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=false
    output.prefix=unscale
    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"
    phil_files = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913//p.eff"
    default_phil = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913//p.eff"
    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"
  }
  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 {
      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 = unscale
    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: 0.62, per 1000 atoms: 0.56
  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: 0.08
  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 {
    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 = "unscale"
  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
revert b_rmsd: 0.0263 a_rmsd: 2.0440 r_work: 0.1495 r_free: 0.1663 wc:  0.062500

====================== 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
 0.1496 0.1672 0.0176  0.026   2.1    4.1   0.0   1.8    0   7.818

Number of minimizer iterations: 26 (27 function evaluations)
end of opt. b_rmsd: 0.0263 a_rmsd: 2.0536 r_work: 0.1496 r_free: 0.1672 wc:  0.062500

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.96 16.72   1.76  1.052  10.819  0.141    0.022
14.78 17.14   2.37  1.865  11.243  0.141    0.021

Number of minimizer iterations: 25 (27 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    4.05  55.52  12.32   1.98   647     0
   Protein:    4.05  27.84   9.16   1.98   518     0
   Water:      6.78  55.52  25.01    N/A   129     0
   Chain  A:   4.05  55.52  12.32    N/A   647     0
   Histogram:
       Values      Number of atoms
     4.05 - 9.20        342
     9.20 - 14.35       149
    14.35 - 19.50        56
    19.50 - 24.64        40
    24.64 - 29.79        20
    29.79 - 34.94        10
    34.94 - 40.08        16
    40.08 - 45.23         8
    45.23 - 50.38         4
    50.38 - 55.52         2


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

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0205076  r_work = 0.1478  r_free = 0.1714      |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0193458  r_work = 0.1465  r_free = 0.1727      |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1465 r_free = 0.1727    target_work(ls_wunit_k1) = 0.019         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1468 r_free = 0.1721    target_work(ls_wunit_k1) = 0.019         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 9 (12 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1468 r_free= 0.1721 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.019484                   |
| target function (ls_wunit_k1) not normalized (work): 564.879899             |
| target function (ls_wunit_k1) not normalized (free): 64.010623              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1485 0.1468 0.1721 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1623 0.1609 0.1820 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1623 0.1609 0.1820 n_refl.: 30991
 overall B=0.01 to atoms: r(all,work,free)=0.1623 0.1609 0.1820 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1481 0.1464 0.1720 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1481 0.1464 0.1720 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.0260

 ======================== 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 0.2354   120.817   111.731 0.708 0.999 0.300
  6.681-5.432    92.59    94     6 0.1197   150.525   148.605 0.791 0.998 0.266
  5.422-4.402    83.85   151    10 0.0959   195.017   194.919 0.894 1.000 0.236
  4.390-3.571    90.83   296    21 0.0890   204.579   203.852 0.947 0.999 0.210
  3.569-2.898    96.33   565    39 0.0964   165.163   164.529 0.956 0.998 0.100
  2.897-2.351    98.71  1071    73 0.1094   127.090   126.559 0.953 0.997 0.000
  2.351-1.908    98.22  1960   136 0.1156    98.405    97.695 0.989 0.997 0.000
  1.908-1.548    96.68  3574   246 0.1311    61.030    60.439 0.974 0.998 0.000
  1.548-1.256    95.43  6500   448 0.1530    38.262    37.614 0.975 0.998 0.000
  1.256-1.020    88.52 11175   771 0.1986    24.661    23.788 0.970 1.001 0.000
  1.020-0.965    71.91  3515   243 0.2772    15.792    14.459 0.940 1.009 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=0.0010  

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

  using refinement target ls_wunit_k1 


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

r_work=0.1464 r_free=0.1720
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1464 r_free=0.1720

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.431905             wxc_scale = 0.500            wc = 0.062         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.237010              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=0.1464 r_free=0.1720
  H omit: r_work=0.1494 r_free=0.1723
  final:  r_work=0.1467 r_free=0.1715
====================== 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 0.1714 0.0260  0.027   2.1    5.1   0.0   1.8    1   8.716

Number of minimizer iterations: 46 (47 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.54 17.14   2.60  1.865  11.252  0.237    0.019
14.46 17.09   2.63  2.028  11.318  0.237    0.019

Number of minimizer iterations: 25 (28 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    4.05  54.50  12.53   2.15   647     0
   Protein:    4.05  30.76   9.30   2.15   518     0
   Water:      6.88  54.50  25.51    N/A   129     0
   Chain  A:   4.05  54.50  12.53    N/A   647     0
   Histogram:
       Values      Number of atoms
     4.05 - 9.09        330
     9.09 - 14.14       148
    14.14 - 19.18        59
    19.18 - 24.23        45
    24.23 - 29.27        19
    29.27 - 34.32        15
    34.32 - 39.36        13
    39.36 - 44.41        11
    44.41 - 49.45         4
    49.45 - 54.50         3


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

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0188117  r_work = 0.1446  r_free = 0.1709      |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0182824  r_work = 0.1440  r_free = 0.1730      |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1440 r_free = 0.1730    target_work(ls_wunit_k1) = 0.018         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1443 r_free = 0.1716    target_work(ls_wunit_k1) = 0.019         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (16 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1443 r_free= 0.1716 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.018512                   |
| target function (ls_wunit_k1) not normalized (work): 536.708255             |
| target function (ls_wunit_k1) not normalized (free): 63.017373              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1461 0.1443 0.1716 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1606 0.1591 0.1814 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1606 0.1591 0.1814 n_refl.: 30991
overall B=-0.00 to atoms: r(all,work,free)=0.1606 0.1591 0.1814 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1461 0.1442 0.1719 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1461 0.1442 0.1719 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.0195

 ======================== 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 0.2117   120.817   111.964 0.728 0.987 0.277
  6.681-5.432    92.59    94     6 0.1133   150.525   148.745 0.796 0.986 0.238
  5.422-4.402    83.85   151    10 0.0907   195.017   195.030 0.901 0.988 0.220
  4.390-3.571    90.83   296    21 0.0851   204.579   204.005 0.958 0.987 0.180
  3.569-2.898    96.33   565    39 0.0938   165.163   164.720 0.968 0.986 0.120
  2.897-2.351    98.71  1071    73 0.1069   127.090   126.636 0.966 0.985 0.000
  2.351-1.908    98.22  1960   136 0.1129    98.405    97.795 1.002 0.985 0.000
  1.908-1.548    96.68  3574   246 0.1282    61.030    60.492 0.986 0.986 0.000
  1.548-1.256    95.43  6500   448 0.1517    38.262    37.644 0.988 0.987 0.000
  1.256-1.020    88.52 11175   771 0.1981    24.661    23.788 0.982 0.990 0.000
  1.020-0.965    71.91  3515   243 0.2778    15.792    14.459 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=-0.0091 

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

  using refinement target ml 


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

r_work=0.1442 r_free=0.1719
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1442 r_free=0.1719

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.395572              wxc_scale = 0.500            wc = 0.062         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.140159              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=0.1442 r_free=0.1719
  H omit: r_work=0.1470 r_free=0.1724
  final:  r_work=0.1444 r_free=0.1716
====================== 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 0.1666 0.0213  0.024   2.0    5.1   0.0   1.8    0   1.198

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
14.53 16.66   2.13  2.028  11.316  0.140    3.423
14.50 16.40   1.90  2.100  11.187  0.140    3.405

Number of minimizer iterations: 25 (28 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.81  54.46  12.40   2.22   647     0
   Protein:    3.81  31.32   9.15   2.22   518     0
   Water:      7.01  54.46  25.48    N/A   129     0
   Chain  A:   3.81  54.46  12.40    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.81 - 8.87        323
     8.87 - 13.94       156
    13.94 - 19.00        57
    19.00 - 24.07        43
    24.07 - 29.13        22
    29.13 - 34.20        16
    34.20 - 39.27        11
    39.27 - 44.33        11
    44.33 - 49.40         5
    49.40 - 54.46         3


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40485  r_work = 0.1450  r_free = 0.1640                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.40046  r_work = 0.1444  r_free = 0.1638                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1444 r_free = 0.1638             target_work(ml) = 3.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       39 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1449 r_free = 0.1635             target_work(ml) = 3.401         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 9 (17 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1449 r_free= 0.1635 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ml) (work): 3.401493                            |
| target function (ml) not normalized (work): 98616.074119                    |
| target function (ml) not normalized (free): 6937.888035                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1462 0.1449 0.1635 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1604 0.1595 0.1735 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1604 0.1595 0.1735 n_refl.: 30991
overall B=-0.02 to atoms: r(all,work,free)=0.1603 0.1593 0.1734 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1463 0.1451 0.1633 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1463 0.1451 0.1633 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0651

 ======================== 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 0.2562   120.817   109.730 0.744 0.957 0.271
  6.681-5.432    92.59    94     6 0.1420   150.525   147.323 0.826 0.955 0.257
  5.422-4.402    83.85   151    10 0.1113   195.017   194.543 0.933 0.958 0.220
  4.390-3.571    90.83   296    21 0.1139   204.579   203.056 0.990 0.956 0.180
  3.569-2.898    96.33   565    39 0.1206   165.163   163.477 1.001 0.955 0.100
  2.897-2.351    98.71  1071    73 0.1298   127.090   125.835 0.998 0.954 0.000
  2.351-1.908    98.22  1960   136 0.1220    98.405    97.326 1.040 0.954 0.000
  1.908-1.548    96.68  3574   246 0.1246    61.030    60.390 1.027 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1383    38.262    37.658 1.031 0.953 0.000
  1.256-1.020    88.52 11175   771 0.1809    24.661    23.892 1.032 0.954 0.000
  1.020-0.965    71.91  3515   243 0.2676    15.792    14.479 0.994 0.960 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0620 

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

  using refinement target ml 


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

r_work=0.1451 r_free=0.1633
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1451 r_free=0.1633

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.201454              wxc_scale = 0.500            wc = 0.062         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.091773              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=0.1451 r_free=0.1633
  H omit: r_work=0.1473 r_free=0.1648
  final:  r_work=0.1452 r_free=0.1633
====================== 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
 0.1450 0.1637 0.0188  0.024   2.1    5.1   0.0   1.8    0   1.101

Number of minimizer iterations: 18 (21 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.50 16.37   1.88  2.100  11.169  0.092    3.402
14.49 16.37   1.88  2.110  11.136  0.092    3.401

Number of minimizer iterations: 14 (19 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.95  54.41  12.37   2.21   647     0
   Protein:    3.95  31.46   9.12   2.21   518     0
   Water:      7.01  54.41  25.43    N/A   129     0
   Chain  A:   3.95  54.41  12.37    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.95 - 9.00        333
     9.00 - 14.04       148
    14.04 - 19.09        56
    19.09 - 24.13        44
    24.13 - 29.18        21
    29.18 - 34.22        15
    34.22 - 39.27        11
    39.27 - 44.32        12
    44.32 - 49.36         4
    49.36 - 54.41         3


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.4007  r_work = 0.1449  r_free = 0.1637                  |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.39855  r_work = 0.1443  r_free = 0.1635                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1443 r_free = 0.1635             target_work(ml) = 3.399         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1448 r_free = 0.1636             target_work(ml) = 3.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (16 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1448 r_free= 0.1636 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.400194                            |
| target function (ml) not normalized (work): 98578.413775                    |
| target function (ml) not normalized (free): 6939.937022                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1461 0.1448 0.1636 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1602 0.1593 0.1735 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1602 0.1593 0.1735 n_refl.: 30991
overall B=-0.01 to atoms: r(all,work,free)=0.1601 0.1591 0.1734 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1461 0.1448 0.1635 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1461 0.1448 0.1635 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0477

 ======================== 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 0.2549   120.817   110.573 0.741 0.956 0.290
  6.681-5.432    92.59    94     6 0.1441   150.525   146.948 0.826 0.955 0.242
  5.422-4.402    83.85   151    10 0.1123   195.017   194.426 0.931 0.958 0.227
  4.390-3.571    90.83   296    21 0.1148   204.579   202.961 0.990 0.956 0.190
  3.569-2.898    96.33   565    39 0.1222   165.163   163.343 1.002 0.955 0.100
  2.897-2.351    98.71  1071    73 0.1308   127.090   125.827 0.998 0.954 0.000
  2.351-1.908    98.22  1960   136 0.1221    98.405    97.308 1.040 0.954 0.000
  1.908-1.548    96.68  3574   246 0.1242    61.030    60.410 1.024 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1366    38.262    37.678 1.029 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1801    24.661    23.906 1.029 0.955 0.000
  1.020-0.965    71.91  3515   243 0.2671    15.792    14.487 0.989 0.961 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0482 

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

  using refinement target ml 


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

r_work=0.1448 r_free=0.1635
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1448 r_free=0.1635

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.077257              wxc_scale = 0.500            wc = 0.062         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.097947              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
 0.1449 0.1635 0.0186  0.024   2.1    5.1   0.0   1.8    0   1.039

Number of minimizer iterations: 7 (9 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.49 16.35   1.86  2.110  11.123  0.098    3.400
14.48 16.35   1.86  2.110  11.123  0.098    3.400

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.94  54.39  12.36   2.21   647     0
   Protein:    3.94  31.44   9.11   2.21   518     0
   Water:      6.99  54.39  25.41    N/A   129     0
   Chain  A:   3.94  54.39  12.36    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.94 - 8.99        333
     8.99 - 14.03       148
    14.03 - 19.08        56
    19.08 - 24.12        44
    24.12 - 29.17        21
    29.17 - 34.21        15
    34.21 - 39.26        11
    39.26 - 44.30        12
    44.30 - 49.35         4
    49.35 - 54.39         3


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40033  r_work = 0.1448  r_free = 0.1635                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.3983  r_work = 0.1442  r_free = 0.1635                  |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1442 r_free = 0.1635             target_work(ml) = 3.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1448 r_free = 0.1636             target_work(ml) = 3.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (10 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1448 r_free= 0.1636 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.400409                            |
| target function (ml) not normalized (work): 98584.663850                    |
| target function (ml) not normalized (free): 6941.488127                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1461 0.1448 0.1636 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1601 0.1591 0.1734 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1601 0.1591 0.1734 n_refl.: 30991
overall B=-0.01 to atoms: r(all,work,free)=0.1600 0.1590 0.1734 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1461 0.1448 0.1634 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1461 0.1448 0.1634 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0362

 ======================== 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 0.2561   120.817   110.489 0.739 0.956 0.290
  6.681-5.432    92.59    94     6 0.1440   150.525   146.943 0.825 0.955 0.238
  5.422-4.402    83.85   151    10 0.1124   195.017   194.377 0.930 0.958 0.223
  4.390-3.571    90.83   296    21 0.1141   204.579   202.942 0.990 0.956 0.190
  3.569-2.898    96.33   565    39 0.1224   165.163   163.347 1.001 0.955 0.047
  2.897-2.351    98.71  1071    73 0.1310   127.090   125.830 0.997 0.955 0.000
  2.351-1.908    98.22  1960   136 0.1221    98.405    97.308 1.039 0.954 0.000
  1.908-1.548    96.68  3574   246 0.1241    61.030    60.412 1.023 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1366    38.262    37.677 1.027 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1801    24.661    23.906 1.027 0.955 0.000
  1.020-0.965    71.91  3515   243 0.2669    15.792    14.487 0.986 0.961 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0380 

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

  using refinement target ml 


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

r_work=0.1448 r_free=0.1634
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1448 r_free=0.1634

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.153753              wxc_scale = 0.500            wc = 0.062         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.101121              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
 0.1448 0.1634 0.0186  0.024   2.1    5.1   0.0   1.8    0   1.077

Number of minimizer iterations: 1 (1 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.48 16.34   1.86  2.110  11.112  0.101    3.400
14.48 16.34   1.86  2.110  11.112  0.101    3.400

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.93  54.38  12.35   2.21   647     0
   Protein:    3.93  31.43   9.09   2.21   518     0
   Water:      6.98  54.38  25.40    N/A   129     0
   Chain  A:   3.93  54.38  12.35    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.93 - 8.97        333
     8.97 - 14.02       148
    14.02 - 19.06        56
    19.06 - 24.11        44
    24.11 - 29.16        21
    29.16 - 34.20        15
    34.20 - 39.25        11
    39.25 - 44.29        12
    44.29 - 49.34         4
    49.34 - 54.38         3


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40028  r_work = 0.1448  r_free = 0.1634                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.3984  r_work = 0.1442  r_free = 0.1634                  |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1442 r_free = 0.1634             target_work(ml) = 3.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1448 r_free = 0.1634             target_work(ml) = 3.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 9 (20 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1448 r_free= 0.1634 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.400238                            |
| target function (ml) not normalized (work): 98579.707588                    |
| target function (ml) not normalized (free): 6941.239849                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1461 0.1448 0.1634 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1600 0.1590 0.1733 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1600 0.1590 0.1733 n_refl.: 30991
overall B=-0.01 to atoms: r(all,work,free)=0.1599 0.1589 0.1732 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1461 0.1448 0.1635 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1461 0.1448 0.1635 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0263

 ======================== 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 0.2554   120.817   110.501 0.739 0.956 0.290
  6.681-5.432    92.59    94     6 0.1445   150.525   146.869 0.824 0.955 0.235
  5.422-4.402    83.85   151    10 0.1123   195.017   194.392 0.929 0.958 0.220
  4.390-3.571    90.83   296    21 0.1139   204.579   202.927 0.990 0.956 0.190
  3.569-2.898    96.33   565    39 0.1225   165.163   163.321 1.002 0.955 0.100
  2.897-2.351    98.71  1071    73 0.1310   127.090   125.829 0.997 0.955 0.000
  2.351-1.908    98.22  1960   136 0.1220    98.405    97.304 1.038 0.954 0.000
  1.908-1.548    96.68  3574   246 0.1241    61.030    60.409 1.023 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1366    38.262    37.677 1.026 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1802    24.661    23.905 1.025 0.955 0.000
  1.020-0.965    71.91  3515   243 0.2669    15.792    14.486 0.983 0.961 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0285 

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

  using refinement target ml 


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

r_work=0.1448 r_free=0.1635
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1448 r_free=0.1635

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.410029              wxc_scale = 0.500            wc = 0.062         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.087908              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
 0.1448 0.1635 0.0187  0.024   2.1    5.1   0.0   1.8    0   1.205

Number of minimizer iterations: 1 (1 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.48 16.35   1.87  2.110  11.104  0.088    3.400
14.48 16.35   1.87  2.110  11.104  0.088    3.400

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.92  54.37  12.34   2.21   647     0
   Protein:    3.92  31.42   9.09   2.21   518     0
   Water:      6.97  54.37  25.39    N/A   129     0
   Chain  A:   3.92  54.37  12.34    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.92 - 8.97        333
     8.97 - 14.01       148
    14.01 - 19.06        56
    19.06 - 24.10        44
    24.10 - 29.15        21
    29.15 - 34.19        15
    34.19 - 39.24        11
    39.24 - 44.28        12
    44.28 - 49.33         4
    49.33 - 54.37         3


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40046  r_work = 0.1448  r_free = 0.1635                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.39844  r_work = 0.1442  r_free = 0.1635                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1442 r_free = 0.1635             target_work(ml) = 3.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1448 r_free = 0.1636             target_work(ml) = 3.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (13 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1448 r_free= 0.1636 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.400459                            |
| target function (ml) not normalized (work): 98586.110360                    |
| target function (ml) not normalized (free): 6941.593262                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1461 0.1448 0.1636 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1599 0.1589 0.1733 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1599 0.1589 0.1733 n_refl.: 30991
overall B=-0.01 to atoms: r(all,work,free)=0.1598 0.1589 0.1732 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1461 0.1448 0.1636 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1461 0.1448 0.1636 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0203

 ======================== 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 0.2550   120.817   110.564 0.739 0.956 0.290
  6.681-5.432    92.59    94     6 0.1447   150.525   146.834 0.824 0.955 0.233
  5.422-4.402    83.85   151    10 0.1119   195.017   194.368 0.929 0.958 0.217
  4.390-3.571    90.83   296    21 0.1138   204.579   202.930 0.990 0.956 0.180
  3.569-2.898    96.33   565    39 0.1226   165.163   163.335 1.001 0.955 0.047
  2.897-2.351    98.71  1071    73 0.1310   127.090   125.825 0.997 0.954 0.000
  2.351-1.908    98.22  1960   136 0.1220    98.405    97.308 1.038 0.954 0.000
  1.908-1.548    96.68  3574   246 0.1241    61.030    60.413 1.022 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1366    38.262    37.677 1.025 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1802    24.661    23.906 1.024 0.955 0.000
  1.020-0.965    71.91  3515   243 0.2669    15.792    14.488 0.982 0.961 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0220 

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

  using refinement target ml 


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

r_work=0.1448 r_free=0.1636
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1448 r_free=0.1636

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.202735              wxc_scale = 0.500            wc = 0.062         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.094274              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
 0.1448 0.1636 0.0188  0.024   2.1    5.1   0.0   1.8    0   1.101

Number of minimizer iterations: 1 (1 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.48 16.36   1.88  2.110  11.098  0.094    3.400
14.48 16.36   1.88  2.110  11.098  0.094    3.400

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.91  54.37  12.33   2.21   647     0
   Protein:    3.91  31.42   9.08   2.21   518     0
   Water:      6.97  54.37  25.39    N/A   129     0
   Chain  A:   3.91  54.37  12.33    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.91 - 8.96        333
     8.96 - 14.01       148
    14.01 - 19.05        56
    19.05 - 24.10        44
    24.10 - 29.14        21
    29.14 - 34.19        15
    34.19 - 39.23        11
    39.23 - 44.28        12
    44.28 - 49.32         4
    49.32 - 54.37         3


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40037  r_work = 0.1448  r_free = 0.1636                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.39838  r_work = 0.1442  r_free = 0.1635                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1442 r_free = 0.1635             target_work(ml) = 3.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1448 r_free = 0.1635             target_work(ml) = 3.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|

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= 0.1448 r_free= 0.1635 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.400252                            |
| target function (ml) not normalized (work): 98580.115156                    |
| target function (ml) not normalized (free): 6940.753604                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1461 0.1448 0.1635 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1598 0.1588 0.1731 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1598 0.1588 0.1731 n_refl.: 30991
overall B=-0.00 to atoms: r(all,work,free)=0.1598 0.1588 0.1731 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1461 0.1448 0.1636 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1461 0.1448 0.1636 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0125

 ======================== 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 0.2548   120.817   110.558 0.738 0.956 0.289
  6.681-5.432    92.59    94     6 0.1447   150.525   146.814 0.824 0.954 0.233
  5.422-4.402    83.85   151    10 0.1122   195.017   194.359 0.929 0.957 0.217
  4.390-3.571    90.83   296    21 0.1140   204.579   202.928 0.990 0.956 0.180
  3.569-2.898    96.33   565    39 0.1227   165.163   163.318 1.002 0.955 0.090
  2.897-2.351    98.71  1071    73 0.1311   127.090   125.826 0.997 0.954 0.000
  2.351-1.908    98.22  1960   136 0.1220    98.405    97.313 1.038 0.953 0.000
  1.908-1.548    96.68  3574   246 0.1242    61.030    60.412 1.022 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1366    38.262    37.676 1.024 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1802    24.661    23.905 1.022 0.955 0.000
  1.020-0.965    71.91  3515   243 0.2669    15.792    14.488 0.980 0.961 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0163 

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

  using refinement target ml 


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

r_work=0.1448 r_free=0.1636
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1448 r_free=0.1636

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.132394              wxc_scale = 0.500            wc = 0.062         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.042691              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
 0.1448 0.1636 0.0187  0.024   2.1    5.1   0.0   1.8    0   1.066

Number of minimizer iterations: 1 (1 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.48 16.36   1.87  2.110  11.093  0.043    3.400
14.48 16.36   1.87  2.110  11.092  0.043    3.400

Number of minimizer iterations: 2 (5 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.92  54.36  12.33   2.21   647     0
   Protein:    3.92  31.41   9.07   2.21   518     0
   Water:      6.96  54.36  25.38    N/A   129     0
   Chain  A:   3.92  54.36  12.33    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.92 - 8.96        333
     8.96 - 14.00       148
    14.00 - 19.05        56
    19.05 - 24.09        44
    24.09 - 29.14        21
    29.14 - 34.18        15
    34.18 - 39.23        11
    39.23 - 44.27        12
    44.27 - 49.32         4
    49.32 - 54.36         3


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.40038  r_work = 0.1448  r_free = 0.1636                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.39837  r_work = 0.1442  r_free = 0.1635                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1442 r_free = 0.1635             target_work(ml) = 3.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1448 r_free = 0.1637             target_work(ml) = 3.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (10 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1448 r_free= 0.1637 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.400487                            |
| target function (ml) not normalized (work): 98586.909677                    |
| target function (ml) not normalized (free): 6941.124180                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1461 0.1448 0.1637 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1597 0.1588 0.1732 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1597 0.1588 0.1732 n_refl.: 30991
overall B=-0.01 to atoms: r(all,work,free)=0.1597 0.1587 0.1732 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1461 0.1448 0.1637 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1461 0.1448 0.1637 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.0013

 ======================== 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 0.2546   120.817   110.718 0.739 0.954 0.300
  6.681-5.432    92.59    94     6 0.1451   150.525   146.633 0.825 0.953 0.230
  5.422-4.402    83.85   151    10 0.1110   195.017   194.160 0.930 0.956 0.230
  4.390-3.571    90.83   296    21 0.1132   204.579   202.747 0.991 0.954 0.180
  3.569-2.898    96.33   565    39 0.1228   165.163   163.202 1.003 0.954 0.090
  2.897-2.351    98.71  1071    73 0.1311   127.090   125.786 0.999 0.953 0.000
  2.351-1.908    98.22  1960   136 0.1219    98.405    97.309 1.039 0.953 0.000
  1.908-1.548    96.68  3574   246 0.1242    61.030    60.442 1.022 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1366    38.262    37.721 1.024 0.955 0.000
  1.256-1.020    88.52 11175   771 0.1802    24.661    23.959 1.021 0.957 0.000
  1.020-0.965    71.91  3515   243 0.2669    15.792    14.532 0.978 0.964 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0220 

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

  using refinement target ml 


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

r_work=0.1448 r_free=0.1637
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1448 r_free=0.1637

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.180120              wxc_scale = 0.500            wc = 0.062         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.094928              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
 0.1448 0.1637 0.0189  0.024   2.1    5.1   0.0   1.8    0   1.090

Number of minimizer iterations: 1 (1 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
14.48 16.37   1.89  2.110  11.086  0.095    3.401
14.48 16.37   1.89  2.110  11.086  0.095    3.401

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.91  54.35  12.32   2.21   647     0
   Protein:    3.91  31.41   9.07   2.21   518     0
   Water:      6.95  54.35  25.37    N/A   129     0
   Chain  A:   3.91  54.35  12.32    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.91 - 8.95        333
     8.95 - 14.00       148
    14.00 - 19.04        56
    19.04 - 24.09        44
    24.09 - 29.13        21
    29.13 - 34.18        15
    34.18 - 39.22        11
    39.22 - 44.27        12
    44.27 - 49.31         4
    49.31 - 54.35         3


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.4005  r_work = 0.1448  r_free = 0.1637                  |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.39833  r_work = 0.1441  r_free = 0.1636                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1441 r_free = 0.1636             target_work(ml) = 3.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1448 r_free = 0.1637             target_work(ml) = 3.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (8 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1448 r_free= 0.1637 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ml) (work): 3.400419                            |
| target function (ml) not normalized (work): 98584.934781                    |
| target function (ml) not normalized (free): 6941.389033                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| 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 0.1287 0.1565      4.6589      4.8302|
|  2:    2.32 -    1.84 0.98   2320  160 0.1227 0.1371       4.196      4.2811|
|  3:    1.84 -    1.61 0.97   2265  156 0.1239 0.1609      3.7334      3.8907|
|  4:    1.61 -    1.46 0.96   2239  154 0.1262 0.1428       3.484      3.5603|
|  5:    1.46 -    1.36 0.96   2218  154 0.1326 0.1353      3.3042        3.34|
|  6:    1.36 -    1.28 0.94   2170  149 0.1461 0.1610      3.2169      3.3528|
|  7:    1.28 -    1.22 0.95   2184  151 0.1465 0.1714      3.1279      3.2373|
|  8:    1.22 -    1.16 0.94   2134  147 0.1528 0.1656      3.1037      3.2082|
|  9:    1.16 -    1.12 0.92   2115  146 0.1633 0.1776      3.0628      3.0886|
| 10:    1.12 -    1.08 0.87   1988  137 0.1928 0.1862      3.1289      3.1322|
| 11:    1.08 -    1.05 0.84   1934  133 0.2168 0.2278      3.0454      3.1247|
| 12:    1.05 -    1.02 0.81   1835  127 0.2496 0.2981      3.0533      3.0647|
| 13:    1.02 -    0.99 0.79   1814  125 0.2577 0.2704      3.0016       2.958|
| 14:    0.99 -    0.96 0.63   1422   98 0.2800 0.2542      2.9725      2.9564|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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  14.65   1.00     1.03       1908.08|
|  2:    2.32 -    1.84  2320   160  0.89  16.58   1.00     1.03        915.81|
|  3:    1.84 -    1.61  2265   156  0.91  14.59   1.00     1.03        333.38|
|  4:    1.61 -    1.46  2239   154  0.93  13.08   1.01     1.03        187.48|
|  5:    1.46 -    1.36  2218   154  0.93  13.08   1.00     1.02        123.62|
|  6:    1.36 -    1.28  2170   149  0.93  13.76   0.99     1.02        101.16|
|  7:    1.28 -    1.22  2184   151  0.92  14.55   1.01     1.01         88.32|
|  8:    1.22 -    1.16  2134   147  0.92  14.47   1.03     1.04         81.25|
|  9:    1.16 -    1.12  2115   146  0.92  14.40   1.00     1.03         70.68|
| 10:    1.12 -    1.08  1988   137  0.92  15.38   0.99     1.02         68.15|
| 11:    1.08 -    1.05  1934   133  0.89  18.49   0.96     0.98         66.50|
| 12:    1.05 -    1.02  1835   127  0.87  21.12   0.96     0.95         67.70|
| 13:    1.02 -    0.99  1814   125  0.85  23.29   1.01     0.94         62.35|
| 14:    0.99 -    0.96  1422    98  0.85  22.83   0.98     0.94         53.61|
|alpha:            min =        0.94 max =            1.04 mean =         1.01|
|beta:             min =       53.61 max =         1908.08 mean =       323.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.87 mean =        16.11|
|phase err.(test): min =        0.00 max =           88.06 mean =        15.51|
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1460 0.1448 0.1637 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1597 0.1587 0.1731 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1597 0.1587 0.1731 n_refl.: 30991
overall B=-0.00 to atoms: r(all,work,free)=0.1597 0.1587 0.1731 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1460 0.1448 0.1635 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1460 0.1448 0.1635 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.0005

 ======================== 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 0.2545   120.817   110.615 0.738 0.956 0.290
  6.681-5.432    92.59    94     6 0.1454   150.525   146.898 0.823 0.954 0.235
  5.422-4.402    83.85   151    10 0.1116   195.017   194.312 0.929 0.957 0.220
  4.390-3.571    90.83   296    21 0.1133   204.579   202.909 0.991 0.955 0.190
  3.569-2.898    96.33   565    39 0.1228   165.163   163.320 1.002 0.954 0.047
  2.897-2.351    98.71  1071    73 0.1311   127.090   125.829 0.997 0.954 0.000
  2.351-1.908    98.22  1960   136 0.1219    98.405    97.313 1.038 0.953 0.000
  1.908-1.548    96.68  3574   246 0.1242    61.030    60.412 1.021 0.954 0.000
  1.548-1.256    95.43  6500   448 0.1366    38.262    37.677 1.022 0.954 0.000
  1.256-1.020    88.52 11175   771 0.1802    24.661    23.906 1.020 0.955 0.000
  1.020-0.965    71.91  3515   243 0.2670    15.792    14.488 0.977 0.961 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0048 

================= 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: 0.1496 0.1672 0.026  2.054   4.1  57.8  12.0 129      0.166
       1_adp: 0.1478 0.1714 0.026  2.054   4.1  55.5  12.3 129      0.166
      1_occh: 0.1465 0.1727 0.026  2.054   4.1  55.5  12.3 129      0.166
       1_occ: 0.1468 0.1721 0.026  2.054   4.1  55.5  12.3 129      0.166
       2_bss: 0.1464 0.1720 0.026  2.054   4.1  55.5  12.3 129      0.166
 2_settarget: 0.1464 0.1720 0.026  2.054   4.1  55.5  12.3 129      0.166
       2_nqh: 0.1464 0.1720 0.026  2.054   4.1  55.5  12.3 129      0.166
    2_weight: 0.1464 0.1720 0.026  2.054   4.1  55.5  12.3 129      0.166
     2_fitrh: 0.1467 0.1715 0.026  2.054   4.1  55.5  12.3 129      0.158
    2_xyzrec: 0.1454 0.1714 0.027  2.054   4.1  55.5  12.3 129      0.160
       2_adp: 0.1446 0.1709 0.027  2.054   4.0  54.5  12.5 129      0.160
      2_occh: 0.1440 0.1730 0.027  2.054   4.0  54.5  12.5 129      0.160
       2_occ: 0.1443 0.1716 0.027  2.054   4.0  54.5  12.5 129      0.160
       3_bss: 0.1442 0.1719 0.027  2.054   4.0  54.5  12.5 129      0.160
 3_settarget: 0.1442 0.1719 0.027  2.054   4.0  54.5  12.5 129      0.160
       3_nqh: 0.1442 0.1719 0.027  2.054   4.0  54.5  12.5 129      0.160
    3_weight: 0.1442 0.1719 0.027  2.054   4.0  54.5  12.5 129      0.160
     3_fitrh: 0.1444 0.1716 0.027  2.054   4.0  54.5  12.5 129      0.182
    3_xyzrec: 0.1453 0.1666 0.024  2.032   4.0  54.5  12.5 129      0.163
       3_adp: 0.1450 0.1640 0.024  2.032   3.8  54.5  12.4 129      0.163
      3_occh: 0.1444 0.1638 0.024  2.032   3.8  54.5  12.4 129      0.163
       3_occ: 0.1449 0.1635 0.024  2.032   3.8  54.5  12.4 129      0.163
       4_bss: 0.1451 0.1633 0.024  2.032   3.8  54.4  12.4 129      0.163
 4_settarget: 0.1451 0.1633 0.024  2.032   3.8  54.4  12.4 129      0.163
       4_nqh: 0.1451 0.1633 0.024  2.032   3.8  54.4  12.4 129      0.163
    4_weight: 0.1451 0.1633 0.024  2.032   3.8  54.4  12.4 129      0.163
     4_fitrh: 0.1452 0.1633 0.024  2.032   3.8  54.4  12.4 129      0.156
    4_xyzrec: 0.1450 0.1637 0.024  2.084   3.8  54.4  12.4 129      0.155
       4_adp: 0.1449 0.1637 0.024  2.084   4.0  54.4  12.4 129      0.155
      4_occh: 0.1443 0.1635 0.024  2.084   4.0  54.4  12.4 129      0.155
       4_occ: 0.1448 0.1636 0.024  2.084   4.0  54.4  12.4 129      0.155
       5_bss: 0.1448 0.1635 0.024  2.084   3.9  54.4  12.4 129      0.155
 5_settarget: 0.1448 0.1635 0.024  2.084   3.9  54.4  12.4 129      0.155
       5_nqh: 0.1448 0.1635 0.024  2.084   3.9  54.4  12.4 129      0.155
    5_weight: 0.1448 0.1635 0.024  2.084   3.9  54.4  12.4 129      0.155
     5_fitrh: 0.1448 0.1635 0.024  2.084   3.9  54.4  12.4 129      0.155
    5_xyzrec: 0.1449 0.1635 0.024  2.081   3.9  54.4  12.4 129      0.155
       5_adp: 0.1448 0.1635 0.024  2.081   3.9  54.4  12.4 129      0.155
      5_occh: 0.1442 0.1635 0.024  2.081   3.9  54.4  12.4 129      0.155
       5_occ: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.4 129      0.155
       6_bss: 0.1448 0.1634 0.024  2.081   3.9  54.4  12.3 129      0.155
 6_settarget: 0.1448 0.1634 0.024  2.081   3.9  54.4  12.3 129      0.155
       6_nqh: 0.1448 0.1634 0.024  2.081   3.9  54.4  12.3 129      0.155
    6_weight: 0.1448 0.1634 0.024  2.081   3.9  54.4  12.3 129      0.155
     6_fitrh: 0.1448 0.1634 0.024  2.081   3.9  54.4  12.3 129      0.155
    6_xyzrec: 0.1448 0.1634 0.024  2.081   3.9  54.4  12.3 129      0.155
       6_adp: 0.1448 0.1634 0.024  2.081   3.9  54.4  12.3 129      0.155
      6_occh: 0.1442 0.1634 0.024  2.081   3.9  54.4  12.3 129      0.155
       6_occ: 0.1448 0.1634 0.024  2.081   3.9  54.4  12.3 129      0.155
       7_bss: 0.1448 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
 7_settarget: 0.1448 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
       7_nqh: 0.1448 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
    7_weight: 0.1448 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
     7_fitrh: 0.1448 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
    7_xyzrec: 0.1448 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
       7_adp: 0.1448 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
      7_occh: 0.1442 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
       7_occ: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
       8_bss: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
 8_settarget: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
       8_nqh: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
    8_weight: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
     8_fitrh: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
    8_xyzrec: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
       8_adp: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
      8_occh: 0.1442 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
       8_occ: 0.1448 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
       9_bss: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
 9_settarget: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
       9_nqh: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
    9_weight: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
     9_fitrh: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
    9_xyzrec: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
       9_adp: 0.1448 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
      9_occh: 0.1442 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
       9_occ: 0.1448 0.1637 0.024  2.081   3.9  54.4  12.3 129      0.155
      10_bss: 0.1448 0.1637 0.024  2.081   3.9  54.4  12.3 129      0.155
10_settarget: 0.1448 0.1637 0.024  2.081   3.9  54.4  12.3 129      0.155
      10_nqh: 0.1448 0.1637 0.024  2.081   3.9  54.4  12.3 129      0.155
   10_weight: 0.1448 0.1637 0.024  2.081   3.9  54.4  12.3 129      0.155
    10_fitrh: 0.1448 0.1637 0.024  2.081   3.9  54.4  12.3 129      0.155
   10_xyzrec: 0.1448 0.1637 0.024  2.081   3.9  54.4  12.3 129      0.155
      10_adp: 0.1448 0.1637 0.024  2.081   3.9  54.4  12.3 129      0.155
     10_occh: 0.1441 0.1636 0.024  2.081   3.9  54.4  12.3 129      0.155
      10_occ: 0.1448 0.1637 0.024  2.081   3.9  54.4  12.3 129      0.155
         end: 0.1448 0.1635 0.024  2.081   3.9  54.4  12.3 129      0.155
------------------------------------------------------------------------

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


Writing refined structure to CIF file:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/unscale_001.cif
Writing default parameters for subsequent refinement:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/unscale_002.def

Timing summary:
  Write initial files (write_before_run_outputs): 0.7500
  Refinement macro-cycles (run)                 : 459.6300
  Write final files (write_after_run_outputs)   : 21.2100
  Total                                         : 481.5900
Total CPU time: 8.23 minutes

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

# Date 2026-07-20 Time 16:50:50 PDT -0700 (1784591450.61 s)

Start R-work = 0.1523, R-free = 0.1485
Final R-work = 0.1448, R-free = 0.1635

===============================================================================
Job complete
usr+sys time: 493.78 seconds
wall clock time: 8 minutes 49.06 seconds (529.06 seconds total)
