Starting phenix.refine
on Mon Jul 20 16:42:04 2026 by afonine
===============================================================================

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

  Found miller_array, /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/1AHO.mtz
  Found model, /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/1AHO.pdb
  Found phil, /net/anaconda/raid1/afonine/work/discamb/varible_weights913//p.eff

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

  Adding PHIL files:
  ------------------
    /net/anaconda/raid1/afonine/work/discamb/varible_weights913//p.eff

  Adding command-line PHIL:
  -------------------------
    local_restraints_scaling=true
    output.prefix=scale
    optimize_xyz_weight=true

No user-defined map coefficients or files defined; will use default map
outputs instead.
Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/1AHO.pdb"
    }
    default_model = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/1AHO.pdb"
    miller_array {
      file = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/1AHO.mtz"
    }
    default_miller_array = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/1AHO.mtz"
    phil_files = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913//p.eff"
    default_phil = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913//p.eff"
  }
  refinement {
    output {
      write_geo_vs_map = True
    }
    electron_density_maps {
      map_coefficients {
        map_type = 2mFo-DFc
        mtz_label_amplitudes = 2FOFCWT
        mtz_label_phases = PH2FOFCWT
        fill_missing_f_obs = True
      }
      map_coefficients {
        map_type = 2mFo-DFc
        mtz_label_amplitudes = 2FOFCWT_no_fill
        mtz_label_phases = PH2FOFCWT_no_fill
      }
      map_coefficients {
        map_type = mFo-DFc
        mtz_label_amplitudes = FOFCWT
        mtz_label_phases = PHFOFCWT
      }
      map_coefficients {
        map_type = anomalous
        mtz_label_amplitudes = ANOM
        mtz_label_phases = PANOM
      }
      map {
        map_type = 2mFo-DFc
        fill_missing_f_obs = True
      }
      map {
        map_type = 2mFo-DFc
      }
      map {
        map_type = mFo-DFc
      }
    }
    refine {
      strategy = *individual_sites individual_sites_real_space rigid_body \
                 *individual_adp group_adp tls *occupancies group_anomalous \
                 den
    }
    main {
      local_restraints_scaling = true
      number_of_macro_cycles = 10
      max_number_of_iterations = 50
      scattering_table = *wk1995 it1992 n_gaussian electron neutron
    }
    hydrogens {
      refine = *individual riding Auto
    }
    pdb_interpretation {
      restraints_library {
        cdl = False
      }
      nonbonded_weight = 16
    }
    target_weights {
      optimize_xyz_weight = true
      wu = 0.1
    }
  }
  output {
    prefix = scale
    overwrite = True
  }


Starting job
===============================================================================
  Monomer Library directory:
    "/net/anaconda/raid1/afonine/phenix/modules/chem_data/mon_lib"
  Total number of atoms: 1106
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 977
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 64, 943
          Classifications: {'peptide': 64}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 60}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 1
      Conformer: "B"
        Number of residues, atoms: 64, 943
          Classifications: {'peptide': 64}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 60}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 1
          bond proxies already assigned to first conformer: 921
    Chain: "A"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 129
          Classifications: {'water': 129}
          Link IDs: {None: 128}
  Residues with excluded nonbonded symmetry interactions: 45
    residue:
      pdb=" N  ACYS A  12 " occ=0.55
      ... (18 atoms not shown)
      pdb=" HB3BCYS A  12 " occ=0.45
    residue:
      pdb=" N  ACYS A  63 " occ=0.55
      ... (18 atoms not shown)
      pdb=" HB3BCYS A  63 " occ=0.45
    residue:
      pdb=" O   HOH A  65 " occ=0.30
    residue:
      pdb=" O   HOH A  66 " occ=0.50
    residue:
      pdb=" O   HOH A  67 " occ=0.50
    residue:
      pdb=" O   HOH A  68 " occ=0.50
    residue:
      pdb=" O   HOH A  69 " occ=0.50
    residue:
      pdb=" O   HOH A  70 " occ=0.50
    residue:
      pdb=" O   HOH A  71 " occ=0.50
    residue:
      pdb=" O   HOH A  72 " occ=0.60
    residue:
      pdb=" O   HOH A  73 " occ=0.40
    residue:
      pdb=" O   HOH A  74 " occ=0.50
    ... (remaining 33 not shown)
  Time building chain proxies: 0.69, per 1000 atoms: 0.62
  Number of scatterers: 1106
  At special positions: 0
  Unit cell: (45.9, 40.7, 30.1, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     O     229      8.00
     N      88      7.00
     C     320      6.00
     H     459      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG ACYS A  12 " - pdb=" SG ACYS A  63 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A  16 " - pdb=" SG  CYS A  36 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  46 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  48 " distance=2.01
    Simple disulfide: pdb=" SG BCYS A  12 " - pdb=" SG BCYS A  63 " distance=2.00

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.07
  Time building geometry restraints manager: 0.11 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 459
        1.04 -     1.24: 49
        1.24 -     1.44: 203
        1.44 -     1.64: 272
        1.64 -     1.84: 10
  Bond restraints: 993
  Sorted by residual:
  bond pdb=" C   ASN A  11 "
       pdb=" N  ACYS A  12 "
    ideal  model  delta    sigma   weight residual
    1.329  1.378 -0.049 1.40e-02 5.10e+03 1.24e+01
  bond pdb=" C   HIS A  64 "
       pdb=" O   HIS A  64 "
    ideal  model  delta    sigma   weight residual
    1.231  1.297 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" C   VAL A  10 "
       pdb=" O   VAL A  10 "
    ideal  model  delta    sigma   weight residual
    1.231  1.167  0.064 2.00e-02 2.50e+03 1.03e+01
  bond pdb=" C  ACYS A  63 "
       pdb=" N   HIS A  64 "
    ideal  model  delta    sigma   weight residual
    1.329  1.371 -0.042 1.40e-02 5.10e+03 8.79e+00
  bond pdb=" C  ACYS A  12 "
       pdb=" N   THR A  13 "
    ideal  model  delta    sigma   weight residual
    1.329  1.290  0.039 1.40e-02 5.10e+03 7.64e+00
  ... (remaining 988 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 1559
        2.16 -     4.32: 167
        4.32 -     6.47: 40
        6.47 -     8.63: 6
        8.63 -    10.79: 3
  Bond angle restraints: 1775
  Sorted by residual:
  angle pdb=" C   ASN A  11 "
        pdb=" N  BCYS A  12 "
        pdb=" CA BCYS A  12 "
      ideal   model   delta    sigma   weight residual
     121.70  110.91   10.79 1.80e+00 3.09e-01 3.59e+01
  angle pdb=" O   ASN A  11 "
        pdb=" C   ASN A  11 "
        pdb=" N  BCYS A  12 "
      ideal   model   delta    sigma   weight residual
     123.00  132.11   -9.11 1.60e+00 3.91e-01 3.24e+01
  angle pdb=" CD  ARG A  62 "
        pdb=" NE  ARG A  62 "
        pdb=" CZ  ARG A  62 "
      ideal   model   delta    sigma   weight residual
     124.40  117.60    6.80 1.40e+00 5.10e-01 2.36e+01
  angle pdb=" CA  PHE A  15 "
        pdb=" CB  PHE A  15 "
        pdb=" CG  PHE A  15 "
      ideal   model   delta    sigma   weight residual
     113.80  109.04    4.76 1.00e+00 1.00e+00 2.27e+01
  angle pdb=" CA  ASP A   8 "
        pdb=" CB  ASP A   8 "
        pdb=" CG  ASP A   8 "
      ideal   model   delta    sigma   weight residual
     112.60  117.16   -4.56 1.00e+00 1.00e+00 2.08e+01
  ... (remaining 1770 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    13.39: 319
       13.39 -    26.76: 30
       26.76 -    40.14: 16
       40.14 -    53.51: 8
       53.51 -    66.89: 5
  Dihedral angle restraints: 378
    sinusoidal: 259
      harmonic: 119
  Sorted by residual:
  dihedral pdb=" CA  ARG A  62 "
           pdb=" C   ARG A  62 "
           pdb=" N  BCYS A  63 "
           pdb=" CA BCYS A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.98   18.02     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" N  ACYS A  12 "
           pdb=" CA ACYS A  12 "
           pdb=" CB ACYS A  12 "
           pdb=" SG ACYS A  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -99.92   39.92     3      1.50e+01 4.44e-03 7.09e+00
  dihedral pdb=" CB  GLU A  32 "
           pdb=" CG  GLU A  32 "
           pdb=" CD  GLU A  32 "
           pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   66.89  -66.89     1      3.00e+01 1.11e-03 6.48e+00
  ... (remaining 375 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.076: 30
       0.076 -    0.151: 25
       0.151 -    0.226: 8
       0.226 -    0.300: 5
       0.300 -    0.375: 1
  Chirality restraints: 69
  Sorted by residual:
  chirality pdb=" CA  LYS A  30 "
            pdb=" N   LYS A  30 "
            pdb=" C   LYS A  30 "
            pdb=" CB  LYS A  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.38 2.00e-01 2.50e+01 3.52e+00
  chirality pdb=" CA  ALA A  39 "
            pdb=" N   ALA A  39 "
            pdb=" C   ALA A  39 "
            pdb=" CB  ALA A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.21    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  LYS A  50 "
            pdb=" N   LYS A  50 "
            pdb=" C   LYS A  50 "
            pdb=" CB  LYS A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  ... (remaining 66 not shown)

  Planarity restraints: 161
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  14 "   -0.054 2.00e-02 2.50e+03   2.34e-02 1.64e+01
        pdb=" CG  TYR A  14 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  14 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  14 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  14 "    0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  14 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  14 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A  14 "   -0.038 2.00e-02 2.50e+03
        pdb=" HD1 TYR A  14 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR A  14 "    0.003 2.00e-02 2.50e+03
        pdb=" HE1 TYR A  14 "    0.000 2.00e-02 2.50e+03
        pdb=" HE2 TYR A  14 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  15 "   -0.052 2.00e-02 2.50e+03   2.31e-02 1.60e+01
        pdb=" CG  PHE A  15 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  15 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  15 "    0.031 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  15 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  15 "   -0.028 2.00e-02 2.50e+03
        pdb=" HD1 PHE A  15 "    0.002 2.00e-02 2.50e+03
        pdb=" HD2 PHE A  15 "    0.003 2.00e-02 2.50e+03
        pdb=" HE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ  PHE A  15 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  35 "   -0.050 2.00e-02 2.50e+03   2.26e-02 1.53e+01
        pdb=" CG  TYR A  35 "    0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  35 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  35 "    0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  35 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  35 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  35 "   -0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A  35 "   -0.038 2.00e-02 2.50e+03
        pdb=" HD1 TYR A  35 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR A  35 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 TYR A  35 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR A  35 "    0.002 2.00e-02 2.50e+03
  ... (remaining 158 not shown)

  Histogram of nonbonded interaction distances:
        1.01 -     1.73: 11
        1.73 -     2.45: 609
        2.45 -     3.16: 3500
        3.16 -     3.88: 5281
        3.88 -     4.60: 8206
  Nonbonded interactions: 17607
  Sorted by model distance:
  nonbonded pdb=" O   HOH A 100 "
            pdb=" O   HOH A 101 "
     model   vdw
     1.012 2.800
  nonbonded pdb=" O   HOH A  99 "
            pdb=" O   HOH A 100 "
     model   vdw
     1.146 2.800
  nonbonded pdb=" O   HOH A  74 "
            pdb=" O   HOH A  76 "
     model   vdw
     1.158 2.800
  nonbonded pdb=" O   HOH A  91 "
            pdb=" O   HOH A  92 "
     model   vdw
     1.272 2.800
  nonbonded pdb=" O   HOH A  66 "
            pdb=" O   HOH A  67 "
     model   vdw
     1.288 2.800
  ... (remaining 17602 not shown)

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

============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 5
  Type Number    sf(0)   Gaussians
   S      10     16.00       5+c
   O     229      8.00       5+c
   N      88      7.00       5+c
   C     320      6.00       5+c
   H     459      1.00       5
  sf(0) = scattering factor at diffraction angle 0.

=========================== Regularize ADP if needed ==========================


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

====================== Modifying start model if requested =====================

n_use            =  1106
n_use_u_iso      =  1106
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
total number of scatterers =  1106

================== Extract refinement strategy and selections =================

Refinement flags and selection counts:
  individual_sites       =  True (1106 atoms)
  torsion_angles         = False (0 atoms)
  rigid_body             = False (0 atoms in 0 groups)
  individual_adp         =  True (iso = 1106 aniso = 0)
  group_adp              = False (0 atoms in 0 groups)
  tls                    = False (0 atoms in 0 groups)
  occupancies            =  True (210 atoms)
  group_anomalous        = False

============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  output {
    write_geo_vs_map = True
  }
  electron_density_maps {
    map_coefficients {
      map_type = "2mFo-DFc"
      mtz_label_amplitudes = "2FOFCWT"
      mtz_label_phases = "PH2FOFCWT"
      fill_missing_f_obs = True
    }
    map_coefficients {
      map_type = "2mFo-DFc"
      mtz_label_amplitudes = "2FOFCWT_no_fill"
      mtz_label_phases = "PH2FOFCWT_no_fill"
    }
    map_coefficients {
      map_type = "mFo-DFc"
      mtz_label_amplitudes = "FOFCWT"
      mtz_label_phases = "PHFOFCWT"
    }
    map_coefficients {
      map_type = "anomalous"
      mtz_label_amplitudes = "ANOM"
      mtz_label_phases = "PANOM"
    }
    map {
      map_type = "2mFo-DFc"
      fill_missing_f_obs = True
    }
    map {
      map_type = "2mFo-DFc"
    }
    map {
      map_type = "mFo-DFc"
    }
  }
  refine {
    strategy = *individual_sites individual_sites_real_space rigid_body \
               *individual_adp group_adp tls *occupancies group_anomalous den
  }
  main {
    local_restraints_scaling = True
    number_of_macro_cycles = 10
    max_number_of_iterations = 50
    scattering_table = *wk1995 it1992 n_gaussian electron neutron
  }
  hydrogens {
    refine = *individual riding Auto
  }
  pdb_interpretation {
    restraints_library {
      cdl = False
    }
    c_beta_restraints = False
    nonbonded_weight = 16
  }
  target_weights {
    optimize_xyz_weight = True
    wu = 0.1
  }
}
output {
  prefix = "scale"
  serial = 1
  target_output_format = None *pdb mmcif
  overwrite = True
}
#phil __OFF__


================================== Hydrogens ==================================

Residue LYS   30 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Total:
  count: 459
  occupancy sum: 439.50 (% of total atoms  42.13)
Rotatable:
  count: 88
  occupancy sum:  88.00 (% of total atoms   8.44)

   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 0.96 - 15.82 A, n_refl.=31001 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1661 r_free= 0.1600 coordinate error (max.-lik. estimate): 0.06 A |
|                                                                             |
| normalized target function (ml) (work): 3.481265                            |
| target function (ml) not normalized (work): 100960.153942                   |
| target function (ml) not normalized (free): 6899.198727                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1:   15.82 -    2.32 0.95   2356  162 0.1689 0.1582      5.0162      4.8542|
|  2:    2.32 -    1.84 0.98   2325  161 0.1382 0.1272      4.2517      4.2211|
|  3:    1.84 -    1.61 0.97   2263  156 0.1315 0.1424      3.7208      3.7679|
|  4:    1.61 -    1.46 0.96   2242  154 0.1418 0.1340      3.5266      3.4782|
|  5:    1.46 -    1.36 0.96   2216  154 0.1477 0.1336       3.364      3.3053|
|  6:    1.36 -    1.28 0.94   2171  149 0.1622 0.1661       3.289      3.3386|
|  7:    1.28 -    1.22 0.95   2184  151 0.1645 0.1712      3.2057      3.2413|
|  8:    1.22 -    1.16 0.94   2133  147 0.1758 0.1620      3.1993       3.197|
|  9:    1.16 -    1.12 0.92   2116  146 0.1852 0.1736      3.1658      3.0427|
| 10:    1.12 -    1.08 0.87   1987  137 0.2112 0.1973      3.2198      3.1838|
| 11:    1.08 -    1.05 0.84   1934  133 0.2296 0.2222      3.1061      3.1009|
| 12:    1.05 -    1.02 0.81   1836  127 0.2558 0.2953      3.0858      3.0583|
| 13:    1.02 -    0.99 0.80   1815  125 0.2596 0.2722      3.0101      2.9643|
| 14:    0.99 -    0.96 0.63   1423   98 0.2837 0.2602      3.0057      2.9812|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1:   15.82 -    2.32  2356   162  0.90  14.89   0.97     0.94       2031.19|
|  2:    2.32 -    1.84  2325   161  0.89  16.32   1.05     0.97        909.52|
|  3:    1.84 -    1.61  2263   156  0.93  12.73   1.04     1.00        276.30|
|  4:    1.61 -    1.46  2242   154  0.94  11.32   1.05     1.00        158.12|
|  5:    1.46 -    1.36  2216   154  0.94  11.33   1.04     0.99        106.10|
|  6:    1.36 -    1.28  2171   149  0.93  12.81   1.04     0.99         93.15|
|  7:    1.28 -    1.22  2184   151  0.93  13.74   1.04     0.98         83.62|
|  8:    1.22 -    1.16  2133   147  0.93  13.85   1.05     0.99         78.14|
|  9:    1.16 -    1.12  2116   146  0.93  13.79   1.04     0.98         67.62|
| 10:    1.12 -    1.08  1987   137  0.93  14.94   1.03     0.99         66.60|
| 11:    1.08 -    1.05  1934   133  0.90  18.30   1.01     0.95         66.72|
| 12:    1.05 -    1.02  1836   127  0.87  20.91   1.01     0.92         67.03|
| 13:    1.02 -    0.99  1815   125  0.86  22.29   1.01     0.89         61.42|
| 14:    0.99 -    0.96  1423    98  0.86  22.32   1.01     0.89         53.08|
|alpha:            min =        0.89 max =            1.00 mean =         0.97|
|beta:             min =       53.08 max =         2031.19 mean =       323.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.33|
|phase err.(test): min =        0.00 max =           87.99 mean =        14.89|
|-----------------------------------------------------------------------------|

        ----------Initial model statistics (before refinement)----------       


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.014   0.066    539  Z= 0.769
    Angle     :  2.117  10.789    735  Z= 1.145
    Chirality :  0.123   0.375     69
    Planarity :  0.012   0.043     97
    Dihedral  : 13.466  66.891    195
    Min Nonbonded Distance : 1.012
  
  Molprobity Statistics.
    All-atom Clashscore : 4.09
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.23 %
      Favored  : 96.77 %
    Rotamer:
      Outliers :  1.79 %
      Allowed  :  0.00 %
      Favored  : 98.21 %
    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: -0.12 (0.85), residues: 67
    helix:  0.91 (1.35), residues: 12
    sheet:  None (None), residues: 0
    loop : -0.31 (0.70), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   ARG   0.008   0.003   ARG A  18 
   TYR   0.053   0.015   TYR A  14 
   PHE   0.049   0.026   PHE A  15 
   TRP   0.021   0.009   TRP A  38 
   HIS   0.012   0.005   HIS A  54 
  
  
  
  Details of bonding type rmsd/Z
    covalent geometry    : bond        0.01433 /  0.77 (  534)
    covalent geometry    : angle       2.12548 /  1.15 (  725)
    SS BOND              : bond        0.01661 /  0.88 (    5)
    SS BOND              : angle       1.40827 /  0.76 (   10)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    4.07  57.76  11.99   1.42   647     0
   Protein:    4.07  22.58   8.67   1.42   518     0
   Water:      6.84  57.76  25.30    N/A   129     0
   Chain  A:   4.07  57.76  11.99    N/A   647     0
   Histogram:
       Values      Number of atoms
     4.07 - 9.44        361
     9.44 - 14.81       149
    14.81 - 20.18        57
    20.18 - 25.55        26
    25.55 - 30.91        15
    30.91 - 36.28        16
    36.28 - 41.65        11
    41.65 - 47.02         5
    47.02 - 52.39         5
    52.39 - 57.76         2

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.20   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

=================== Write initial parameters into .eff file ===================



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

|--(resolution: 0.96 - 15.82 A, n_refl.=31001 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1661 r_free= 0.1600 coordinate error (max.-lik. estimate): 0.06 A |
|                                                                             |
| normalized target function (ml) (work): 3.481265                            |
| target function (ml) not normalized (work): 100960.153942                   |
| target function (ml) not normalized (free): 6899.198727                     |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1656 0.1661 0.1600 n_refl.: 31001
       re-set all scales: r(all,work,free)=0.1656 0.1661 0.1600 n_refl.: 31001
         remove outliers: r(all,work,free)=0.1656 0.1661 0.1600 n_refl.: 31001
overall B=-0.00 to atoms: r(all,work,free)=0.1656 0.1660 0.1600 n_refl.: 31001
bulk-solvent and scaling: r(all,work,free)=0.1528 0.1531 0.1496 n_refl.: 31001
         remove outliers: r(all,work,free)=0.1521 0.1523 0.1485 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.2132

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.3227   120.817   103.445 0.680 1.001 0.320
  6.681-5.432    92.59    94     6 0.1913   150.525   145.609 0.803 1.000 0.258
  5.422-4.402    83.85   151    10 0.1452   195.017   193.117 0.900 1.003 0.243
  4.390-3.571    90.83   296    21 0.1409   204.579   202.491 0.947 1.003 0.220
  3.569-2.898    96.33   565    39 0.1396   165.163   163.234 0.951 1.004 0.060
  2.897-2.351    98.71  1071    73 0.1335   127.090   126.077 0.942 1.006 0.000
  2.351-1.908    98.22  1960   136 0.1254    98.405    97.302 0.971 1.010 0.000
  1.908-1.548    96.68  3574   246 0.1258    61.030    60.560 0.960 1.017 0.000
  1.548-1.256    95.43  6500   448 0.1423    38.262    37.796 0.953 1.027 0.000
  1.256-1.020    88.52 11175   771 0.1862    24.661    23.975 0.933 1.043 0.000
  1.020-0.965    71.91  3515   243 0.2664    15.792    14.592 0.889 1.062 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9647   b_overall=-0.0113 

============================ Set refinement target ============================

  using refinement target ls_wunit_k1 


================================== NQH flips ==================================

r_work=0.1523 r_free=0.1485
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1523 r_free=0.1485

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.635274             wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.141343              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


============================= Fit rotatable H or D ============================

Residue LYS   30 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Real-space grid search fit H (or D) atoms:
  start:  r_work=0.1523 r_free=0.1485
  H omit: r_work=0.1531 r_free=0.1481
  final:  r_work=0.1519 r_free=0.1478
====================== Weight optimization ====================================
start b_rmsd: 0.0144 a_rmsd: 2.1173 r_work: 0.1519 r_free: 0.1478 wc:  1.000000
final b_rmsd: 0.0065 a_rmsd: 1.0830 r_work: 0.1575 r_free: 0.1693 wc:  1.000000

start b_rmsd: 0.0144 a_rmsd: 2.1173 r_work: 0.1519 r_free: 0.1478 wc:  0.500000
final b_rmsd: 0.0093 a_rmsd: 1.2295 r_work: 0.1551 r_free: 0.1690 wc:  0.500000

start b_rmsd: 0.0144 a_rmsd: 2.1173 r_work: 0.1519 r_free: 0.1478 wc:  0.250000
final b_rmsd: 0.0135 a_rmsd: 1.4083 r_work: 0.1531 r_free: 0.1674 wc:  0.250000

start b_rmsd: 0.0144 a_rmsd: 2.1173 r_work: 0.1519 r_free: 0.1478 wc:  0.125000
final b_rmsd: 0.0192 a_rmsd: 1.6717 r_work: 0.1512 r_free: 0.1664 wc:  0.125000

start b_rmsd: 0.0144 a_rmsd: 2.1173 r_work: 0.1519 r_free: 0.1478 wc:  0.062500
final b_rmsd: 0.0263 a_rmsd: 2.0440 r_work: 0.1495 r_free: 0.1663 wc:  0.062500

start b_rmsd: 0.0144 a_rmsd: 2.1173 r_work: 0.1519 r_free: 0.1478 wc:  0.031250
final b_rmsd: 0.0336 a_rmsd: 2.4898 r_work: 0.1480 r_free: 0.1665 wc:  0.031250

====================== XYZ individual (reciprocal space) ======================

Weight selection criteria:
  R_free deviation:  0.0000
  R_free-R_work gap: 4.0000
  Bond RMSD:         0.0250
  Angle RMSD:        3.0000

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.1519 0.1681 0.0163  0.016   2.0    4.1   0.0   1.8    1   7.818

Number of minimizer iterations: 50 (52 function evaluations)
end of opt. b_rmsd: 0.0162 a_rmsd: 2.0119 r_work: 0.1519 r_free: 0.1681 wc:  0.031250

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
15.19 16.81   1.63  1.052  10.819  0.141    0.022
15.01 17.20   2.19  1.885  11.268  0.141    0.021

Number of minimizer iterations: 25 (27 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    4.03  55.37  12.36   2.02   647     0
   Protein:    4.03  27.76   9.20   2.02   518     0
   Water:      6.81  55.37  25.05    N/A   129     0
   Chain  A:   4.03  55.37  12.36    N/A   647     0
   Histogram:
       Values      Number of atoms
     4.03 - 9.16        337
     9.16 - 14.30       151
    14.30 - 19.43        60
    19.43 - 24.56        37
    24.56 - 29.70        21
    29.70 - 34.83        12
    34.83 - 39.97        15
    39.97 - 45.10         8
    45.10 - 50.24         3
    50.24 - 55.37         3


======================== Occupancy refinement (H only) ========================

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0213126  r_work = 0.1501  r_free = 0.1720      |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0200716  r_work = 0.1486  r_free = 0.1735      |
|-----------------------------------------------------------------------------|

============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1486 r_free = 0.1735    target_work(ls_wunit_k1) = 0.020         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1488 r_free = 0.1728    target_work(ls_wunit_k1) = 0.020         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (16 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1488 r_free= 0.1728 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.020218                   |
| target function (ls_wunit_k1) not normalized (work): 586.151046             |
| target function (ls_wunit_k1) not normalized (free): 64.755069              |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1504 0.1488 0.1728 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1642 0.1629 0.1828 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1642 0.1629 0.1828 n_refl.: 30991
 overall B=0.01 to atoms: r(all,work,free)=0.1643 0.1630 0.1829 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1501 0.1485 0.1728 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1501 0.1485 0.1728 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.0312

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2342   120.817   111.258 0.722 0.981 0.290
  6.681-5.432    92.59    94     6 0.1184   150.525   148.686 0.807 0.980 0.270
  5.422-4.402    83.85   151    10 0.0970   195.017   194.656 0.910 0.982 0.260
  4.390-3.571    90.83   296    21 0.0916   204.579   204.047 0.965 0.980 0.190
  3.569-2.898    96.33   565    39 0.0995   165.163   164.443 0.974 0.979 0.110
  2.897-2.351    98.71  1071    73 0.1121   127.090   126.464 0.972 0.979 0.000
  2.351-1.908    98.22  1960   136 0.1192    98.405    97.672 1.008 0.979 0.000
  1.908-1.548    96.68  3574   246 0.1329    61.030    60.427 0.992 0.980 0.000
  1.548-1.256    95.43  6500   448 0.1548    38.262    37.601 0.993 0.980 0.000
  1.256-1.020    88.52 11175   771 0.2002    24.661    23.773 0.987 0.984 0.000
  1.020-0.965    71.91  3515   243 0.2771    15.792    14.470 0.956 0.991 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=0.0013  

============================ Set refinement target ============================

  using refinement target ls_wunit_k1 


================================== NQH flips ==================================

r_work=0.1485 r_free=0.1728
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1485 r_free=0.1728

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.551346             wxc_scale = 0.500            wc = 0.031         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.273709              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


============================= Fit rotatable H or D ============================

Residue LYS   30 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Real-space grid search fit H (or D) atoms:
  start:  r_work=0.1485 r_free=0.1728
  H omit: r_work=0.1512 r_free=0.1737
  final:  r_work=0.1488 r_free=0.1725
====================== Weight optimization ====================================

====================== XYZ individual (reciprocal space) ======================

Weight selection criteria:
  R_free deviation:  0.0000
  R_free-R_work gap: 4.0000
  Bond RMSD:         0.0250
  Angle RMSD:        3.0000

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.1459 0.1730 0.0271  0.040   2.0    5.1   0.0   1.8    0   8.776

Number of minimizer iterations: 50 (53 function evaluations)

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.59 17.30   2.71  1.885  11.279  0.274    0.019
14.49 17.22   2.73  2.057  11.339  0.274    0.019

Number of minimizer iterations: 25 (29 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    4.11  54.49  12.58   2.16   647     0
   Protein:    4.11  31.98   9.33   2.16   518     0
   Water:      6.86  54.49  25.64    N/A   129     0
   Chain  A:   4.11  54.49  12.58    N/A   647     0
   Histogram:
       Values      Number of atoms
     4.11 - 9.14        329
     9.14 - 14.18       149
    14.18 - 19.22        60
    19.22 - 24.26        43
    24.26 - 29.30        22
    29.30 - 34.34        15
    34.34 - 39.38        11
    39.38 - 44.42        11
    44.42 - 49.45         4
    49.45 - 54.49         3


======================== Occupancy refinement (H only) ========================

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0187752  r_work = 0.1449  r_free = 0.1722      |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0182134  r_work = 0.1442  r_free = 0.1744      |
|-----------------------------------------------------------------------------|

============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1442 r_free = 0.1744    target_work(ls_wunit_k1) = 0.018         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1445 r_free = 0.1729    target_work(ls_wunit_k1) = 0.018         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (18 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1445 r_free= 0.1729 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.018463                   |
| target function (ls_wunit_k1) not normalized (work): 535.284540             |
| target function (ls_wunit_k1) not normalized (free): 63.763211              |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1464 0.1445 0.1729 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1609 0.1593 0.1823 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1609 0.1593 0.1823 n_refl.: 30991
overall B=-0.00 to atoms: r(all,work,free)=0.1609 0.1593 0.1823 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1464 0.1445 0.1731 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1464 0.1445 0.1731 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.0153

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2081   120.817   112.403 0.729 0.988 0.281
  6.681-5.432    92.59    94     6 0.1101   150.525   148.754 0.796 0.987 0.243
  5.422-4.402    83.85   151    10 0.0907   195.017   194.797 0.899 0.989 0.224
  4.390-3.571    90.83   296    21 0.0840   204.579   203.981 0.959 0.987 0.172
  3.569-2.898    96.33   565    39 0.0942   165.163   164.714 0.967 0.986 0.130
  2.897-2.351    98.71  1071    73 0.1052   127.090   126.742 0.967 0.986 0.000
  2.351-1.908    98.22  1960   136 0.1126    98.405    97.802 1.002 0.985 0.000
  1.908-1.548    96.68  3574   246 0.1288    61.030    60.484 0.986 0.986 0.000
  1.548-1.256    95.43  6500   448 0.1529    38.262    37.645 0.987 0.987 0.000
  1.256-1.020    88.52 11175   771 0.1990    24.661    23.777 0.982 0.990 0.000
  1.020-0.965    71.91  3515   243 0.2789    15.792    14.454 0.955 0.997 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0090 

============================ Set refinement target ============================

  using refinement target ml 


================================== NQH flips ==================================

r_work=0.1445 r_free=0.1731
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1445 r_free=0.1731

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.374399              wxc_scale = 0.500            wc = 0.031         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.109259              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


============================= Fit rotatable H or D ============================

Residue LYS   30 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Real-space grid search fit H (or D) atoms:
  start:  r_work=0.1445 r_free=0.1731
  H omit: r_work=0.1472 r_free=0.1739
  final:  r_work=0.1447 r_free=0.1731
====================== Weight optimization ====================================

====================== XYZ individual (reciprocal space) ======================

Weight selection criteria:
  R_free deviation:  0.0000
  R_free-R_work gap: 4.0000
  Bond RMSD:         0.0250
  Angle RMSD:        3.0000

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.1461 0.1678 0.0217  0.027   2.0    4.1   0.0   1.8    0   1.187

Number of minimizer iterations: 50 (53 function evaluations)

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.61 16.78   2.17  2.057  11.336  0.109    3.425
14.56 16.49   1.92  2.101  11.199  0.109    3.407

Number of minimizer iterations: 25 (28 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.94  54.45  12.42   2.21   647     0
   Protein:    3.94  32.32   9.16   2.21   518     0
   Water:      7.02  54.45  25.53    N/A   129     0
   Chain  A:   3.94  54.45  12.42    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.94 - 8.99        329
     8.99 - 14.04       151
    14.04 - 19.09        58
    19.09 - 24.14        42
    24.14 - 29.19        22
    29.19 - 34.25        16
    34.25 - 39.30        10
    39.30 - 44.35        12
    44.35 - 49.40         4
    49.40 - 54.45         3


======================== Occupancy refinement (H only) ========================

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40658  r_work = 0.1456  r_free = 0.1649                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.40156  r_work = 0.1450  r_free = 0.1647                 |
|-----------------------------------------------------------------------------|

============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1450 r_free = 0.1647             target_work(ml) = 3.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1456 r_free = 0.1648             target_work(ml) = 3.404         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (13 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1456 r_free= 0.1648 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ml) (work): 3.403693                            |
| target function (ml) not normalized (work): 98679.868822                    |
| target function (ml) not normalized (free): 6944.817521                     |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1469 0.1456 0.1648 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1611 0.1601 0.1747 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1611 0.1601 0.1747 n_refl.: 30991
overall B=-0.05 to atoms: r(all,work,free)=0.1607 0.1597 0.1744 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1470 0.1457 0.1645 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1470 0.1457 0.1645 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0571

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2547   120.817   110.509 0.750 0.955 0.290
  6.681-5.432    92.59    94     6 0.1443   150.525   147.103 0.828 0.954 0.263
  5.422-4.402    83.85   151    10 0.1117   195.017   195.198 0.942 0.956 0.223
  4.390-3.571    90.83   296    21 0.1162   204.579   203.710 0.998 0.955 0.170
  3.569-2.898    96.33   565    39 0.1230   165.163   163.384 1.005 0.954 0.052
  2.897-2.351    98.71  1071    73 0.1307   127.090   125.610 1.001 0.953 0.000
  2.351-1.908    98.22  1960   136 0.1239    98.405    97.064 1.042 0.953 0.000
  1.908-1.548    96.68  3574   246 0.1248    61.030    60.319 1.027 0.953 0.000
  1.548-1.256    95.43  6500   448 0.1384    38.262    37.623 1.029 0.953 0.000
  1.256-1.020    88.52 11175   771 0.1808    24.661    23.940 1.031 0.955 0.000
  1.020-0.965    71.91  3515   243 0.2670    15.792    14.656 0.998 0.961 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0672 

============================ Set refinement target ============================

  using refinement target ml 


================================== NQH flips ==================================

r_work=0.1457 r_free=0.1645
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1457 r_free=0.1645

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.167466              wxc_scale = 0.500            wc = 0.031         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.080816              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


============================= Fit rotatable H or D ============================

Residue LYS   30 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Real-space grid search fit H (or D) atoms:
  start:  r_work=0.1457 r_free=0.1645
  H omit: r_work=0.1479 r_free=0.1658
  final:  r_work=0.1458 r_free=0.1647
====================== Weight optimization ====================================

====================== XYZ individual (reciprocal space) ======================

Weight selection criteria:
  R_free deviation:  0.0000
  R_free-R_work gap: 4.0000
  Bond RMSD:         0.0250
  Angle RMSD:        3.0000

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.1456 0.1643 0.0187  0.024   1.8    5.1   0.0   1.8    0   1.084

Number of minimizer iterations: 30 (31 function evaluations)

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.56 16.43   1.87  2.101  11.152  0.081    3.405
14.54 16.40   1.86  2.140  11.013  0.081    3.403

Number of minimizer iterations: 25 (29 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.76  54.18  12.31   2.12   647     0
   Protein:    3.76  32.79   9.07   2.12   518     0
   Water:      6.98  54.18  25.34    N/A   129     0
   Chain  A:   3.76  54.18  12.31    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.76 - 8.80        325
     8.80 - 13.84       157
    13.84 - 18.88        59
    18.88 - 23.93        40
    23.93 - 28.97        21
    28.97 - 34.01        16
    34.01 - 39.05         9
    39.05 - 44.09        11
    44.09 - 49.13         6
    49.13 - 54.18         3


======================== Occupancy refinement (H only) ========================

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40267  r_work = 0.1454  r_free = 0.1640                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.40122  r_work = 0.1447  r_free = 0.1638                 |
|-----------------------------------------------------------------------------|

============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1447 r_free = 0.1638             target_work(ml) = 3.401         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1453 r_free = 0.1637             target_work(ml) = 3.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 9 (18 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1453 r_free= 0.1637 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.401940                            |
| target function (ml) not normalized (work): 98629.056603                    |
| target function (ml) not normalized (free): 6941.098696                     |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1465 0.1453 0.1637 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1604 0.1594 0.1737 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1604 0.1594 0.1737 n_refl.: 30991
overall B=-0.00 to atoms: r(all,work,free)=0.1604 0.1594 0.1737 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1465 0.1453 0.1637 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1465 0.1453 0.1637 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0226

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2515   120.817   110.330 0.747 0.956 0.281
  6.681-5.432    92.59    94     6 0.1440   150.525   147.149 0.824 0.955 0.267
  5.422-4.402    83.85   151    10 0.1119   195.017   194.275 0.932 0.958 0.227
  4.390-3.571    90.83   296    21 0.1164   204.579   203.022 0.990 0.956 0.180
  3.569-2.898    96.33   565    39 0.1235   165.163   163.300 1.001 0.955 0.110
  2.897-2.351    98.71  1071    73 0.1309   127.090   125.899 0.998 0.954 0.000
  2.351-1.908    98.22  1960   136 0.1230    98.405    97.273 1.038 0.954 0.000
  1.908-1.548    96.68  3574   246 0.1247    61.030    60.389 1.021 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1372    38.262    37.661 1.025 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1801    24.661    23.912 1.026 0.956 0.000
  1.020-0.965    71.91  3515   243 0.2670    15.792    14.486 0.979 0.962 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0289 

============================ Set refinement target ============================

  using refinement target ml 


================================== NQH flips ==================================

r_work=0.1453 r_free=0.1637
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1453 r_free=0.1637

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.109335              wxc_scale = 0.500            wc = 0.031         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.105432              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


============================= Fit rotatable H or D ============================

====================== Weight optimization ====================================

====================== XYZ individual (reciprocal space) ======================

Weight selection criteria:
  R_free deviation:  0.0000
  R_free-R_work gap: 4.0000
  Bond RMSD:         0.0250
  Angle RMSD:        3.0000

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.1453 0.1639 0.0185  0.020   1.8    5.1   0.0   1.8    0   1.055

Number of minimizer iterations: 20 (22 function evaluations)

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.53 16.39   1.85  2.140  11.013  0.105    3.403
14.53 16.39   1.86  2.144  11.005  0.105    3.403

Number of minimizer iterations: 7 (15 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.76  54.17  12.31   2.11   647     0
   Protein:    3.76  32.81   9.06   2.11   518     0
   Water:      6.96  54.17  25.34    N/A   129     0
   Chain  A:   3.76  54.17  12.31    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.76 - 8.80        325
     8.80 - 13.84       157
    13.84 - 18.88        58
    18.88 - 23.92        40
    23.92 - 28.96        22
    28.96 - 34.00        16
    34.00 - 39.04         9
    39.04 - 44.08        11
    44.08 - 49.12         6
    49.12 - 54.17         3


======================== Occupancy refinement (H only) ========================

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.4028  r_work = 0.1453  r_free = 0.1639                  |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.40088  r_work = 0.1446  r_free = 0.1636                 |
|-----------------------------------------------------------------------------|

============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1446 r_free = 0.1636             target_work(ml) = 3.401         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1452 r_free = 0.1641             target_work(ml) = 3.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (13 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1452 r_free= 0.1641 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.402420                            |
| target function (ml) not normalized (work): 98642.964687                    |
| target function (ml) not normalized (free): 6943.503709                     |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1464 0.1452 0.1641 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1603 0.1593 0.1737 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1603 0.1593 0.1737 n_refl.: 30991
overall B=-0.00 to atoms: r(all,work,free)=0.1603 0.1593 0.1737 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1464 0.1451 0.1642 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1464 0.1451 0.1642 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0146

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2479   120.817   110.796 0.746 0.956 0.283
  6.681-5.432    92.59    94     6 0.1465   150.525   146.871 0.821 0.955 0.250
  5.422-4.402    83.85   151    10 0.1110   195.017   194.166 0.929 0.958 0.233
  4.390-3.571    90.83   296    21 0.1150   204.579   203.092 0.991 0.956 0.153
  3.569-2.898    96.33   565    39 0.1239   165.163   163.298 1.001 0.955 0.057
  2.897-2.351    98.71  1071    73 0.1316   127.090   125.863 0.999 0.954 0.000
  2.351-1.908    98.22  1960   136 0.1226    98.405    97.286 1.038 0.954 0.000
  1.908-1.548    96.68  3574   246 0.1249    61.030    60.390 1.020 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1370    38.262    37.665 1.024 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1799    24.661    23.908 1.024 0.955 0.000
  1.020-0.965    71.91  3515   243 0.2662    15.792    14.498 0.978 0.962 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0200 

============================ Set refinement target ============================

  using refinement target ml 


================================== NQH flips ==================================

r_work=0.1451 r_free=0.1642
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1451 r_free=0.1642

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.140735              wxc_scale = 0.500            wc = 0.031         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.125542              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


============================= Fit rotatable H or D ============================

====================== Weight optimization ====================================

====================== XYZ individual (reciprocal space) ======================

Weight selection criteria:
  R_free deviation:  0.0000
  R_free-R_work gap: 4.0000
  Bond RMSD:         0.0250
  Angle RMSD:        3.0000

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.1453 0.1640 0.0187  0.017   1.8    5.1   0.0   1.8    0   1.070

Number of minimizer iterations: 11 (14 function evaluations)

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.53 16.40   1.87  2.144  11.005  0.126    3.403
14.53 16.40   1.87  2.144  11.005  0.126    3.403

Number of minimizer iterations: 2 (6 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.76  54.16  12.31   2.11   647     0
   Protein:    3.76  32.81   9.06   2.11   518     0
   Water:      6.96  54.16  25.34    N/A   129     0
   Chain  A:   3.76  54.16  12.31    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.76 - 8.80        325
     8.80 - 13.84       157
    13.84 - 18.88        58
    18.88 - 23.92        40
    23.92 - 28.96        22
    28.96 - 34.00        16
    34.00 - 39.04         9
    39.04 - 44.08        11
    44.08 - 49.12         6
    49.12 - 54.16         3


======================== Occupancy refinement (H only) ========================

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40271  r_work = 0.1453  r_free = 0.1640                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.40118  r_work = 0.1447  r_free = 0.1640                 |
|-----------------------------------------------------------------------------|

============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1447 r_free = 0.1640             target_work(ml) = 3.401         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1453 r_free = 0.1639             target_work(ml) = 3.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (19 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1453 r_free= 0.1639 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.402458                            |
| target function (ml) not normalized (work): 98644.066296                    |
| target function (ml) not normalized (free): 6943.215852                     |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1465 0.1453 0.1639 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1603 0.1593 0.1734 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1603 0.1593 0.1734 n_refl.: 30991
overall B=-0.00 to atoms: r(all,work,free)=0.1603 0.1593 0.1734 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1465 0.1453 0.1638 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1465 0.1453 0.1638 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0145

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2460   120.817   111.076 0.741 0.957 0.290
  6.681-5.432    92.59    94     6 0.1466   150.525   146.817 0.820 0.955 0.242
  5.422-4.402    83.85   151    10 0.1109   195.017   194.170 0.928 0.958 0.227
  4.390-3.571    90.83   296    21 0.1143   204.579   203.115 0.991 0.956 0.147
  3.569-2.898    96.33   565    39 0.1238   165.163   163.308 1.001 0.955 0.052
  2.897-2.351    98.71  1071    73 0.1318   127.090   125.874 0.999 0.955 0.000
  2.351-1.908    98.22  1960   136 0.1228    98.405    97.284 1.037 0.954 0.000
  1.908-1.548    96.68  3574   246 0.1251    61.030    60.383 1.020 0.955 0.000
  1.548-1.256    95.43  6500   448 0.1373    38.262    37.665 1.023 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1801    24.661    23.906 1.023 0.956 0.000
  1.020-0.965    71.91  3515   243 0.2664    15.792    14.496 0.978 0.962 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0181 

============================ Set refinement target ============================

  using refinement target ml 


================================== NQH flips ==================================

r_work=0.1453 r_free=0.1638
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1453 r_free=0.1638

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.362847              wxc_scale = 0.500            wc = 0.031         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.099632              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


============================= Fit rotatable H or D ============================

====================== Weight optimization ====================================

====================== XYZ individual (reciprocal space) ======================

Weight selection criteria:
  R_free deviation:  0.0000
  R_free-R_work gap: 4.0000
  Bond RMSD:         0.0250
  Angle RMSD:        3.0000

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.1452 0.1641 0.0189  0.017   1.8    5.1   0.0   1.8    0   1.181

Number of minimizer iterations: 10 (11 function evaluations)

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.52 16.41   1.89  2.144  11.005  0.100    3.403
14.52 16.41   1.89  2.144  11.003  0.100    3.402

Number of minimizer iterations: 2 (5 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.76  54.16  12.31   2.11   647     0
   Protein:    3.76  32.81   9.06   2.11   518     0
   Water:      6.96  54.16  25.33    N/A   129     0
   Chain  A:   3.76  54.16  12.31    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.76 - 8.80        325
     8.80 - 13.84       157
    13.84 - 18.88        58
    18.88 - 23.92        40
    23.92 - 28.96        22
    28.96 - 34.00        16
    34.00 - 39.04         9
    39.04 - 44.08        11
    44.08 - 49.12         6
    49.12 - 54.16         3


======================== Occupancy refinement (H only) ========================

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40245  r_work = 0.1452  r_free = 0.1641                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.40099  r_work = 0.1446  r_free = 0.1641                 |
|-----------------------------------------------------------------------------|

============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1446 r_free = 0.1641             target_work(ml) = 3.401         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1452 r_free = 0.1642             target_work(ml) = 3.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (12 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1452 r_free= 0.1642 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.402456                            |
| target function (ml) not normalized (work): 98644.009246                    |
| target function (ml) not normalized (free): 6943.941712                     |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1465 0.1452 0.1642 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1602 0.1592 0.1736 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1602 0.1592 0.1736 n_refl.: 30991
overall B=-0.00 to atoms: r(all,work,free)=0.1602 0.1592 0.1736 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1465 0.1452 0.1642 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1465 0.1452 0.1642 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0034

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2459   120.817   110.683 0.744 0.957 0.273
  6.681-5.432    92.59    94     6 0.1468   150.525   146.819 0.819 0.955 0.242
  5.422-4.402    83.85   151    10 0.1110   195.017   194.128 0.928 0.958 0.227
  4.390-3.571    90.83   296    21 0.1144   204.579   203.118 0.990 0.956 0.147
  3.569-2.898    96.33   565    39 0.1237   165.163   163.282 1.001 0.955 0.052
  2.897-2.351    98.71  1071    73 0.1318   127.090   125.866 0.998 0.955 0.000
  2.351-1.908    98.22  1960   136 0.1227    98.405    97.288 1.037 0.954 0.000
  1.908-1.548    96.68  3574   246 0.1250    61.030    60.389 1.019 0.955 0.000
  1.548-1.256    95.43  6500   448 0.1371    38.262    37.664 1.021 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1801    24.661    23.908 1.021 0.956 0.000
  1.020-0.965    71.91  3515   243 0.2665    15.792    14.494 0.975 0.962 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0088 

============================ Set refinement target ============================

  using refinement target ml 


================================== NQH flips ==================================

r_work=0.1452 r_free=0.1642
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1452 r_free=0.1642

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.205696              wxc_scale = 0.500            wc = 0.031         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.108035              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


============================= Fit rotatable H or D ============================

====================== Weight optimization ====================================

====================== XYZ individual (reciprocal space) ======================

Weight selection criteria:
  R_free deviation:  0.0000
  R_free-R_work gap: 4.0000
  Bond RMSD:         0.0250
  Angle RMSD:        3.0000

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.1454 0.1642 0.0188  0.016   1.8    5.1   0.0   1.8    0   1.103

Number of minimizer iterations: 8 (9 function evaluations)

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.54 16.42   1.88  2.144  11.003  0.108    3.403
14.54 16.41   1.88  2.150  10.992  0.108    3.403

Number of minimizer iterations: 6 (9 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.87  54.16  12.29   2.11   647     0
   Protein:    3.87  32.84   9.05   2.11   518     0
   Water:      6.95  54.16  25.32    N/A   129     0
   Chain  A:   3.87  54.16  12.29    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.87 - 8.90        331
     8.90 - 13.93       151
    13.93 - 18.96        61
    18.96 - 23.99        37
    23.99 - 29.02        22
    29.02 - 34.04        16
    34.04 - 39.07         9
    39.07 - 44.10        11
    44.10 - 49.13         6
    49.13 - 54.16         3


======================== Occupancy refinement (H only) ========================

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40285  r_work = 0.1454  r_free = 0.1641                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.40124  r_work = 0.1447  r_free = 0.1641                 |
|-----------------------------------------------------------------------------|

============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1447 r_free = 0.1641             target_work(ml) = 3.401         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1454 r_free = 0.1641             target_work(ml) = 3.403         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (8 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1454 r_free= 0.1641 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.402742                            |
| target function (ml) not normalized (work): 98652.302734                    |
| target function (ml) not normalized (free): 6942.393345                     |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1466 0.1454 0.1641 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1601 0.1592 0.1734 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1601 0.1592 0.1734 n_refl.: 30991
 overall B=0.01 to atoms: r(all,work,free)=0.1602 0.1592 0.1734 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1466 0.1454 0.1641 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1466 0.1454 0.1641 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.0039

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2454   120.817   110.721 0.744 0.956 0.273
  6.681-5.432    92.59    94     6 0.1462   150.525   146.814 0.819 0.955 0.242
  5.422-4.402    83.85   151    10 0.1114   195.017   194.120 0.928 0.958 0.227
  4.390-3.571    90.83   296    21 0.1147   204.579   203.124 0.991 0.956 0.147
  3.569-2.898    96.33   565    39 0.1238   165.163   163.292 1.001 0.955 0.052
  2.897-2.351    98.71  1071    73 0.1320   127.090   125.850 0.998 0.954 0.000
  2.351-1.908    98.22  1960   136 0.1229    98.405    97.287 1.037 0.954 0.000
  1.908-1.548    96.68  3574   246 0.1252    61.030    60.387 1.019 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1374    38.262    37.663 1.021 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1801    24.661    23.907 1.020 0.955 0.000
  1.020-0.965    71.91  3515   243 0.2665    15.792    14.494 0.974 0.961 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=0.0009  

============================ Set refinement target ============================

  using refinement target ml 


================================== NQH flips ==================================

r_work=0.1454 r_free=0.1641
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1454 r_free=0.1641

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.153576              wxc_scale = 0.500            wc = 0.031         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.044552              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


============================= Fit rotatable H or D ============================

====================== Weight optimization ====================================

====================== XYZ individual (reciprocal space) ======================

Weight selection criteria:
  R_free deviation:  0.0000
  R_free-R_work gap: 4.0000
  Bond RMSD:         0.0250
  Angle RMSD:        3.0000

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.1454 0.1641 0.0187  0.016   1.8    5.1   0.0   1.8    0   1.077

Number of minimizer iterations: 3 (4 function evaluations)

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.54 16.41   1.87  2.150  11.000  0.045    3.403
14.54 16.41   1.87  2.150  11.000  0.045    3.403

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.88  54.17  12.30   2.11   647     0
   Protein:    3.88  32.85   9.06   2.11   518     0
   Water:      6.96  54.17  25.33    N/A   129     0
   Chain  A:   3.88  54.17  12.30    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.88 - 8.91        331
     8.91 - 13.94       151
    13.94 - 18.97        61
    18.97 - 24.00        37
    24.00 - 29.02        22
    29.02 - 34.05        16
    34.05 - 39.08         9
    39.08 - 44.11        11
    44.11 - 49.14         6
    49.14 - 54.17         3


======================== Occupancy refinement (H only) ========================

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40276  r_work = 0.1454  r_free = 0.1641                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.4012  r_work = 0.1447  r_free = 0.1641                  |
|-----------------------------------------------------------------------------|

============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1447 r_free = 0.1641             target_work(ml) = 3.401         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1453 r_free = 0.1641             target_work(ml) = 3.403         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 9 (13 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1453 r_free= 0.1641 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.402836                            |
| target function (ml) not normalized (work): 98655.024283                    |
| target function (ml) not normalized (free): 6942.648492                     |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1466 0.1453 0.1641 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1602 0.1592 0.1735 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1602 0.1592 0.1735 n_refl.: 30991
 overall B=0.00 to atoms: r(all,work,free)=0.1602 0.1592 0.1735 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1466 0.1453 0.1642 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1466 0.1453 0.1642 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.0007

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2443   120.817   110.821 0.743 0.956 0.275
  6.681-5.432    92.59    94     6 0.1474   150.525   146.903 0.819 0.955 0.245
  5.422-4.402    83.85   151    10 0.1109   195.017   194.072 0.927 0.958 0.230
  4.390-3.571    90.83   296    21 0.1140   204.579   203.132 0.991 0.956 0.147
  3.569-2.898    96.33   565    39 0.1240   165.163   163.232 1.002 0.955 0.110
  2.897-2.351    98.71  1071    73 0.1321   127.090   125.844 0.998 0.954 0.000
  2.351-1.908    98.22  1960   136 0.1228    98.405    97.280 1.037 0.953 0.000
  1.908-1.548    96.68  3574   246 0.1251    61.030    60.388 1.019 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1373    38.262    37.662 1.021 0.953 0.000
  1.256-1.020    88.52 11175   771 0.1802    24.661    23.906 1.021 0.954 0.000
  1.020-0.965    71.91  3515   243 0.2665    15.792    14.494 0.975 0.960 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=0.0001  

============================ Set refinement target ============================

  using refinement target ml 


================================== NQH flips ==================================

r_work=0.1453 r_free=0.1642
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1453 r_free=0.1642

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.129254              wxc_scale = 0.500            wc = 0.031         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.108690              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


============================= Fit rotatable H or D ============================

====================== Weight optimization ====================================

====================== XYZ individual (reciprocal space) ======================

Weight selection criteria:
  R_free deviation:  0.0000
  R_free-R_work gap: 4.0000
  Bond RMSD:         0.0250
  Angle RMSD:        3.0000

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.1454 0.1645 0.0190  0.015   1.8    5.1   0.0   1.8    0   1.065

Number of minimizer iterations: 9 (10 function evaluations)

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.54 16.45   1.90  2.150  11.001  0.109    3.404
14.54 16.45   1.90  2.150  11.001  0.109    3.404

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.88  54.17  12.30   2.11   647     0
   Protein:    3.88  32.85   9.06   2.11   518     0
   Water:      6.96  54.17  25.33    N/A   129     0
   Chain  A:   3.88  54.17  12.30    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.88 - 8.91        331
     8.91 - 13.94       151
    13.94 - 18.97        61
    18.97 - 24.00        37
    24.00 - 29.03        22
    29.03 - 34.05        16
    34.05 - 39.08         9
    39.08 - 44.11        11
    44.11 - 49.14         6
    49.14 - 54.17         3


======================== Occupancy refinement (H only) ========================

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40368  r_work = 0.1454  r_free = 0.1645                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.40204  r_work = 0.1448  r_free = 0.1644                 |
|-----------------------------------------------------------------------------|

============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1448 r_free = 0.1644             target_work(ml) = 3.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1454 r_free = 0.1644             target_work(ml) = 3.404         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (15 function evaluations)

                         ----------X-ray data----------                        

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1454 r_free= 0.1644 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.403609                            |
| target function (ml) not normalized (work): 98677.443111                    |
| target function (ml) not normalized (free): 6945.507771                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1:   14.12 -    2.32 0.95   2354  162 0.1292 0.1585       4.661      4.8321|
|  2:    2.32 -    1.84 0.98   2320  160 0.1238 0.1361      4.2013      4.2781|
|  3:    1.84 -    1.61 0.97   2265  156 0.1252 0.1616      3.7397      3.8931|
|  4:    1.61 -    1.46 0.96   2239  154 0.1272 0.1438      3.4913      3.5686|
|  5:    1.46 -    1.36 0.96   2218  154 0.1334 0.1354      3.3123      3.3478|
|  6:    1.36 -    1.28 0.94   2170  149 0.1471 0.1631      3.2227      3.3559|
|  7:    1.28 -    1.22 0.95   2184  151 0.1476 0.1721      3.1332      3.2348|
|  8:    1.22 -    1.16 0.94   2134  147 0.1529 0.1642      3.1037      3.1981|
|  9:    1.16 -    1.12 0.92   2115  146 0.1630 0.1750      3.0619      3.0826|
| 10:    1.12 -    1.08 0.87   1988  137 0.1932 0.1896      3.1316      3.1548|
| 11:    1.08 -    1.05 0.84   1934  133 0.2169 0.2273      3.0475      3.1215|
| 12:    1.05 -    1.02 0.81   1835  127 0.2487 0.3025      3.0515      3.0755|
| 13:    1.02 -    0.99 0.79   1814  125 0.2570 0.2694      3.0005      2.9547|
| 14:    0.99 -    0.96 0.63   1422   98 0.2801 0.2531      2.9723      2.9571|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1:   14.12 -    2.32  2354   162  0.90  14.72   1.00     1.02       1918.37|
|  2:    2.32 -    1.84  2320   160  0.89  16.63   1.00     1.03        921.44|
|  3:    1.84 -    1.61  2265   156  0.91  14.72   1.00     1.03        336.38|
|  4:    1.61 -    1.46  2239   154  0.93  13.13   1.01     1.03        189.53|
|  5:    1.46 -    1.36  2218   154  0.93  13.09   1.00     1.02        124.72|
|  6:    1.36 -    1.28  2170   149  0.93  13.83   0.99     1.02        101.53|
|  7:    1.28 -    1.22  2184   151  0.92  14.54   1.01     1.02         88.43|
|  8:    1.22 -    1.16  2134   147  0.92  14.42   1.03     1.04         81.10|
|  9:    1.16 -    1.12  2115   146  0.92  14.38   1.01     1.03         70.63|
| 10:    1.12 -    1.08  1988   137  0.92  15.40   0.99     1.02         68.33|
| 11:    1.08 -    1.05  1934   133  0.89  18.67   0.96     0.97         67.48|
| 12:    1.05 -    1.02  1835   127  0.87  21.29   0.96     0.95         68.56|
| 13:    1.02 -    0.99  1814   125  0.85  23.37   1.01     0.94         62.84|
| 14:    0.99 -    0.96  1422    98  0.86  22.69   0.99     0.95         53.18|
|alpha:            min =        0.94 max =            1.04 mean =         1.01|
|beta:             min =       53.18 max =         1918.37 mean =       325.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.16|
|phase err.(test): min =        0.00 max =           88.21 mean =        15.59|
|-----------------------------------------------------------------------------|

==================================== Final ====================================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1467 0.1454 0.1644 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1603 0.1593 0.1736 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1603 0.1593 0.1736 n_refl.: 30991
 overall B=0.00 to atoms: r(all,work,free)=0.1603 0.1593 0.1736 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1467 0.1454 0.1644 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1467 0.1454 0.1644 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0051

 ======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2445   120.817   110.764 0.742 0.956 0.275
  6.681-5.432    92.59    94     6 0.1471   150.525   146.876 0.818 0.955 0.245
  5.422-4.402    83.85   151    10 0.1113   195.017   194.111 0.927 0.958 0.230
  4.390-3.571    90.83   296    21 0.1143   204.579   203.092 0.991 0.956 0.153
  3.569-2.898    96.33   565    39 0.1239   165.163   163.246 1.002 0.955 0.120
  2.897-2.351    98.71  1071    73 0.1321   127.090   125.841 0.998 0.954 0.000
  2.351-1.908    98.22  1960   136 0.1229    98.405    97.280 1.037 0.953 0.000
  1.908-1.548    96.68  3574   246 0.1252    61.030    60.390 1.019 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1375    38.262    37.662 1.021 0.953 0.000
  1.256-1.020    88.52 11175   771 0.1803    24.661    23.903 1.022 0.954 0.000
  1.020-0.965    71.91  3515   243 0.2665    15.792    14.495 0.976 0.959 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=0.0001  

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of occupancies                                        
------------------------------------------------------------------------
 stage r-work r-free bonds angles b_min b_max b_ave n_water shift
       0    : 0.1661 0.1600 0.014  2.117   4.1  57.8  12.0 129      0.000
       1_bss: 0.1523 0.1485 0.014  2.117   4.1  57.8  12.0 129      0.000
 1_settarget: 0.1523 0.1485 0.014  2.117   4.1  57.8  12.0 129      0.000
       1_nqh: 0.1523 0.1485 0.014  2.117   4.1  57.8  12.0 129      0.000
    1_weight: 0.1523 0.1485 0.014  2.117   4.1  57.8  12.0 129      0.000
     1_fitrh: 0.1519 0.1478 0.014  2.117   4.1  57.8  12.0 129      0.091
    1_xyzrec: 0.1519 0.1681 0.016  2.012   4.1  57.8  12.0 129      0.168
       1_adp: 0.1501 0.1720 0.016  2.012   4.0  55.4  12.4 129      0.168
      1_occh: 0.1486 0.1735 0.016  2.012   4.0  55.4  12.4 129      0.168
       1_occ: 0.1488 0.1728 0.016  2.012   4.0  55.4  12.4 129      0.168
       2_bss: 0.1485 0.1728 0.016  2.012   4.0  55.4  12.4 129      0.168
 2_settarget: 0.1485 0.1728 0.016  2.012   4.0  55.4  12.4 129      0.168
       2_nqh: 0.1485 0.1728 0.016  2.012   4.0  55.4  12.4 129      0.168
    2_weight: 0.1485 0.1728 0.016  2.012   4.0  55.4  12.4 129      0.168
     2_fitrh: 0.1488 0.1725 0.016  2.012   4.0  55.4  12.4 129      0.163
    2_xyzrec: 0.1459 0.1730 0.040  1.995   4.0  55.4  12.4 129      0.167
       2_adp: 0.1449 0.1722 0.040  1.995   4.1  54.5  12.6 129      0.167
      2_occh: 0.1442 0.1744 0.040  1.995   4.1  54.5  12.6 129      0.167
       2_occ: 0.1445 0.1729 0.040  1.995   4.1  54.5  12.6 129      0.167
       3_bss: 0.1445 0.1731 0.040  1.995   4.1  54.5  12.6 129      0.167
 3_settarget: 0.1445 0.1731 0.040  1.995   4.1  54.5  12.6 129      0.167
       3_nqh: 0.1445 0.1731 0.040  1.995   4.1  54.5  12.6 129      0.167
    3_weight: 0.1445 0.1731 0.040  1.995   4.1  54.5  12.6 129      0.167
     3_fitrh: 0.1447 0.1731 0.040  1.995   4.1  54.5  12.6 129      0.178
    3_xyzrec: 0.1461 0.1678 0.027  1.968   4.1  54.5  12.6 129      0.159
       3_adp: 0.1456 0.1649 0.027  1.968   3.9  54.5  12.4 129      0.159
      3_occh: 0.1450 0.1647 0.027  1.968   3.9  54.5  12.4 129      0.159
       3_occ: 0.1456 0.1648 0.027  1.968   3.9  54.5  12.4 129      0.159
       4_bss: 0.1457 0.1645 0.027  1.968   3.9  54.4  12.4 129      0.159
 4_settarget: 0.1457 0.1645 0.027  1.968   3.9  54.4  12.4 129      0.159
       4_nqh: 0.1457 0.1645 0.027  1.968   3.9  54.4  12.4 129      0.159
    4_weight: 0.1457 0.1645 0.027  1.968   3.9  54.4  12.4 129      0.159
     4_fitrh: 0.1458 0.1647 0.027  1.968   3.9  54.4  12.4 129      0.154
    4_xyzrec: 0.1456 0.1643 0.024  1.836   3.9  54.4  12.4 129      0.149
       4_adp: 0.1454 0.1640 0.024  1.836   3.8  54.2  12.3 129      0.149
      4_occh: 0.1447 0.1638 0.024  1.836   3.8  54.2  12.3 129      0.149
       4_occ: 0.1453 0.1637 0.024  1.836   3.8  54.2  12.3 129      0.149
       5_bss: 0.1453 0.1637 0.024  1.836   3.8  54.2  12.3 129      0.149
 5_settarget: 0.1453 0.1637 0.024  1.836   3.8  54.2  12.3 129      0.149
       5_nqh: 0.1453 0.1637 0.024  1.836   3.8  54.2  12.3 129      0.149
    5_weight: 0.1453 0.1637 0.024  1.836   3.8  54.2  12.3 129      0.149
     5_fitrh: 0.1453 0.1637 0.024  1.836   3.8  54.2  12.3 129      0.149
    5_xyzrec: 0.1453 0.1639 0.020  1.761   3.8  54.2  12.3 129      0.149
       5_adp: 0.1453 0.1639 0.020  1.761   3.8  54.2  12.3 129      0.149
      5_occh: 0.1446 0.1636 0.020  1.761   3.8  54.2  12.3 129      0.149
       5_occ: 0.1452 0.1641 0.020  1.761   3.8  54.2  12.3 129      0.149
       6_bss: 0.1451 0.1642 0.020  1.761   3.8  54.2  12.3 129      0.149
 6_settarget: 0.1451 0.1642 0.020  1.761   3.8  54.2  12.3 129      0.149
       6_nqh: 0.1451 0.1642 0.020  1.761   3.8  54.2  12.3 129      0.149
    6_weight: 0.1451 0.1642 0.020  1.761   3.8  54.2  12.3 129      0.149
     6_fitrh: 0.1451 0.1642 0.020  1.761   3.8  54.2  12.3 129      0.149
    6_xyzrec: 0.1453 0.1640 0.017  1.811   3.8  54.2  12.3 129      0.148
       6_adp: 0.1453 0.1640 0.017  1.811   3.8  54.2  12.3 129      0.148
      6_occh: 0.1447 0.1640 0.017  1.811   3.8  54.2  12.3 129      0.148
       6_occ: 0.1453 0.1639 0.017  1.811   3.8  54.2  12.3 129      0.148
       7_bss: 0.1453 0.1638 0.017  1.811   3.8  54.2  12.3 129      0.148
 7_settarget: 0.1453 0.1638 0.017  1.811   3.8  54.2  12.3 129      0.148
       7_nqh: 0.1453 0.1638 0.017  1.811   3.8  54.2  12.3 129      0.148
    7_weight: 0.1453 0.1638 0.017  1.811   3.8  54.2  12.3 129      0.148
     7_fitrh: 0.1453 0.1638 0.017  1.811   3.8  54.2  12.3 129      0.148
    7_xyzrec: 0.1452 0.1641 0.017  1.830   3.8  54.2  12.3 129      0.148
       7_adp: 0.1452 0.1641 0.017  1.830   3.8  54.2  12.3 129      0.148
      7_occh: 0.1446 0.1641 0.017  1.830   3.8  54.2  12.3 129      0.148
       7_occ: 0.1452 0.1642 0.017  1.830   3.8  54.2  12.3 129      0.148
       8_bss: 0.1452 0.1642 0.017  1.830   3.8  54.2  12.3 129      0.148
 8_settarget: 0.1452 0.1642 0.017  1.830   3.8  54.2  12.3 129      0.148
       8_nqh: 0.1452 0.1642 0.017  1.830   3.8  54.2  12.3 129      0.148
    8_weight: 0.1452 0.1642 0.017  1.830   3.8  54.2  12.3 129      0.148
     8_fitrh: 0.1452 0.1642 0.017  1.830   3.8  54.2  12.3 129      0.148
    8_xyzrec: 0.1454 0.1642 0.016  1.835   3.8  54.2  12.3 129      0.148
       8_adp: 0.1454 0.1641 0.016  1.835   3.9  54.2  12.3 129      0.148
      8_occh: 0.1447 0.1641 0.016  1.835   3.9  54.2  12.3 129      0.148
       8_occ: 0.1454 0.1641 0.016  1.835   3.9  54.2  12.3 129      0.148
       9_bss: 0.1454 0.1641 0.016  1.835   3.9  54.2  12.3 129      0.148
 9_settarget: 0.1454 0.1641 0.016  1.835   3.9  54.2  12.3 129      0.148
       9_nqh: 0.1454 0.1641 0.016  1.835   3.9  54.2  12.3 129      0.148
    9_weight: 0.1454 0.1641 0.016  1.835   3.9  54.2  12.3 129      0.148
     9_fitrh: 0.1454 0.1641 0.016  1.835   3.9  54.2  12.3 129      0.148
    9_xyzrec: 0.1454 0.1641 0.016  1.838   3.9  54.2  12.3 129      0.148
       9_adp: 0.1454 0.1641 0.016  1.838   3.9  54.2  12.3 129      0.148
      9_occh: 0.1447 0.1641 0.016  1.838   3.9  54.2  12.3 129      0.148
       9_occ: 0.1453 0.1641 0.016  1.838   3.9  54.2  12.3 129      0.148
      10_bss: 0.1453 0.1642 0.016  1.838   3.9  54.2  12.3 129      0.148
10_settarget: 0.1453 0.1642 0.016  1.838   3.9  54.2  12.3 129      0.148
      10_nqh: 0.1453 0.1642 0.016  1.838   3.9  54.2  12.3 129      0.148
   10_weight: 0.1453 0.1642 0.016  1.838   3.9  54.2  12.3 129      0.148
    10_fitrh: 0.1453 0.1642 0.016  1.838   3.9  54.2  12.3 129      0.148
   10_xyzrec: 0.1454 0.1645 0.015  1.848   3.9  54.2  12.3 129      0.148
      10_adp: 0.1454 0.1645 0.015  1.848   3.9  54.2  12.3 129      0.148
     10_occh: 0.1448 0.1644 0.015  1.848   3.9  54.2  12.3 129      0.148
      10_occ: 0.1454 0.1644 0.015  1.848   3.9  54.2  12.3 129      0.148
         end: 0.1454 0.1644 0.015  1.848   3.9  54.2  12.3 129      0.148
------------------------------------------------------------------------

============================== Exporting results ==============================


Writing refined structure to CIF file:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/scale_001.cif
Writing default parameters for subsequent refinement:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/scale_002.def

Timing summary:
  Write initial files (write_before_run_outputs): 0.7500
  Refinement macro-cycles (run)                 : 489.9700
  Write final files (write_after_run_outputs)   : 22.9300
  Total                                         : 513.6500
Total CPU time: 8.77 minutes

=========================== phenix.refine: finished ===========================

# Date 2026-07-20 Time 16:51:23 PDT -0700 (1784591483.17 s)

Start R-work = 0.1523, R-free = 0.1485
Final R-work = 0.1454, R-free = 0.1644

===============================================================================
Job complete
usr+sys time: 526.17 seconds
wall clock time: 9 minutes 21.62 seconds (561.62 seconds total)
