 LYS cc_start: 0.8540 (mttt) cc_final: 0.8095 (mtmt) REVERT: B 234 GLU cc_start: 0.7748 (pm20) cc_final: 0.7231 (pm20) REVERT: B 277 SER cc_start: 0.8933 (p) cc_final: 0.8643 (m) REVERT: B 323 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8142 (mt-10) REVERT: B 365 GLU cc_start: 0.8226 (mp0) cc_final: 0.7926 (pm20) REVERT: B 387 MET cc_start: 0.8754 (mtm) cc_final: 0.8185 (mtm) REVERT: B 400 GLU cc_start: 0.8275 (tt0) cc_final: 0.7894 (tt0) REVERT: B 402 LYS cc_start: 0.7099 (mtpt) cc_final: 0.6779 (mptt) REVERT: C 3 GLN cc_start: 0.7844 (tt0) cc_final: 0.7382 (mm-40) REVERT: C 32 TYR cc_start: 0.8178 (m-80) cc_final: 0.7806 (m-80) REVERT: C 63 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8004 (tttt) REVERT: D 103 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8117 (ttpp) REVERT: D 205 VAL cc_start: 0.6047 (OUTLIER) cc_final: 0.5700 (p) outliers start: 30 outliers final: 21 residues processed: 166 average time/residue: 0.5450 time to fit residues: 97.2396 Evaluate side-chains 164 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [21, 62, 92, 99, 18, 44, 122, 87, 14, 54, 51] chunk 21 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.149590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.104364 restraints weight = 9740.128| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.97 r_work: 0.2705 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9948 Z= 0.170 Angle : 0.548 11.634 13534 Z= 0.286 Chirality : 0.045 0.147 1496 Planarity : 0.004 0.046 1758 Dihedral : 6.506 58.746 1383 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.70 % Allowed : 17.86 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.23), residues: 1254 helix: -0.34 (0.46), residues: 122 sheet: -0.30 (0.24), residues: 452 loop : -0.38 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 91 TYR 0.014 0.002 TYR D 50 PHE 0.014 0.002 PHE A 19 TRP 0.016 0.002 TRP C 33 HIS 0.007 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 9938) covalent geometry : angle 0.54582 / 0.28 (13514) SS BOND : bond 0.00670 / 0.33 ( 10) SS BOND : angle 1.50649 / 0.66 ( 20) hydrogen bonds : bond 0.03304 / 2.24 ( 329) hydrogen bonds : angle 5.92615 / 4.29 ( 888) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7702 (mpt180) cc_final: 0.6769 (ttt-90) REVERT: A 120 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7312 (mt-10) REVERT: A 125 THR cc_start: 0.8959 (p) cc_final: 0.8615 (p) REVERT: A 192 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 208 ARG cc_start: 0.8467 (mpt180) cc_final: 0.8218 (mmp80) REVERT: A 400 ARG cc_start: 0.8394 (mmt180) cc_final: 0.7769 (mmt90) REVERT: B 62 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7411 (mtm110) REVERT: B 72 LYS cc_start: 0.8047 (ptmm) cc_final: 0.7797 (ttpt) REVERT: B 93 ARG cc_start: 0.7146 (ptm160) cc_final: 0.5932 (ttt180) REVERT: B 137 LYS cc_start: 0.8533 (mttt) cc_final: 0.8089 (mtmt) REVERT: B 234 GLU cc_start: 0.7740 (pm20) cc_final: 0.7171 (mp0) REVERT: B 277 SER cc_start: 0.8932 (p) cc_final: 0.8638 (m) REVERT: B 323 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8148 (mt-10) REVERT: B 365 GLU cc_start: 0.8230 (mp0) cc_final: 0.7970 (pm20) REVERT: B 387 MET cc_start: 0.8808 (mtm) cc_final: 0.8249 (mtm) REVERT: B 400 GLU cc_start: 0.8291 (tt0) cc_final: 0.7930 (tt0) REVERT: B 402 LYS cc_start: 0.7098 (mtpt) cc_final: 0.6790 (mptt) REVERT: C 3 GLN cc_start: 0.7854 (tt0) cc_final: 0.7385 (mm-40) REVERT: C 32 TYR cc_start: 0.8192 (m-80) cc_final: 0.7807 (m-80) REVERT: C 63 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8084 (tttt) REVERT: D 103 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8108 (ttpp) REVERT: D 105 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7521 (mp0) REVERT: D 205 VAL cc_start: 0.6062 (OUTLIER) cc_final: 0.5720 (p) outliers start: 29 outliers final: 24 residues processed: 164 average time/residue: 0.5545 time to fit residues: 97.8037 Evaluate side-chains 166 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [93, 95, 45, 11, 25, 74, 107, 94, 48, 26, 73] chunk 93 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.148476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.096889 restraints weight = 9743.678| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.61 r_work: 0.2688 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9948 Z= 0.171 Angle : 0.544 11.330 13534 Z= 0.285 Chirality : 0.045 0.141 1496 Planarity : 0.004 0.045 1758 Dihedral : 6.513 59.387 1383 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.98 % Allowed : 17.77 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1254 helix: -0.35 (0.46), residues: 122 sheet: -0.28 (0.24), residues: 452 loop : -0.37 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 91 TYR 0.014 0.001 TYR D 50 PHE 0.015 0.002 PHE A 19 TRP 0.015 0.002 TRP C 33 HIS 0.007 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 9938) covalent geometry : angle 0.54082 / 0.28 (13514) SS BOND : bond 0.00674 / 0.33 ( 10) SS BOND : angle 1.50347 / 0.65 ( 20) hydrogen bonds : bond 0.03325 / 2.25 ( 329) hydrogen bonds : angle 5.92184 / 4.29 ( 888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3885.23 seconds wall clock time: 66 minutes 55.02 seconds (4015.02 seconds total)