Starting phenix.real_space_refine
on Fri Jun 13 17:25:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xt9_33443/06_2025/7xt9_33443_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xt9_33443/06_2025/7xt9_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xt9_33443/06_2025/7xt9_33443.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xt9_33443/06_2025/7xt9_33443.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xt9_33443/06_2025/7xt9_33443_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xt9_33443/06_2025/7xt9_33443_trim.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.27, per 1000 atoms: 0.49
  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: 3.72
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.27
  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: 4.93

  Time building geometry restraints manager: 4.50 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:             0.530
  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:             0.230
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     32.630
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.890
-------------------------------------------------------------------------------
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 : 5.49
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.009   0.001   TRP R 298 
 HIS   0.002   0.000   HIS B  54 
 PHE   0.007   0.001   PHE B 234 
 TYR   0.009   0.001   TYR B 105 
 ARG   0.009   0.001   ARG A  20 

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

*********************** 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  : 1.093 
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: 0.7453 (tptp) cc_final: 0.7164 (tptt)
REVERT: G   36 ASP cc_start: 0.7606 (m-30) cc_final: 0.7336 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.5216
  time to fit residues: 91.4659
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  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 46 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 70 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  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 = 0.3685 r_free = 0.3685 target = 0.155562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.117916 restraints weight = 22845.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.02
r_work: 0.3076 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7686  Z= 0.192
  Angle     :  0.541   7.098  10423  Z= 0.291
  Chirality :  0.042   0.149   1187
  Planarity :  0.004   0.035   1294
  Dihedral  :  6.377  51.878   1300
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  5.37 %
    Favored  : 93.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.29), residues: 913
  helix:  2.47 (0.25), residues: 418
  sheet:  0.55 (0.40), residues: 167
  loop :  0.60 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.006   0.001   HIS R 109 
 PHE   0.021   0.002   PHE R 275 
 TYR   0.013   0.002   TYR A 339 
 ARG   0.004   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04765 (  404)
  hydrogen bonds       : angle       5.02909 ( 1176)
  SS BOND              : bond        0.00010 (    1)
  SS BOND              : angle       1.31491 (    2)
  covalent geometry    : bond        0.00429 ( 7685)
  covalent geometry    : angle       0.54035 (10421)

*********************** 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
  134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 ASP cc_start: 0.8638 (m-30) cc_final: 0.8391 (m-30)
REVERT: B   10 GLU cc_start: 0.6704 (tp30) cc_final: 0.6482 (tp30)
REVERT: B   69 LEU cc_start: 0.8851 (mt) cc_final: 0.8581 (mm)
REVERT: B  258 ASP cc_start: 0.7569 (t0) cc_final: 0.6985 (t0)
REVERT: G   36 ASP cc_start: 0.7834 (m-30) cc_final: 0.7480 (m-30)
REVERT: R   55 ASN cc_start: 0.8862 (m-40) cc_final: 0.8604 (m-40)
  outliers start: 6
  outliers final: 6
  residues processed: 132
  average time/residue: 0.5355
  time to fit residues: 90.9732
Evaluate side-chains
  124 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  189 SER
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 72 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 87 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 85 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3698 r_free = 0.3698 target = 0.156367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.119404 restraints weight = 22773.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.98
r_work: 0.3094 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7686  Z= 0.133
  Angle     :  0.478   5.531  10423  Z= 0.257
  Chirality :  0.040   0.142   1187
  Planarity :  0.004   0.031   1294
  Dihedral  :  5.751  56.734   1300
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  7.87 %
    Favored  : 91.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.29), residues: 913
  helix:  2.57 (0.25), residues: 417
  sheet:  0.40 (0.40), residues: 169
  loop :  0.61 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 109 
 PHE   0.015   0.001   PHE R  63 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.006   0.000   ARG R 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04143 (  404)
  hydrogen bonds       : angle       4.69760 ( 1176)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       1.03346 (    2)
  covalent geometry    : bond        0.00286 ( 7685)
  covalent geometry    : angle       0.47753 (10421)

*********************** 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
  143 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7314 (tt0)
REVERT: A  378 ASP cc_start: 0.8605 (m-30) cc_final: 0.8387 (m-30)
REVERT: B   69 LEU cc_start: 0.8903 (mt) cc_final: 0.8638 (mm)
REVERT: B  258 ASP cc_start: 0.7488 (t0) cc_final: 0.6853 (t0)
REVERT: B  333 ASP cc_start: 0.8756 (p0) cc_final: 0.8287 (p0)
REVERT: G   36 ASP cc_start: 0.7768 (m-30) cc_final: 0.7504 (m-30)
REVERT: R  139 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7552 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 139
  average time/residue: 0.5515
  time to fit residues: 97.3655
Evaluate side-chains
  135 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 129
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
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 G residue   19 LEU
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 36 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.152195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.114817 restraints weight = 22827.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.04
r_work: 0.3029 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7686  Z= 0.193
  Angle     :  0.529   6.444  10423  Z= 0.285
  Chirality :  0.041   0.147   1187
  Planarity :  0.004   0.041   1294
  Dihedral  :  6.368  51.499   1300
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.28), residues: 913
  helix:  2.29 (0.25), residues: 417
  sheet: -0.20 (0.38), residues: 181
  loop :  0.50 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  99 
 HIS   0.005   0.001   HIS R 109 
 PHE   0.017   0.002   PHE R 275 
 TYR   0.015   0.001   TYR A 339 
 ARG   0.008   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04328 (  404)
  hydrogen bonds       : angle       4.78522 ( 1176)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       1.02678 (    2)
  covalent geometry    : bond        0.00433 ( 7685)
  covalent geometry    : angle       0.52876 (10421)

*********************** 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
  141 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7412 (tt0)
REVERT: A   28 LYS cc_start: 0.7831 (ptpp) cc_final: 0.7575 (mtpt)
REVERT: A  378 ASP cc_start: 0.8625 (m-30) cc_final: 0.8373 (m-30)
REVERT: B   69 LEU cc_start: 0.8933 (mt) cc_final: 0.8650 (mm)
REVERT: B  254 ASP cc_start: 0.8355 (t0) cc_final: 0.8140 (t0)
REVERT: B  258 ASP cc_start: 0.7487 (t0) cc_final: 0.6877 (t0)
REVERT: R  139 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7604 (mp)
  outliers start: 10
  outliers final: 7
  residues processed: 135
  average time/residue: 0.5897
  time to fit residues: 102.4428
Evaluate side-chains
  133 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
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  321 THR
Chi-restraints excluded: chain G residue   25 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3687 r_free = 0.3687 target = 0.155590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.118846 restraints weight = 22878.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.00
r_work: 0.3068 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2573

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= 0.104
  Angle     :  0.457   5.274  10423  Z= 0.244
  Chirality :  0.039   0.137   1187
  Planarity :  0.004   0.049   1294
  Dihedral  :  5.442  49.556   1300
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.61 %
    Favored  : 88.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.29), residues: 913
  helix:  2.61 (0.26), residues: 417
  sheet: -0.12 (0.39), residues: 175
  loop :  0.58 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 298 
 HIS   0.004   0.001   HIS R 109 
 PHE   0.013   0.001   PHE R  63 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.008   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03758 (  404)
  hydrogen bonds       : angle       4.47182 ( 1176)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.76922 (    2)
  covalent geometry    : bond        0.00221 ( 7685)
  covalent geometry    : angle       0.45699 (10421)

*********************** 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
  139 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7403 (tt0)
REVERT: A   28 LYS cc_start: 0.7838 (ptpp) cc_final: 0.7586 (mtpt)
REVERT: A  378 ASP cc_start: 0.8566 (m-30) cc_final: 0.8337 (m-30)
REVERT: B   69 LEU cc_start: 0.8952 (mt) cc_final: 0.8696 (mm)
REVERT: B  258 ASP cc_start: 0.7509 (t0) cc_final: 0.6935 (t0)
REVERT: B  333 ASP cc_start: 0.8763 (p0) cc_final: 0.8311 (p0)
REVERT: R  139 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7565 (mp)
REVERT: R  182 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6204 (p90)
  outliers start: 7
  outliers final: 4
  residues processed: 136
  average time/residue: 0.5468
  time to fit residues: 94.1871
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  : 1.217 
-------------------------------------------------------------------------------
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  259 GLN
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.153437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.116712 restraints weight = 22843.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.98
r_work: 0.3060 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7686  Z= 0.145
  Angle     :  0.478   5.803  10423  Z= 0.257
  Chirality :  0.039   0.139   1187
  Planarity :  0.004   0.055   1294
  Dihedral  :  5.554  48.357   1300
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.86 %
    Favored  : 88.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.29), residues: 913
  helix:  2.56 (0.25), residues: 417
  sheet: -0.07 (0.39), residues: 173
  loop :  0.40 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.015   0.001   PHE R  63 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.009   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03918 (  404)
  hydrogen bonds       : angle       4.51683 ( 1176)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.82634 (    2)
  covalent geometry    : bond        0.00322 ( 7685)
  covalent geometry    : angle       0.47834 (10421)

*********************** 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
  134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7425 (tt0)
REVERT: A   28 LYS cc_start: 0.7887 (ptpp) cc_final: 0.7625 (mtpt)
REVERT: A  378 ASP cc_start: 0.8612 (m-30) cc_final: 0.8378 (m-30)
REVERT: B   69 LEU cc_start: 0.8934 (mt) cc_final: 0.8677 (mm)
REVERT: B  258 ASP cc_start: 0.7405 (t0) cc_final: 0.6936 (t0)
REVERT: R  139 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7579 (mp)
REVERT: R  182 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6275 (p90)
  outliers start: 9
  outliers final: 7
  residues processed: 131
  average time/residue: 0.6413
  time to fit residues: 107.4466
Evaluate side-chains
  134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
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  139 LEU
Chi-restraints excluded: chain R residue  182 TYR
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:    0.9990
   chunk 57 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.3646 r_free = 0.3646 target = 0.151569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.114896 restraints weight = 23165.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.98
r_work: 0.3025 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7686  Z= 0.163
  Angle     :  0.499   6.045  10423  Z= 0.269
  Chirality :  0.040   0.142   1187
  Planarity :  0.004   0.065   1294
  Dihedral  :  5.798  50.114   1300
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.28), residues: 913
  helix:  2.44 (0.25), residues: 417
  sheet: -0.16 (0.40), residues: 173
  loop :  0.32 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 109 
 PHE   0.015   0.002   PHE R  63 
 TYR   0.013   0.001   TYR A 339 
 ARG   0.010   0.001   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04058 (  404)
  hydrogen bonds       : angle       4.56580 ( 1176)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.89565 (    2)
  covalent geometry    : bond        0.00366 ( 7685)
  covalent geometry    : angle       0.49919 (10421)

*********************** 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
  137 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7444 (tt0)
REVERT: A  378 ASP cc_start: 0.8616 (m-30) cc_final: 0.8384 (m-30)
REVERT: B   69 LEU cc_start: 0.8933 (mt) cc_final: 0.8663 (mm)
REVERT: B  258 ASP cc_start: 0.7588 (t0) cc_final: 0.7004 (t0)
REVERT: R  139 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7566 (mp)
REVERT: R  182 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6290 (p90)
  outliers start: 11
  outliers final: 8
  residues processed: 133
  average time/residue: 0.5668
  time to fit residues: 96.6826
Evaluate side-chains
  131 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
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 G residue   19 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   chunk 55 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.154239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.117794 restraints weight = 22911.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.98
r_work: 0.3087 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2851

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= 0.112
  Angle     :  0.461   5.240  10423  Z= 0.247
  Chirality :  0.039   0.133   1187
  Planarity :  0.004   0.066   1294
  Dihedral  :  5.327  49.386   1300
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.49 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.29), residues: 913
  helix:  2.65 (0.26), residues: 411
  sheet: -0.16 (0.40), residues: 173
  loop :  0.45 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 298 
 HIS   0.004   0.001   HIS R 109 
 PHE   0.012   0.001   PHE R 275 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.010   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03740 (  404)
  hydrogen bonds       : angle       4.37202 ( 1176)
  SS BOND              : bond        0.00070 (    1)
  SS BOND              : angle       0.81371 (    2)
  covalent geometry    : bond        0.00242 ( 7685)
  covalent geometry    : angle       0.46137 (10421)

*********************** 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
  134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7398 (tt0)
REVERT: A  378 ASP cc_start: 0.8563 (m-30) cc_final: 0.8336 (m-30)
REVERT: B   69 LEU cc_start: 0.8932 (mt) cc_final: 0.8678 (mm)
REVERT: B  258 ASP cc_start: 0.7468 (t0) cc_final: 0.6902 (t0)
REVERT: R  182 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6149 (p90)
  outliers start: 9
  outliers final: 7
  residues processed: 132
  average time/residue: 0.5691
  time to fit residues: 96.5907
Evaluate side-chains
  130 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.152304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.116000 restraints weight = 22867.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.92
r_work: 0.3058 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7686  Z= 0.162
  Angle     :  0.498   6.015  10423  Z= 0.269
  Chirality :  0.040   0.140   1187
  Planarity :  0.004   0.060   1294
  Dihedral  :  5.698  52.026   1300
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.74 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.29), residues: 913
  helix:  2.44 (0.26), residues: 417
  sheet: -0.20 (0.40), residues: 173
  loop :  0.30 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 109 
 PHE   0.016   0.002   PHE R 275 
 TYR   0.013   0.001   TYR A 339 
 ARG   0.009   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04010 (  404)
  hydrogen bonds       : angle       4.50376 ( 1176)
  SS BOND              : bond        0.00117 (    1)
  SS BOND              : angle       0.84934 (    2)
  covalent geometry    : bond        0.00363 ( 7685)
  covalent geometry    : angle       0.49832 (10421)

*********************** 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
  132 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 1.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7449 (tt0)
REVERT: A  378 ASP cc_start: 0.8585 (m-30) cc_final: 0.8346 (m-30)
REVERT: B   69 LEU cc_start: 0.8922 (mt) cc_final: 0.8670 (mm)
REVERT: B  258 ASP cc_start: 0.7489 (t0) cc_final: 0.6939 (t0)
REVERT: R  139 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7520 (mp)
REVERT: R  182 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6302 (p90)
  outliers start: 9
  outliers final: 7
  residues processed: 129
  average time/residue: 0.6970
  time to fit residues: 116.6325
Evaluate side-chains
  129 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
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  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 83 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 82 optimal weight:    0.2980
   chunk 17 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.155507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.119061 restraints weight = 22808.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.97
r_work: 0.3078 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2936

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= 0.100
  Angle     :  0.460   5.310  10423  Z= 0.246
  Chirality :  0.039   0.129   1187
  Planarity :  0.004   0.052   1294
  Dihedral  :  5.190  51.286   1300
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 12.61 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.29), residues: 913
  helix:  2.68 (0.26), residues: 415
  sheet: -0.23 (0.40), residues: 175
  loop :  0.42 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 298 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.009   0.000   ARG R  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03622 (  404)
  hydrogen bonds       : angle       4.26524 ( 1176)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.80709 (    2)
  covalent geometry    : bond        0.00213 ( 7685)
  covalent geometry    : angle       0.45990 (10421)

********************** 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: 5
    poor density    : 126
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7394 (tt0)
REVERT: A  378 ASP cc_start: 0.8607 (m-30) cc_final: 0.8402 (m-30)
REVERT: B   69 LEU cc_start: 0.8927 (mt) cc_final: 0.8691 (mm)
REVERT: B  258 ASP cc_start: 0.7483 (t0) cc_final: 0.6964 (t0)
REVERT: B  333 ASP cc_start: 0.8763 (p0) cc_final: 0.8350 (p0)
REVERT: R  182 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6198 (p90)
  outliers start: 5
  outliers final: 4
  residues processed: 130
  average time/residue: 0.5754
  time to fit residues: 96.1779
Evaluate side-chains
  129 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
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  234 PHE
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 41 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 42 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.151495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.115108 restraints weight = 23009.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.93
r_work: 0.3022 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7686  Z= 0.182
  Angle     :  0.518   5.985  10423  Z= 0.279
  Chirality :  0.041   0.143   1187
  Planarity :  0.004   0.047   1294
  Dihedral  :  5.825  54.584   1300
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 12.23 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.28), residues: 913
  helix:  2.48 (0.26), residues: 411
  sheet: -0.21 (0.40), residues: 173
  loop :  0.25 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 109 
 PHE   0.014   0.002   PHE R 275 
 TYR   0.013   0.001   TYR A 339 
 ARG   0.008   0.001   ARG R  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  404)
  hydrogen bonds       : angle       4.52143 ( 1176)
  SS BOND              : bond        0.00153 (    1)
  SS BOND              : angle       1.14384 (    2)
  covalent geometry    : bond        0.00410 ( 7685)
  covalent geometry    : angle       0.51749 (10421)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9233.22 seconds
wall clock time: 161 minutes 58.87 seconds (9718.87 seconds total)