Starting phenix.real_space_refine
on Wed Mar  4 17:44:59 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7xt9_33443/03_2026/7xt9_33443_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xt9_33443/03_2026/7xt9_33443.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xt9_33443/03_2026/7xt9_33443_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xt9_33443/03_2026/7xt9_33443_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xt9_33443/03_2026/7xt9_33443.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xt9_33443/03_2026/7xt9_33443.map"
  }
  resolution = 3.2
  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=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    4840      2.51       5
     N    1276      2.21       5
     O    1351      1.98       5
     H    7351      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14875
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 3928
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5108
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 885
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 4793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 4793
          Classifications: {'peptide': 294}
          Link IDs: {'PTRANS': 11, 'TRANS': 282}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 161
          Unusual residues: {'CLR': 4, 'PLM': 2, 'SRO': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 2.67, per 1000 atoms: 0.18
  Number of scatterers: 14875
  At special positions: 0
  Unit cell: (96.12, 102.6, 119.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     O    1351      8.00
     N    1276      7.00
     C    4840      6.00
     H    7351      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  92 " - pdb=" SG  CYS R 183 " 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: 1.01
  Conformation dependent library (CDL) restraints added in 478.9 milliseconds
  

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1758

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 8 sheets defined
      49.6% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 3.960A  pdb=" N   ARG A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.966A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.513A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.761A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 46
      removed outlier: 4.528A  pdb=" N   LYS G  46 " --> pdb=" O   GLU G  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 19 through 46
      removed outlier: 4.021A  pdb=" N   THR R  23 " --> pdb=" O   VAL R  19 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 46 through 51
      removed outlier: 3.522A  pdb=" N   LYS R  51 " --> pdb=" O   ARG R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 53 through 72
      removed outlier: 4.029A  pdb=" N   PHE R  57 " --> pdb=" O   LYS R  53 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ILE R  58 " --> pdb=" O   THR R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 83
    Processing helix  chain 'R' and resid 88 through 123
    Processing helix  chain 'R' and resid 124 through 126
      No H-bonds generated for 'chain 'R' and resid 124 through 126'
    Processing helix  chain 'R' and resid 127 through 132
    Processing helix  chain 'R' and resid 133 through 159
      Proline residue:  R 148  - end of helix
      removed outlier: 3.816A  pdb=" N   ILE R 151 " --> pdb=" O   ILE R 147 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   LEU R 154 " --> pdb=" O   PHE R 150 " (cutoff:3.500A)
      Proline residue:  R 155  - end of helix
      removed outlier: 3.578A  pdb=" N   GLN R 158 " --> pdb=" O   LEU R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 174
      removed outlier: 4.013A  pdb=" N   PHE R 174 " --> pdb=" O   GLU R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 188 through 200
    Processing helix  chain 'R' and resid 200 through 233
    Processing helix  chain 'R' and resid 254 through 281
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 282 through 285
      removed outlier: 3.746A  pdb=" N   ASP R 285 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 282 through 285'
    Processing helix  chain 'R' and resid 289 through 307
      removed outlier: 3.607A  pdb=" N   ASN R 303 " --> pdb=" O   LEU R 299 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   SER R 304 " --> pdb=" O   GLY R 300 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLY R 305 " --> pdb=" O   TYR R 301 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 307 through 312
      removed outlier: 3.649A  pdb=" N   ALA R 312 " --> pdb=" O   PRO R 308 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 315 through 328
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 9.655A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.478A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.439A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.647A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.693A  pdb=" N   CYS B 121 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.600A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.935A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.502A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.703A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1176 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: 3.39

  Time building geometry restraints manager: 1.44 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 7319
        1.03 -     1.23: 56
        1.23 -     1.43: 3163
        1.43 -     1.62: 4418
        1.62 -     1.82: 80
  Bond restraints: 15036
  Sorted by residual:
  bond pdb=" CZ2 SRO R 407 "
       pdb=" CH2 SRO R 407 "
    ideal  model  delta    sigma   weight residual
    1.386  1.522 -0.136 2.00e-02 2.50e+03 4.62e+01
  bond pdb=" CG  SRO R 407 "
       pdb=" CD2 SRO R 407 "
    ideal  model  delta    sigma   weight residual
    1.438  1.510 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C13 CLR R 404 "
       pdb=" C17 CLR R 404 "
    ideal  model  delta    sigma   weight residual
    1.550  1.487  0.063 2.00e-02 2.50e+03 1.00e+01
  bond pdb=" C13 CLR R 402 "
       pdb=" C17 CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.550  1.487  0.063 2.00e-02 2.50e+03 9.87e+00
  bond pdb=" CD1 SRO R 407 "
       pdb=" NE1 SRO R 407 "
    ideal  model  delta    sigma   weight residual
    1.377  1.315  0.062 2.00e-02 2.50e+03 9.73e+00
  ... (remaining 15031 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 26853
        2.08 -     4.15: 143
        4.15 -     6.23: 18
        6.23 -     8.31: 6
        8.31 -    10.38: 1
  Bond angle restraints: 27021
  Sorted by residual:
  angle pdb=" CA  PRO G  55 "
        pdb=" N   PRO G  55 "
        pdb=" CD  PRO G  55 "
      ideal   model   delta    sigma   weight residual
     112.00  105.20    6.80 1.40e+00 5.10e-01 2.36e+01
  angle pdb=" N   PRO G  55 "
        pdb=" CD  PRO G  55 "
        pdb=" CG  PRO G  55 "
      ideal   model   delta    sigma   weight residual
     103.20   97.04    6.16 1.50e+00 4.44e-01 1.69e+01
  angle pdb=" CD1 SRO R 407 "
        pdb=" NE1 SRO R 407 "
        pdb=" CE2 SRO R 407 "
      ideal   model   delta    sigma   weight residual
     109.10  119.48  -10.38 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" C20 CLR R 403 "
        pdb=" C22 CLR R 403 "
        pdb=" C23 CLR R 403 "
      ideal   model   delta    sigma   weight residual
     115.57  107.47    8.10 3.00e+00 1.11e-01 7.30e+00
  angle pdb=" CG  SRO R 407 "
        pdb=" CD1 SRO R 407 "
        pdb=" NE1 SRO R 407 "
      ideal   model   delta    sigma   weight residual
     110.16  102.33    7.83 3.00e+00 1.11e-01 6.81e+00
  ... (remaining 27016 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.08: 6895
       24.08 -    48.16: 302
       48.16 -    72.24: 57
       72.24 -    96.33: 19
       96.33 -   120.41: 3
  Dihedral angle restraints: 7276
    sinusoidal: 4047
      harmonic: 3229
  Sorted by residual:
  dihedral pdb=" C1  CLR R 402 "
           pdb=" C2  CLR R 402 "
           pdb=" C3  CLR R 402 "
           pdb=" O1  CLR R 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.04   59.63  120.41     1      3.00e+01 1.11e-03 1.61e+01
  dihedral pdb=" C1  CLR R 402 "
           pdb=" C2  CLR R 402 "
           pdb=" C3  CLR R 402 "
           pdb=" C4  CLR R 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.41  -60.87  118.28     1      3.00e+01 1.11e-03 1.57e+01
  dihedral pdb=" C10 CLR R 402 "
           pdb=" C1  CLR R 402 "
           pdb=" C2  CLR R 402 "
           pdb=" C3  CLR R 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.83   41.82  -98.65     1      3.00e+01 1.11e-03 1.23e+01
  ... (remaining 7273 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1047
       0.068 -    0.136: 124
       0.136 -    0.204: 12
       0.204 -    0.271: 0
       0.271 -    0.339: 4
  Chirality restraints: 1187
  Sorted by residual:
  chirality pdb=" C14 CLR R 403 "
            pdb=" C13 CLR R 403 "
            pdb=" C15 CLR R 403 "
            pdb=" C8  CLR R 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.66    0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" C14 CLR R 402 "
            pdb=" C13 CLR R 402 "
            pdb=" C15 CLR R 402 "
            pdb=" C8  CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.63    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" C14 CLR R 401 "
            pdb=" C13 CLR R 401 "
            pdb=" C15 CLR R 401 "
            pdb=" C8  CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.63    0.31 2.00e-01 2.50e+01 2.40e+00
  ... (remaining 1184 not shown)

  Planarity restraints: 2188
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G  54 "   -0.043 5.00e-02 4.00e+02   6.27e-02 6.29e+00
        pdb=" N   PRO G  55 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO G  55 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO G  55 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 202 "    0.020 5.00e-02 4.00e+02   3.04e-02 1.47e+00
        pdb=" N   PRO R 203 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO R 203 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO R 203 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "   -0.017 5.00e-02 4.00e+02   2.54e-02 1.03e+00
        pdb=" N   PRO B  39 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 2185 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 812
        2.19 -     2.80: 30374
        2.80 -     3.40: 42406
        3.40 -     4.00: 54476
        4.00 -     4.60: 84912
  Nonbonded interactions: 212980
  Sorted by model distance:
  nonbonded pdb=" H   PHE B 235 "
            pdb=" O   ALA B 240 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" HG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     1.600 2.450
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" HG1 THR B 165 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" HH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     1.637 2.450
  nonbonded pdb=" O   ASP B 186 "
            pdb=" H   CYS B 204 "
     model   vdw
     1.642 2.450
  ... (remaining 212975 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.100
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.780
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
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      :  0.004   0.136   7686  Z= 0.221
  Angle     :  0.599  10.383  10423  Z= 0.318
  Chirality :  0.046   0.339   1187
  Planarity :  0.003   0.063   1294
  Dihedral  : 13.994 120.407   3017
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.29), residues: 913
  helix:  2.69 (0.26), residues: 426
  sheet:  0.95 (0.41), residues: 169
  loop :  0.63 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  20 
 TYR   0.009   0.001   TYR B 105 
 PHE   0.007   0.001   PHE B 234 
 TRP   0.009   0.001   TRP R 298 
 HIS   0.002   0.000   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 7685)
  covalent geometry    : angle       0.59858 (10421)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       1.33468 (    2)
  hydrogen bonds       : bond        0.15735 (  404)
  hydrogen bonds       : angle       6.02256 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 ASP cc_start: 0.7744 (m-30) cc_final: 0.7491 (m-30)
REVERT: G   32 LYS cc_start: 0.7454 (tptp) cc_final: 0.7164 (tptt)
REVERT: G   36 ASP cc_start: 0.7606 (m-30) cc_final: 0.7335 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.2402
  time to fit residues: 42.1649
Evaluate side-chains
  125 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.0060
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    2.0004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
R 278 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.155946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.118451 restraints weight = 22781.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.00
r_work: 0.3071 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7686  Z= 0.188
  Angle     :  0.543   7.548  10423  Z= 0.291
  Chirality :  0.042   0.148   1187
  Planarity :  0.004   0.036   1294
  Dihedral  :  6.304  50.190   1300
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  5.37 %
    Favored  : 94.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.15 (0.29), residues: 913
  helix:  2.49 (0.25), residues: 418
  sheet:  0.57 (0.40), residues: 167
  loop :  0.61 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  38 
 TYR   0.013   0.002   TYR A 339 
 PHE   0.022   0.002   PHE R 275 
 TRP   0.017   0.002   TRP B  82 
 HIS   0.007   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 7685)
  covalent geometry    : angle       0.54264 (10421)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       1.24921 (    2)
  hydrogen bonds       : bond        0.04585 (  404)
  hydrogen bonds       : angle       5.00408 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 ASP cc_start: 0.8647 (m-30) cc_final: 0.8389 (m-30)
REVERT: B   10 GLU cc_start: 0.6714 (tp30) cc_final: 0.6499 (tp30)
REVERT: B   69 LEU cc_start: 0.8863 (mt) cc_final: 0.8592 (mm)
REVERT: B  254 ASP cc_start: 0.8342 (t0) cc_final: 0.8136 (t0)
REVERT: B  258 ASP cc_start: 0.7500 (t0) cc_final: 0.6907 (t0)
REVERT: G   32 LYS cc_start: 0.7323 (tptp) cc_final: 0.7102 (tptt)
REVERT: G   36 ASP cc_start: 0.7828 (m-30) cc_final: 0.7450 (m-30)
REVERT: R   55 ASN cc_start: 0.8809 (m-40) cc_final: 0.8585 (m-40)
REVERT: R  319 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7134 (ttt180)
  outliers start: 4
  outliers final: 4
  residues processed: 130
  average time/residue: 0.2509
  time to fit residues: 41.1916
Evaluate side-chains
  121 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.155574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.118215 restraints weight = 23029.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.02
r_work: 0.3088 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7686  Z= 0.136
  Angle     :  0.476   5.469  10423  Z= 0.256
  Chirality :  0.040   0.142   1187
  Planarity :  0.004   0.037   1294
  Dihedral  :  5.744  57.713   1300
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  7.87 %
    Favored  : 91.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.29), residues: 913
  helix:  2.58 (0.25), residues: 417
  sheet:  0.35 (0.40), residues: 169
  loop :  0.61 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 129 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.014   0.001   PHE R 275 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7685)
  covalent geometry    : angle       0.47625 (10421)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       1.02873 (    2)
  hydrogen bonds       : bond        0.04148 (  404)
  hydrogen bonds       : angle       4.67300 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7344 (tt0)
REVERT: A  378 ASP cc_start: 0.8628 (m-30) cc_final: 0.8408 (m-30)
REVERT: B   69 LEU cc_start: 0.8920 (mt) cc_final: 0.8653 (mm)
REVERT: B   74 SER cc_start: 0.9179 (t) cc_final: 0.8923 (p)
REVERT: B  258 ASP cc_start: 0.7497 (t0) cc_final: 0.6920 (t0)
REVERT: G   32 LYS cc_start: 0.7156 (tptp) cc_final: 0.6838 (tptt)
REVERT: G   36 ASP cc_start: 0.7872 (m-30) cc_final: 0.7513 (m-30)
REVERT: R   50 ARG cc_start: 0.7367 (ttp-110) cc_final: 0.7148 (ttp-110)
REVERT: R  139 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7535 (mp)
  outliers start: 5
  outliers final: 4
  residues processed: 139
  average time/residue: 0.2509
  time to fit residues: 44.2104
Evaluate side-chains
  133 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 70 optimal weight:    0.5980
   chunk 36 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.156049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.119065 restraints weight = 22719.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.99
r_work: 0.3117 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7686  Z= 0.117
  Angle     :  0.461   5.122  10423  Z= 0.247
  Chirality :  0.039   0.137   1187
  Planarity :  0.003   0.032   1294
  Dihedral  :  5.523  56.262   1300
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  9.86 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.29), residues: 913
  helix:  2.62 (0.25), residues: 420
  sheet:  0.09 (0.39), residues: 174
  loop :  0.64 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 317 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.013   0.001   PHE R  63 
 TRP   0.011   0.001   TRP R 298 
 HIS   0.004   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7685)
  covalent geometry    : angle       0.46082 (10421)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       0.69759 (    2)
  hydrogen bonds       : bond        0.03837 (  404)
  hydrogen bonds       : angle       4.51974 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7340 (tt0)
REVERT: A  378 ASP cc_start: 0.8561 (m-30) cc_final: 0.8324 (m-30)
REVERT: B   69 LEU cc_start: 0.8921 (mt) cc_final: 0.8663 (mm)
REVERT: B   74 SER cc_start: 0.9152 (t) cc_final: 0.8932 (p)
REVERT: B  254 ASP cc_start: 0.8259 (t0) cc_final: 0.8038 (t0)
REVERT: B  258 ASP cc_start: 0.7518 (t0) cc_final: 0.6932 (t0)
REVERT: B  333 ASP cc_start: 0.8758 (p0) cc_final: 0.8291 (p0)
REVERT: G   32 LYS cc_start: 0.7194 (tptp) cc_final: 0.6881 (tptt)
REVERT: G   36 ASP cc_start: 0.7913 (m-30) cc_final: 0.7574 (m-30)
REVERT: R  139 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7565 (mp)
  outliers start: 8
  outliers final: 5
  residues processed: 138
  average time/residue: 0.2616
  time to fit residues: 45.4969
Evaluate side-chains
  131 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 125
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 58 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.153018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.116057 restraints weight = 22992.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 1.96
r_work: 0.3033 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7686  Z= 0.177
  Angle     :  0.498   5.699  10423  Z= 0.269
  Chirality :  0.040   0.144   1187
  Planarity :  0.004   0.043   1294
  Dihedral  :  5.864  53.641   1300
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.49 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.28), residues: 913
  helix:  2.47 (0.25), residues: 417
  sheet: -0.20 (0.38), residues: 180
  loop :  0.54 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 129 
 TYR   0.014   0.001   TYR A 339 
 PHE   0.017   0.002   PHE R 275 
 TRP   0.011   0.002   TRP R 298 
 HIS   0.005   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 7685)
  covalent geometry    : angle       0.49769 (10421)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.80393 (    2)
  hydrogen bonds       : bond        0.04135 (  404)
  hydrogen bonds       : angle       4.63311 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7453 (tt0)
REVERT: A   28 LYS cc_start: 0.7867 (ptpp) cc_final: 0.7612 (mtpt)
REVERT: A  378 ASP cc_start: 0.8634 (m-30) cc_final: 0.8385 (m-30)
REVERT: B   69 LEU cc_start: 0.8945 (mt) cc_final: 0.8667 (mm)
REVERT: B  258 ASP cc_start: 0.7522 (t0) cc_final: 0.6965 (t0)
REVERT: G   32 LYS cc_start: 0.7227 (tptp) cc_final: 0.6973 (tptt)
REVERT: G   36 ASP cc_start: 0.8021 (m-30) cc_final: 0.7760 (m-30)
REVERT: R   55 ASN cc_start: 0.8897 (m-40) cc_final: 0.8652 (m-40)
REVERT: R  139 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7626 (mp)
  outliers start: 9
  outliers final: 7
  residues processed: 135
  average time/residue: 0.2478
  time to fit residues: 42.1697
Evaluate side-chains
  132 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.6984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.152773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.115637 restraints weight = 22850.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.02
r_work: 0.3038 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7686  Z= 0.157
  Angle     :  0.487   6.208  10423  Z= 0.262
  Chirality :  0.040   0.142   1187
  Planarity :  0.004   0.044   1294
  Dihedral  :  5.737  52.888   1300
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.11 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.79 (0.28), residues: 913
  helix:  2.47 (0.25), residues: 417
  sheet: -0.19 (0.39), residues: 175
  loop :  0.39 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 129 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.015   0.001   PHE R 275 
 TRP   0.011   0.001   TRP R 298 
 HIS   0.005   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7685)
  covalent geometry    : angle       0.48731 (10421)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.79639 (    2)
  hydrogen bonds       : bond        0.04013 (  404)
  hydrogen bonds       : angle       4.58760 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7415 (tt0)
REVERT: A   28 LYS cc_start: 0.7816 (ptpp) cc_final: 0.7554 (mtpt)
REVERT: A  378 ASP cc_start: 0.8618 (m-30) cc_final: 0.8375 (m-30)
REVERT: B   69 LEU cc_start: 0.8943 (mt) cc_final: 0.8676 (mm)
REVERT: B  258 ASP cc_start: 0.7501 (t0) cc_final: 0.7011 (t0)
REVERT: G   32 LYS cc_start: 0.7237 (tptp) cc_final: 0.6995 (tptt)
REVERT: G   36 ASP cc_start: 0.8027 (m-30) cc_final: 0.7757 (m-30)
REVERT: R   55 ASN cc_start: 0.8900 (m-40) cc_final: 0.8648 (m-40)
REVERT: R  139 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7598 (mp)
  outliers start: 8
  outliers final: 5
  residues processed: 132
  average time/residue: 0.2579
  time to fit residues: 42.9270
Evaluate side-chains
  130 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 124
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 54 optimal weight:    0.2980
   chunk 59 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.154218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.117878 restraints weight = 22582.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.92
r_work: 0.3066 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7686  Z= 0.118
  Angle     :  0.457   5.410  10423  Z= 0.246
  Chirality :  0.039   0.135   1187
  Planarity :  0.004   0.036   1294
  Dihedral  :  5.351  52.463   1300
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.11 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.94 (0.29), residues: 913
  helix:  2.62 (0.25), residues: 417
  sheet: -0.15 (0.39), residues: 173
  loop :  0.45 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 129 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.012   0.001   PHE R 275 
 TRP   0.011   0.001   TRP R 298 
 HIS   0.004   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7685)
  covalent geometry    : angle       0.45727 (10421)
  SS BOND              : bond        0.00052 (    1)
  SS BOND              : angle       0.75350 (    2)
  hydrogen bonds       : bond        0.03766 (  404)
  hydrogen bonds       : angle       4.42757 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7449 (tt0)
REVERT: A  378 ASP cc_start: 0.8593 (m-30) cc_final: 0.8357 (m-30)
REVERT: B   69 LEU cc_start: 0.8944 (mt) cc_final: 0.8689 (mm)
REVERT: B  258 ASP cc_start: 0.7555 (t0) cc_final: 0.7068 (t0)
REVERT: G   32 LYS cc_start: 0.7231 (tptp) cc_final: 0.6995 (tptt)
REVERT: G   36 ASP cc_start: 0.8016 (m-30) cc_final: 0.7750 (m-30)
REVERT: R   55 ASN cc_start: 0.8880 (m-40) cc_final: 0.8664 (m-40)
REVERT: R  139 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7589 (mp)
  outliers start: 8
  outliers final: 6
  residues processed: 131
  average time/residue: 0.2511
  time to fit residues: 41.6791
Evaluate side-chains
  130 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 23 optimal weight:    8.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.154682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.118062 restraints weight = 22930.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.99
r_work: 0.3073 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7686  Z= 0.111
  Angle     :  0.452   4.946  10423  Z= 0.244
  Chirality :  0.039   0.134   1187
  Planarity :  0.004   0.051   1294
  Dihedral  :  5.207  53.270   1300
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 11.36 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.98 (0.29), residues: 913
  helix:  2.74 (0.26), residues: 414
  sheet: -0.27 (0.39), residues: 179
  loop :  0.46 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 129 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.012   0.001   PHE R 275 
 TRP   0.011   0.001   TRP R 298 
 HIS   0.004   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7685)
  covalent geometry    : angle       0.45181 (10421)
  SS BOND              : bond        0.00048 (    1)
  SS BOND              : angle       0.82552 (    2)
  hydrogen bonds       : bond        0.03703 (  404)
  hydrogen bonds       : angle       4.35283 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 127
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7395 (tt0)
REVERT: A  378 ASP cc_start: 0.8589 (m-30) cc_final: 0.8353 (m-30)
REVERT: B   69 LEU cc_start: 0.8939 (mt) cc_final: 0.8689 (mm)
REVERT: B  258 ASP cc_start: 0.7530 (t0) cc_final: 0.7023 (t0)
REVERT: B  333 ASP cc_start: 0.8760 (p0) cc_final: 0.8354 (p0)
REVERT: G   32 LYS cc_start: 0.7281 (tptp) cc_final: 0.7043 (tptt)
REVERT: G   36 ASP cc_start: 0.8005 (m-30) cc_final: 0.7741 (m-30)
REVERT: R   55 ASN cc_start: 0.8851 (m-40) cc_final: 0.8607 (m-40)
  outliers start: 6
  outliers final: 6
  residues processed: 131
  average time/residue: 0.2667
  time to fit residues: 43.9219
Evaluate side-chains
  132 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   chunk 47 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.153602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.116764 restraints weight = 23015.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.00
r_work: 0.3048 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7686  Z= 0.132
  Angle     :  0.470   5.309  10423  Z= 0.253
  Chirality :  0.039   0.137   1187
  Planarity :  0.004   0.044   1294
  Dihedral  :  5.426  56.381   1300
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.11 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.87 (0.29), residues: 913
  helix:  2.69 (0.25), residues: 411
  sheet: -0.41 (0.38), residues: 185
  loop :  0.45 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 129 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.014   0.001   PHE R 275 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7685)
  covalent geometry    : angle       0.46965 (10421)
  SS BOND              : bond        0.00055 (    1)
  SS BOND              : angle       0.78428 (    2)
  hydrogen bonds       : bond        0.03829 (  404)
  hydrogen bonds       : angle       4.38583 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7450 (tt0)
REVERT: A  378 ASP cc_start: 0.8610 (m-30) cc_final: 0.8372 (m-30)
REVERT: B   69 LEU cc_start: 0.8933 (mt) cc_final: 0.8687 (mm)
REVERT: B  258 ASP cc_start: 0.7449 (t0) cc_final: 0.6839 (t0)
REVERT: G   32 LYS cc_start: 0.7328 (tptp) cc_final: 0.7111 (tptt)
REVERT: G   36 ASP cc_start: 0.8037 (m-30) cc_final: 0.7789 (m-30)
REVERT: R   55 ASN cc_start: 0.8905 (m-40) cc_final: 0.8698 (m-40)
REVERT: R  182 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.6337 (p90)
  outliers start: 8
  outliers final: 7
  residues processed: 133
  average time/residue: 0.2649
  time to fit residues: 44.6037
Evaluate side-chains
  129 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  182 TYR
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.155136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.118559 restraints weight = 22798.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.98
r_work: 0.3078 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7686  Z= 0.109
  Angle     :  0.461   5.071  10423  Z= 0.248
  Chirality :  0.039   0.131   1187
  Planarity :  0.004   0.045   1294
  Dihedral  :  5.203  58.683   1300
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.36 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.99 (0.29), residues: 913
  helix:  2.77 (0.25), residues: 414
  sheet: -0.30 (0.39), residues: 180
  loop :  0.46 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 129 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.011   0.001   PHE A 212 
 TRP   0.011   0.001   TRP R 298 
 HIS   0.003   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 7685)
  covalent geometry    : angle       0.46042 (10421)
  SS BOND              : bond        0.00035 (    1)
  SS BOND              : angle       0.81749 (    2)
  hydrogen bonds       : bond        0.03640 (  404)
  hydrogen bonds       : angle       4.27053 ( 1176)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7355 (tt0)
REVERT: A  378 ASP cc_start: 0.8573 (m-30) cc_final: 0.8339 (m-30)
REVERT: B   69 LEU cc_start: 0.8932 (mt) cc_final: 0.8690 (mm)
REVERT: B  153 ASP cc_start: 0.8063 (p0) cc_final: 0.7849 (p0)
REVERT: B  181 THR cc_start: 0.7983 (p) cc_final: 0.7500 (m)
REVERT: B  258 ASP cc_start: 0.7410 (t0) cc_final: 0.6859 (t0)
REVERT: B  333 ASP cc_start: 0.8761 (p0) cc_final: 0.8351 (p0)
REVERT: G   32 LYS cc_start: 0.7278 (tptp) cc_final: 0.7040 (tptt)
REVERT: G   36 ASP cc_start: 0.8031 (m-30) cc_final: 0.7763 (m-30)
REVERT: R   55 ASN cc_start: 0.8833 (m-40) cc_final: 0.8608 (m-40)
REVERT: R  139 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7461 (mp)
REVERT: R  182 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.6329 (p90)
  outliers start: 9
  outliers final: 6
  residues processed: 129
  average time/residue: 0.2747
  time to fit residues: 44.6771
Evaluate side-chains
  129 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  182 TYR
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    1.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.153140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.116866 restraints weight = 22812.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.89
r_work: 0.3072 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7686  Z= 0.157
  Angle     :  0.492   5.584  10423  Z= 0.266
  Chirality :  0.040   0.138   1187
  Planarity :  0.004   0.040   1294
  Dihedral  :  5.567  58.686   1300
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.61 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.29), residues: 913
  helix:  2.64 (0.25), residues: 411
  sheet: -0.43 (0.39), residues: 185
  loop :  0.38 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 129 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.014   0.001   PHE R  91 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7685)
  covalent geometry    : angle       0.49202 (10421)
  SS BOND              : bond        0.00099 (    1)
  SS BOND              : angle       0.79888 (    2)
  hydrogen bonds       : bond        0.03929 (  404)
  hydrogen bonds       : angle       4.43733 ( 1176)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4281.45 seconds
wall clock time: 73 minutes 6.76 seconds (4386.76 seconds total)