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=default
    optimize_xyz_weight=false

No user-defined map coefficients or files defined; will use default map
outputs instead.
Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    phil_files = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913//p.eff"
    default_phil = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913//p.eff"
    model {
      file = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/1AHO.pdb"
    }
    default_model = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/1AHO.pdb"
    miller_array {
      file = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/1AHO.mtz"
    }
    default_miller_array = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/1AHO.mtz"
  }
  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 {
      wu = 0.1
    }
  }
  output {
    prefix = default
    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: 0.59, per 1000 atoms: 0.53
  Number of scatterers: 1106
  At special positions: 0
  Unit cell: (45.9, 40.7, 30.1, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     O     229      8.00
     N      88      7.00
     C     320      6.00
     H     459      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

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

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

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

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

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

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

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

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

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


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

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

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


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

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

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

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

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

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

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

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

#phil __ON__
refinement {
  output {
    write_geo_vs_map = True
  }
  electron_density_maps {
    map_coefficients {
      map_type = "2mFo-DFc"
      mtz_label_amplitudes = "2FOFCWT"
      mtz_label_phases = "PH2FOFCWT"
      fill_missing_f_obs = True
    }
    map_coefficients {
      map_type = "2mFo-DFc"
      mtz_label_amplitudes = "2FOFCWT_no_fill"
      mtz_label_phases = "PH2FOFCWT_no_fill"
    }
    map_coefficients {
      map_type = "mFo-DFc"
      mtz_label_amplitudes = "FOFCWT"
      mtz_label_phases = "PHFOFCWT"
    }
    map_coefficients {
      map_type = "anomalous"
      mtz_label_amplitudes = "ANOM"
      mtz_label_phases = "PANOM"
    }
    map {
      map_type = "2mFo-DFc"
      fill_missing_f_obs = True
    }
    map {
      map_type = "2mFo-DFc"
    }
    map {
      map_type = "mFo-DFc"
    }
  }
  refine {
    strategy = *individual_sites individual_sites_real_space rigid_body \
               *individual_adp group_adp tls *occupancies group_anomalous den
  }
  main {
    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 {
    wu = 0.1
  }
}
output {
  prefix = "default"
  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

====================== 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
 0.1575 0.1693 0.0118  0.006   1.1    3.1   0.0   1.8    0   7.818

Number of minimizer iterations: 50 (55 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
15.75 16.93   1.18  1.052  10.819  0.141    0.025
15.54 17.33   1.79  1.994  11.398  0.141    0.024

Number of minimizer iterations: 25 (27 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    4.06  55.41  12.49   2.07   647     0
   Protein:    4.06  28.70   9.27   2.07   518     0
   Water:      6.82  55.41  25.39    N/A   129     0
   Chain  A:   4.06  55.41  12.49    N/A   647     0
   Histogram:
       Values      Number of atoms
     4.06 - 9.19        336
     9.19 - 14.33       146
    14.33 - 19.46        60
    19.46 - 24.60        41
    24.60 - 29.73        21
    29.73 - 34.87        14
    34.87 - 40.00        14
    40.00 - 45.14         9
    45.14 - 50.27         4
    50.27 - 55.41         2


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

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0235897  r_work = 0.1554  r_free = 0.1733      |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0219403  r_work = 0.1532  r_free = 0.1758      |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1532 r_free = 0.1758    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1539 r_free = 0.1745    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (16 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1539 r_free= 0.1745 coordinate error (max.-lik. estimate): 0.09 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.022127                   |
| target function (ls_wunit_k1) not normalized (work): 641.513877             |
| target function (ls_wunit_k1) not normalized (free): 64.901184              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1553 0.1539 0.1745 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1684 0.1674 0.1831 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1684 0.1674 0.1831 n_refl.: 30991
 overall B=0.01 to atoms: r(all,work,free)=0.1685 0.1674 0.1831 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1550 0.1536 0.1744 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1550 0.1536 0.1744 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.0284

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

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

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 14.116-6.710    82.91    91     6 0.2454   120.817   111.742 0.715 0.987 0.290
  6.681-5.432    92.59    94     6 0.1341   150.525   147.976 0.805 0.986 0.245
  5.422-4.402    83.85   151    10 0.1051   195.017   194.699 0.903 0.989 0.232
  4.390-3.571    90.83   296    21 0.0987   204.579   203.400 0.963 0.987 0.200
  3.569-2.898    96.33   565    39 0.1082   165.163   164.381 0.971 0.986 0.060
  2.897-2.351    98.71  1071    73 0.1190   127.090   126.374 0.965 0.986 0.000
  2.351-1.908    98.22  1960   136 0.1264    98.405    97.379 0.999 0.985 0.000
  1.908-1.548    96.68  3574   246 0.1388    61.030    60.348 0.986 0.986 0.000
  1.548-1.256    95.43  6500   448 0.1581    38.262    37.564 0.987 0.987 0.000
  1.256-1.020    88.52 11175   771 0.2021    24.661    23.743 0.980 0.990 0.000
  1.020-0.965    71.91  3515   243 0.2781    15.792    14.447 0.952 0.998 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=0.0008  

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

  using refinement target ls_wunit_k1 


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

r_work=0.1536 r_free=0.1744
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1536 r_free=0.1744

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.923848             wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.278884              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=0.1536 r_free=0.1744
  H omit: r_work=0.1558 r_free=0.1747
  final:  r_work=0.1538 r_free=0.1743

====================== 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
 0.1530 0.1745 0.0214  0.006   1.1    3.1   0.0   1.8    0   7.962

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
15.30 17.45   2.14  1.994  11.406  0.279    0.022
15.16 17.32   2.16  2.124  11.490  0.279    0.021

Number of minimizer iterations: 25 (28 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    4.03  54.42  12.77   2.23   647     0
   Protein:    4.03  31.30   9.40   2.23   518     0
   Water:      6.88  54.42  26.30    N/A   129     0
   Chain  A:   4.03  54.42  12.77    N/A   647     0
   Histogram:
       Values      Number of atoms
     4.03 - 9.07        326
     9.07 - 14.11       147
    14.11 - 19.15        57
    19.15 - 24.19        47
    24.19 - 29.22        22
    29.22 - 34.26        15
    34.26 - 39.30        15
    39.30 - 44.34        10
    44.34 - 49.38         6
    49.38 - 54.42         2


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

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0214628  r_work = 0.1516  r_free = 0.1732      |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0208106  r_work = 0.1508  r_free = 0.1754      |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1508 r_free = 0.1754    target_work(ls_wunit_k1) = 0.021         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1513 r_free = 0.1735    target_work(ls_wunit_k1) = 0.021         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 14 (24 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1513 r_free= 0.1735 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.021036                   |
| target function (ls_wunit_k1) not normalized (work): 609.867782             |
| target function (ls_wunit_k1) not normalized (free): 65.026885              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1527 0.1513 0.1735 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1665 0.1654 0.1822 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1665 0.1654 0.1822 n_refl.: 30991
overall B=-0.00 to atoms: r(all,work,free)=0.1665 0.1653 0.1822 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1527 0.1512 0.1737 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1527 0.1512 0.1737 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: 0.0170

 ======================== 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 0.2157   120.817   113.014 0.723 0.988 0.280
  6.681-5.432    92.59    94     6 0.1249   150.525   148.086 0.800 0.987 0.240
  5.422-4.402    83.85   151    10 0.0995   195.017   194.639 0.896 0.989 0.230
  4.390-3.571    90.83   296    21 0.0924   204.579   203.700 0.961 0.988 0.180
  3.569-2.898    96.33   565    39 0.1064   165.163   164.545 0.971 0.987 0.090
  2.897-2.351    98.71  1071    73 0.1157   127.090   126.430 0.966 0.986 0.000
  2.351-1.908    98.22  1960   136 0.1240    98.405    97.454 0.999 0.986 0.000
  1.908-1.548    96.68  3574   246 0.1363    61.030    60.410 0.986 0.987 0.000
  1.548-1.256    95.43  6500   448 0.1563    38.262    37.580 0.988 0.988 0.000
  1.256-1.020    88.52 11175   771 0.2013    24.661    23.741 0.980 0.990 0.000
  1.020-0.965    71.91  3515   243 0.2789    15.792    14.449 0.956 0.998 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0087 

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

  using refinement target ml 


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

r_work=0.1512 r_free=0.1737
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1512 r_free=0.1737

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.514124              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.170403              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=0.1512 r_free=0.1737
  H omit: r_work=0.1534 r_free=0.1749
  final:  r_work=0.1515 r_free=0.1740

====================== 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
 0.1513 0.1683 0.0170  0.007   1.2    4.1   0.0   1.8    0   1.257

Number of minimizer iterations: 36 (37 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
15.13 16.83   1.70  2.124  11.488  0.170    3.450
15.07 16.58   1.51  2.159  11.395  0.170    3.431

Number of minimizer iterations: 25 (28 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.87  54.37  12.66   2.28   647     0
   Protein:    3.87  31.62   9.27   2.28   518     0
   Water:      7.05  54.37  26.26    N/A   129     0
   Chain  A:   3.87  54.37  12.66    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.87 - 8.92        322
     8.92 - 13.97       152
    13.97 - 19.02        52
    19.02 - 24.07        51
    24.07 - 29.12        22
    29.12 - 34.17        14
    34.17 - 39.22        16
    39.22 - 44.27        10
    44.27 - 49.32         6
    49.32 - 54.37         2


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.4314  r_work = 0.1507  r_free = 0.1658                  |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.42577  r_work = 0.1502  r_free = 0.1651                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1502 r_free = 0.1651             target_work(ml) = 3.426         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       60 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1507 r_free = 0.1643             target_work(ml) = 3.428         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 12 (15 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1507 r_free= 0.1643 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ml) (work): 3.427632                            |
| target function (ml) not normalized (work): 99373.900088                    |
| target function (ml) not normalized (free): 6954.505473                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1516 0.1507 0.1643 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1649 0.1642 0.1742 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1649 0.1642 0.1742 n_refl.: 30991
overall B=-0.02 to atoms: r(all,work,free)=0.1648 0.1641 0.1741 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1518 0.1509 0.1644 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1518 0.1509 0.1644 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0555

 ======================== 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 0.2630   120.817   110.397 0.732 0.960 0.270
  6.681-5.432    92.59    94     6 0.1522   150.525   146.103 0.824 0.958 0.210
  5.422-4.402    83.85   151    10 0.1146   195.017   194.420 0.923 0.961 0.203
  4.390-3.571    90.83   296    21 0.1139   204.579   203.133 0.993 0.959 0.149
  3.569-2.898    96.33   565    39 0.1263   165.163   163.471 1.005 0.958 0.140
  2.897-2.351    98.71  1071    73 0.1342   127.090   125.903 0.994 0.958 0.000
  2.351-1.908    98.22  1960   136 0.1298    98.405    97.120 1.034 0.957 0.000
  1.908-1.548    96.68  3574   246 0.1315    61.030    60.399 1.023 0.958 0.000
  1.548-1.256    95.43  6500   448 0.1452    38.262    37.620 1.027 0.957 0.000
  1.256-1.020    88.52 11175   771 0.1860    24.661    23.858 1.026 0.959 0.000
  1.020-0.965    71.91  3515   243 0.2698    15.792    14.450 0.990 0.965 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0606 

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

  using refinement target ml 


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

r_work=0.1509 r_free=0.1644
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1509 r_free=0.1644

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.400242              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.109672              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=0.1509 r_free=0.1644
  H omit: r_work=0.1524 r_free=0.1660
  final:  r_work=0.1510 r_free=0.1640

====================== 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
 0.1505 0.1638 0.0132  0.007   1.2    3.1   0.0   1.8    0   1.200

Number of minimizer iterations: 36 (42 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
15.05 16.38   1.32  2.159  11.378  0.110    3.428
15.04 16.42   1.39  2.214  11.253  0.110    3.426

Number of minimizer iterations: 25 (31 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    4.01  54.19  12.58   2.20   647     0
   Protein:    4.01  32.34   9.23   2.20   518     0
   Water:      7.09  54.19  26.06    N/A   129     0
   Chain  A:   4.01  54.19  12.58    N/A   647     0
   Histogram:
       Values      Number of atoms
     4.01 - 9.03        331
     9.03 - 14.05       149
    14.05 - 19.07        51
    19.07 - 24.08        44
    24.08 - 29.10        23
    29.10 - 34.12        15
    34.12 - 39.13        16
    39.13 - 44.15        10
    44.15 - 49.17         6
    49.17 - 54.19         2


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.42573  r_work = 0.1504  r_free = 0.1642                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.42406  r_work = 0.1498  r_free = 0.1645                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1498 r_free = 0.1645             target_work(ml) = 3.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       62 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1502 r_free = 0.1641             target_work(ml) = 3.425         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (18 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1502 r_free= 0.1641 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ml) (work): 3.425076                            |
| target function (ml) not normalized (work): 99299.814040                    |
| target function (ml) not normalized (free): 6956.892753                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1511 0.1502 0.1641 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1646 0.1639 0.1744 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1646 0.1639 0.1744 n_refl.: 30991
overall B=-0.02 to atoms: r(all,work,free)=0.1644 0.1637 0.1743 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1511 0.1501 0.1641 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1511 0.1501 0.1641 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0637

 ======================== 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 0.2611   120.817   110.639 0.730 0.961 0.272
  6.681-5.432    92.59    94     6 0.1495   150.525   146.458 0.821 0.960 0.220
  5.422-4.402    83.85   151    10 0.1146   195.017   194.503 0.922 0.963 0.200
  4.390-3.571    90.83   296    21 0.1139   204.579   202.955 0.993 0.961 0.154
  3.569-2.898    96.33   565    39 0.1268   165.163   163.449 1.007 0.960 0.140
  2.897-2.351    98.71  1071    73 0.1366   127.090   125.801 0.994 0.959 0.000
  2.351-1.908    98.22  1960   136 0.1290    98.405    97.134 1.034 0.959 0.000
  1.908-1.548    96.68  3574   246 0.1306    61.030    60.407 1.020 0.959 0.000
  1.548-1.256    95.43  6500   448 0.1431    38.262    37.628 1.025 0.959 0.000
  1.256-1.020    88.52 11175   771 0.1846    24.661    23.874 1.028 0.961 0.000
  1.020-0.965    71.91  3515   243 0.2693    15.792    14.463 0.987 0.967 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0726 

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

  using refinement target ml 


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

r_work=0.1501 r_free=0.1641
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1501 r_free=0.1641

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.266074              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.179650              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


====================== 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
 0.1502 0.1641 0.0140  0.007   1.2    3.1   0.0   1.8    0   1.133

Number of minimizer iterations: 3 (4 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
15.02 16.41   1.40  2.214  11.232  0.180    3.425
15.01 16.39   1.37  2.211  11.233  0.180    3.425

Number of minimizer iterations: 8 (11 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.95  54.16  12.57   2.19   647     0
   Protein:    3.95  32.36   9.22   2.19   518     0
   Water:      7.04  54.16  26.04    N/A   129     0
   Chain  A:   3.95  54.16  12.57    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.95 - 8.98        330
     8.98 - 14.00       150
    14.00 - 19.02        51
    19.02 - 24.04        44
    24.04 - 29.06        23
    29.06 - 34.08        15
    34.08 - 39.10        16
    39.10 - 44.12        10
    44.12 - 49.14         6
    49.14 - 54.16         2


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.42456  r_work = 0.1501  r_free = 0.1639                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.42294  r_work = 0.1497  r_free = 0.1641                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1497 r_free = 0.1641             target_work(ml) = 3.423         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       60 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1501 r_free = 0.1636             target_work(ml) = 3.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 15 (23 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1501 r_free= 0.1636 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ml) (work): 3.424173                            |
| target function (ml) not normalized (work): 99273.625952                    |
| target function (ml) not normalized (free): 6953.457926                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1644 0.1638 0.1738 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1644 0.1638 0.1738 n_refl.: 30991
overall B=-0.02 to atoms: r(all,work,free)=0.1643 0.1636 0.1737 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0590

 ======================== 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 0.2608   120.817   110.857 0.725 0.962 0.280
  6.681-5.432    92.59    94     6 0.1520   150.525   146.348 0.817 0.961 0.210
  5.422-4.402    83.85   151    10 0.1144   195.017   194.470 0.918 0.964 0.210
  4.390-3.571    90.83   296    21 0.1135   204.579   202.876 0.992 0.962 0.149
  3.569-2.898    96.33   565    39 0.1270   165.163   163.477 1.006 0.961 0.130
  2.897-2.351    98.71  1071    73 0.1364   127.090   125.805 0.993 0.960 0.000
  2.351-1.908    98.22  1960   136 0.1288    98.405    97.145 1.033 0.959 0.000
  1.908-1.548    96.68  3574   246 0.1304    61.030    60.417 1.019 0.960 0.000
  1.548-1.256    95.43  6500   448 0.1431    38.262    37.628 1.023 0.959 0.000
  1.256-1.020    88.52 11175   771 0.1846    24.661    23.872 1.026 0.960 0.000
  1.020-0.965    71.91  3515   243 0.2694    15.792    14.462 0.985 0.967 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0602 

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

  using refinement target ml 


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

r_work=0.1501 r_free=0.1636
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1501 r_free=0.1636

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.204122              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.123851              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


====================== 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
 0.1501 0.1636 0.0136  0.007   1.2    3.1   0.0   1.8    0   1.102

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
15.01 16.36   1.36  2.211  11.216  0.124    3.424
15.01 16.36   1.36  2.211  11.216  0.124    3.424

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.94  54.14  12.55   2.19   647     0
   Protein:    3.94  32.34   9.20   2.19   518     0
   Water:      7.02  54.14  26.02    N/A   129     0
   Chain  A:   3.94  54.14  12.55    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.94 - 8.96        330
     8.96 - 13.98       150
    13.98 - 19.00        51
    19.00 - 24.02        44
    24.02 - 29.04        23
    29.04 - 34.06        15
    34.06 - 39.08        16
    39.08 - 44.10        10
    44.10 - 49.12         6
    49.12 - 54.14         2


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.42429  r_work = 0.1501  r_free = 0.1636                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.42261  r_work = 0.1496  r_free = 0.1638                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1496 r_free = 0.1638             target_work(ml) = 3.423         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       61 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1501 r_free = 0.1637             target_work(ml) = 3.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (12 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1501 r_free= 0.1637 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ml) (work): 3.424281                            |
| target function (ml) not normalized (work): 99276.748573                    |
| target function (ml) not normalized (free): 6953.282349                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1510 0.1501 0.1637 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1643 0.1636 0.1736 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1643 0.1636 0.1736 n_refl.: 30991
overall B=-0.01 to atoms: r(all,work,free)=0.1642 0.1635 0.1735 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1510 0.1501 0.1637 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1510 0.1501 0.1637 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0459

 ======================== 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 0.2602   120.817   110.888 0.725 0.962 0.280
  6.681-5.432    92.59    94     6 0.1518   150.525   146.310 0.817 0.961 0.210
  5.422-4.402    83.85   151    10 0.1143   195.017   194.451 0.918 0.964 0.210
  4.390-3.571    90.83   296    21 0.1140   204.579   202.879 0.991 0.962 0.144
  3.569-2.898    96.33   565    39 0.1271   165.163   163.470 1.006 0.961 0.130
  2.897-2.351    98.71  1071    73 0.1363   127.090   125.802 0.993 0.960 0.000
  2.351-1.908    98.22  1960   136 0.1287    98.405    97.152 1.032 0.959 0.000
  1.908-1.548    96.68  3574   246 0.1305    61.030    60.419 1.018 0.960 0.000
  1.548-1.256    95.43  6500   448 0.1431    38.262    37.628 1.022 0.959 0.000
  1.256-1.020    88.52 11175   771 0.1846    24.661    23.873 1.023 0.960 0.000
  1.020-0.965    71.91  3515   243 0.2694    15.792    14.463 0.981 0.966 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0466 

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

  using refinement target ml 


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

r_work=0.1501 r_free=0.1637
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1501 r_free=0.1637

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.487737              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.150085              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


====================== 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
 0.1501 0.1637 0.0136  0.007   1.2    3.1   0.0   1.8    0   1.244

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
15.01 16.37   1.36  2.211  11.203  0.150    3.424
15.01 16.37   1.36  2.211  11.203  0.150    3.424

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.92  54.13  12.54   2.19   647     0
   Protein:    3.92  32.33   9.19   2.19   518     0
   Water:      7.01  54.13  26.01    N/A   129     0
   Chain  A:   3.92  54.13  12.54    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.92 - 8.95        330
     8.95 - 13.97       150
    13.97 - 18.99        51
    18.99 - 24.01        44
    24.01 - 29.03        23
    29.03 - 34.05        15
    34.05 - 39.07        16
    39.07 - 44.09        10
    44.09 - 49.11         6
    49.11 - 54.13         2


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.42438  r_work = 0.1501  r_free = 0.1637                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.42277  r_work = 0.1496  r_free = 0.1639                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1496 r_free = 0.1639             target_work(ml) = 3.423         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       61 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1501 r_free = 0.1636             target_work(ml) = 3.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (14 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1501 r_free= 0.1636 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ml) (work): 3.424276                            |
| target function (ml) not normalized (work): 99276.621197                    |
| target function (ml) not normalized (free): 6953.531308                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1642 0.1635 0.1735 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1642 0.1635 0.1735 n_refl.: 30991
overall B=-0.01 to atoms: r(all,work,free)=0.1641 0.1634 0.1734 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0366

 ======================== 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 0.2602   120.817   110.877 0.725 0.962 0.280
  6.681-5.432    92.59    94     6 0.1521   150.525   146.325 0.816 0.961 0.210
  5.422-4.402    83.85   151    10 0.1145   195.017   194.457 0.918 0.964 0.210
  4.390-3.571    90.83   296    21 0.1138   204.579   202.866 0.991 0.962 0.144
  3.569-2.898    96.33   565    39 0.1271   165.163   163.478 1.005 0.961 0.130
  2.897-2.351    98.71  1071    73 0.1364   127.090   125.806 0.992 0.960 0.000
  2.351-1.908    98.22  1960   136 0.1287    98.405    97.147 1.031 0.959 0.000
  1.908-1.548    96.68  3574   246 0.1304    61.030    60.418 1.017 0.960 0.000
  1.548-1.256    95.43  6500   448 0.1431    38.262    37.628 1.020 0.959 0.000
  1.256-1.020    88.52 11175   771 0.1846    24.661    23.873 1.021 0.960 0.000
  1.020-0.965    71.91  3515   243 0.2694    15.792    14.462 0.979 0.966 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0366 

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

  using refinement target ml 


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

r_work=0.1501 r_free=0.1636
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1501 r_free=0.1636

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.363939              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.118777              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


====================== 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
 0.1501 0.1636 0.0136  0.007   1.2    3.1   0.0   1.8    0   1.182

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
15.01 16.36   1.36  2.211  11.192  0.119    3.424
15.01 16.36   1.36  2.211  11.192  0.119    3.424

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.91  54.12  12.53   2.19   647     0
   Protein:    3.91  32.32   9.18   2.19   518     0
   Water:      7.00  54.12  26.00    N/A   129     0
   Chain  A:   3.91  54.12  12.53    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.91 - 8.93        330
     8.93 - 13.96       150
    13.96 - 18.98        51
    18.98 - 24.00        44
    24.00 - 29.02        23
    29.02 - 34.04        15
    34.04 - 39.06        16
    39.06 - 44.08        10
    44.08 - 49.10         6
    49.10 - 54.12         2


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.42428  r_work = 0.1501  r_free = 0.1636                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.42269  r_work = 0.1496  r_free = 0.1639                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1496 r_free = 0.1639             target_work(ml) = 3.423         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       61 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1501 r_free = 0.1636             target_work(ml) = 3.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (14 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1501 r_free= 0.1636 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ml) (work): 3.424239                            |
| target function (ml) not normalized (work): 99275.535536                    |
| target function (ml) not normalized (free): 6953.395864                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1641 0.1634 0.1734 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1641 0.1634 0.1734 n_refl.: 30991
overall B=-0.01 to atoms: r(all,work,free)=0.1640 0.1634 0.1733 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0286

 ======================== 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 0.2602   120.817   110.886 0.724 0.962 0.280
  6.681-5.432    92.59    94     6 0.1522   150.525   146.322 0.816 0.961 0.210
  5.422-4.402    83.85   151    10 0.1145   195.017   194.444 0.918 0.964 0.210
  4.390-3.571    90.83   296    21 0.1138   204.579   202.853 0.991 0.962 0.144
  3.569-2.898    96.33   565    39 0.1271   165.163   163.484 1.005 0.961 0.130
  2.897-2.351    98.71  1071    73 0.1363   127.090   125.808 0.992 0.960 0.000
  2.351-1.908    98.22  1960   136 0.1287    98.405    97.148 1.031 0.960 0.000
  1.908-1.548    96.68  3574   246 0.1305    61.030    60.419 1.016 0.960 0.000
  1.548-1.256    95.43  6500   448 0.1431    38.262    37.628 1.019 0.960 0.000
  1.256-1.020    88.52 11175   771 0.1846    24.661    23.872 1.019 0.961 0.000
  1.020-0.965    71.91  3515   243 0.2694    15.792    14.462 0.977 0.967 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0284 

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

  using refinement target ml 


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

r_work=0.1501 r_free=0.1636
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1501 r_free=0.1636

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.151033              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.051588              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


====================== 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
 0.1501 0.1636 0.0136  0.007   1.2    3.1   0.0   1.8    0   1.076

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
15.01 16.36   1.36  2.211  11.184  0.052    3.424
15.01 16.36   1.36  2.211  11.184  0.052    3.424

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.91  54.11  12.52   2.19   647     0
   Protein:    3.91  32.31   9.17   2.19   518     0
   Water:      6.99  54.11  25.99    N/A   129     0
   Chain  A:   3.91  54.11  12.52    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.91 - 8.93        330
     8.93 - 13.95       150
    13.95 - 18.97        51
    18.97 - 23.99        44
    23.99 - 29.01        23
    29.01 - 34.03        15
    34.03 - 39.05        16
    39.05 - 44.07        10
    44.07 - 49.09         6
    49.09 - 54.11         2


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.42424  r_work = 0.1501  r_free = 0.1636                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.42269  r_work = 0.1496  r_free = 0.1639                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1496 r_free = 0.1639             target_work(ml) = 3.423         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       61 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1501 r_free = 0.1636             target_work(ml) = 3.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (14 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1501 r_free= 0.1636 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ml) (work): 3.424230                            |
| target function (ml) not normalized (work): 99275.279397                    |
| target function (ml) not normalized (free): 6953.400876                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1640 0.1634 0.1733 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1640 0.1634 0.1733 n_refl.: 30991
overall B=-0.01 to atoms: r(all,work,free)=0.1640 0.1633 0.1733 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0209

 ======================== 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 0.2602   120.817   110.889 0.724 0.962 0.280
  6.681-5.432    92.59    94     6 0.1522   150.525   146.330 0.816 0.961 0.210
  5.422-4.402    83.85   151    10 0.1144   195.017   194.436 0.917 0.964 0.210
  4.390-3.571    90.83   296    21 0.1137   204.579   202.848 0.991 0.962 0.144
  3.569-2.898    96.33   565    39 0.1271   165.163   163.484 1.005 0.961 0.130
  2.897-2.351    98.71  1071    73 0.1364   127.090   125.809 0.992 0.960 0.000
  2.351-1.908    98.22  1960   136 0.1287    98.405    97.150 1.030 0.960 0.000
  1.908-1.548    96.68  3574   246 0.1305    61.030    60.419 1.015 0.960 0.000
  1.548-1.256    95.43  6500   448 0.1431    38.262    37.628 1.018 0.960 0.000
  1.256-1.020    88.52 11175   771 0.1846    24.661    23.872 1.018 0.961 0.000
  1.020-0.965    71.91  3515   243 0.2694    15.792    14.462 0.975 0.967 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0221 

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

  using refinement target ml 


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

r_work=0.1501 r_free=0.1636
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1501 r_free=0.1636

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.212052              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.143872              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


====================== 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
 0.1501 0.1636 0.0136  0.007   1.2    3.1   0.0   1.8    0   1.106

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
15.01 16.36   1.36  2.211  11.178  0.144    3.424
15.01 16.36   1.36  2.211  11.178  0.144    3.424

Number of minimizer iterations: 1 (1 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    3.90  54.11  12.51   2.19   647     0
   Protein:    3.90  32.30   9.16   2.19   518     0
   Water:      6.98  54.11  25.98    N/A   129     0
   Chain  A:   3.90  54.11  12.51    N/A   647     0
   Histogram:
       Values      Number of atoms
     3.90 - 8.92        330
     8.92 - 13.94       150
    13.94 - 18.96        51
    18.96 - 23.98        44
    23.98 - 29.00        23
    29.00 - 34.02        15
    34.02 - 39.04        16
    39.04 - 44.06        10
    44.06 - 49.08         6
    49.08 - 54.11         2


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 3.42424  r_work = 0.1501  r_free = 0.1636                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 3.4226  r_work = 0.1496  r_free = 0.1638                  |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.1496 r_free = 0.1638             target_work(ml) = 3.423         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       61 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1501 r_free = 0.1636             target_work(ml) = 3.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (14 function evaluations)

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

|--(resolution: 0.96 - 14.12 A, n_refl.=30991 (all), 6.45  % free)------------|
|                                                                             |
| r_work= 0.1501 r_free= 0.1636 coordinate error (max.-lik. estimate): 0.08 A |
|                                                                             |
| normalized target function (ml) (work): 3.424211                            |
| target function (ml) not normalized (work): 99274.723140                    |
| target function (ml) not normalized (free): 6953.297184                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| 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 0.1328 0.1564      4.6827      4.8485|
|  2:    2.32 -    1.84 0.98   2320  160 0.1297 0.1362      4.2314      4.2815|
|  3:    1.84 -    1.61 0.97   2265  156 0.1295 0.1614      3.7626      3.9198|
|  4:    1.61 -    1.46 0.96   2239  154 0.1344 0.1442       3.527       3.558|
|  5:    1.46 -    1.36 0.96   2218  154 0.1394 0.1386      3.3452      3.3621|
|  6:    1.36 -    1.28 0.94   2170  149 0.1510 0.1561      3.2428      3.3301|
|  7:    1.28 -    1.22 0.95   2184  151 0.1518 0.1708      3.1518      3.2429|
|  8:    1.22 -    1.16 0.94   2134  147 0.1578 0.1674      3.1239      3.2035|
|  9:    1.16 -    1.12 0.92   2115  146 0.1684 0.1751      3.0866      3.0932|
| 10:    1.12 -    1.08 0.87   1988  137 0.1959 0.1864      3.1454      3.1424|
| 11:    1.08 -    1.05 0.84   1934  133 0.2208 0.2313      3.0599        3.14|
| 12:    1.05 -    1.02 0.81   1835  127 0.2528 0.2968      3.0617      3.0646|
| 13:    1.02 -    0.99 0.79   1814  125 0.2603 0.2674      3.0096      2.9484|
| 14:    0.99 -    0.96 0.63   1422   98 0.2822 0.2562      2.9764      2.9732|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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  14.93   1.00     1.03       1989.45|
|  2:    2.32 -    1.84  2320   160  0.89  16.93   1.00     1.03        953.25|
|  3:    1.84 -    1.61  2265   156  0.91  14.90   1.00     1.03        346.19|
|  4:    1.61 -    1.46  2239   154  0.93  13.18   1.01     1.03        191.68|
|  5:    1.46 -    1.36  2218   154  0.93  13.08   1.00     1.02        126.34|
|  6:    1.36 -    1.28  2170   149  0.93  13.70   0.99     1.02        100.83|
|  7:    1.28 -    1.22  2184   151  0.92  14.52   1.01     1.02         88.12|
|  8:    1.22 -    1.16  2134   147  0.92  14.49   1.03     1.04         81.29|
|  9:    1.16 -    1.12  2115   146  0.92  14.52   1.01     1.04         71.86|
| 10:    1.12 -    1.08  1988   137  0.92  15.43   0.99     1.03         68.87|
| 11:    1.08 -    1.05  1934   133  0.89  18.77   0.96     0.98         67.92|
| 12:    1.05 -    1.02  1835   127  0.87  21.36   0.96     0.95         68.68|
| 13:    1.02 -    0.99  1814   125  0.84  23.61   1.01     0.94         63.44|
| 14:    0.99 -    0.96  1422    98  0.85  23.01   0.99     0.95         54.08|
|alpha:            min =        0.94 max =            1.04 mean =         1.01|
|beta:             min =       54.08 max =         1989.45 mean =       334.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.26|
|phase err.(test): min =        0.00 max =           87.42 mean =        15.77|
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991
       re-set all scales: r(all,work,free)=0.1640 0.1633 0.1732 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1640 0.1633 0.1732 n_refl.: 30991
overall B=-0.00 to atoms: r(all,work,free)=0.1639 0.1633 0.1732 n_refl.: 30991
bulk-solvent and scaling: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991
         remove outliers: r(all,work,free)=0.1510 0.1501 0.1636 n_refl.: 30991

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0155

 ======================== 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 0.2601   120.817   110.886 0.724 0.962 0.280
  6.681-5.432    92.59    94     6 0.1524   150.525   146.328 0.816 0.961 0.210
  5.422-4.402    83.85   151    10 0.1144   195.017   194.427 0.917 0.964 0.210
  4.390-3.571    90.83   296    21 0.1137   204.579   202.845 0.991 0.962 0.144
  3.569-2.898    96.33   565    39 0.1271   165.163   163.485 1.005 0.961 0.130
  2.897-2.351    98.71  1071    73 0.1363   127.090   125.810 0.992 0.960 0.000
  2.351-1.908    98.22  1960   136 0.1287    98.405    97.151 1.030 0.959 0.000
  1.908-1.548    96.68  3574   246 0.1305    61.030    60.419 1.015 0.960 0.000
  1.548-1.256    95.43  6500   448 0.1431    38.262    37.628 1.017 0.960 0.000
  1.256-1.020    88.52 11175   771 0.1846    24.661    23.872 1.017 0.961 0.000
  1.020-0.965    71.91  3515   243 0.2694    15.792    14.462 0.974 0.967 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0171 

================= 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: 0.1575 0.1693 0.006  1.083   4.1  57.8  12.0 129      0.159
       1_adp: 0.1554 0.1733 0.006  1.083   4.1  55.4  12.5 129      0.159
      1_occh: 0.1532 0.1758 0.006  1.083   4.1  55.4  12.5 129      0.159
       1_occ: 0.1539 0.1745 0.006  1.083   4.1  55.4  12.5 129      0.159
       2_bss: 0.1536 0.1744 0.006  1.083   4.1  55.4  12.5 129      0.159
 2_settarget: 0.1536 0.1744 0.006  1.083   4.1  55.4  12.5 129      0.159
       2_nqh: 0.1536 0.1744 0.006  1.083   4.1  55.4  12.5 129      0.159
    2_weight: 0.1536 0.1744 0.006  1.083   4.1  55.4  12.5 129      0.159
     2_fitrh: 0.1538 0.1743 0.006  1.083   4.1  55.4  12.5 129      0.163
    2_xyzrec: 0.1530 0.1745 0.006  1.061   4.1  55.4  12.5 129      0.168
       2_adp: 0.1516 0.1732 0.006  1.061   4.0  54.4  12.8 129      0.168
      2_occh: 0.1508 0.1754 0.006  1.061   4.0  54.4  12.8 129      0.168
       2_occ: 0.1513 0.1735 0.006  1.061   4.0  54.4  12.8 129      0.168
       3_bss: 0.1512 0.1737 0.006  1.061   4.0  54.4  12.8 129      0.168
 3_settarget: 0.1512 0.1737 0.006  1.061   4.0  54.4  12.8 129      0.168
       3_nqh: 0.1512 0.1737 0.006  1.061   4.0  54.4  12.8 129      0.168
    3_weight: 0.1512 0.1737 0.006  1.061   4.0  54.4  12.8 129      0.168
     3_fitrh: 0.1515 0.1740 0.006  1.061   4.0  54.4  12.8 129      0.167
    3_xyzrec: 0.1513 0.1683 0.007  1.164   4.0  54.4  12.8 129      0.152
       3_adp: 0.1507 0.1658 0.007  1.164   3.9  54.4  12.7 129      0.152
      3_occh: 0.1502 0.1651 0.007  1.164   3.9  54.4  12.7 129      0.152
       3_occ: 0.1507 0.1643 0.007  1.164   3.9  54.4  12.7 129      0.152
       4_bss: 0.1509 0.1644 0.007  1.164   3.9  54.3  12.6 129      0.152
 4_settarget: 0.1509 0.1644 0.007  1.164   3.9  54.3  12.6 129      0.152
       4_nqh: 0.1509 0.1644 0.007  1.164   3.9  54.3  12.6 129      0.152
    4_weight: 0.1509 0.1644 0.007  1.164   3.9  54.3  12.6 129      0.152
     4_fitrh: 0.1510 0.1640 0.007  1.164   3.9  54.3  12.6 129      0.155
    4_xyzrec: 0.1505 0.1638 0.007  1.186   3.9  54.3  12.6 129      0.153
       4_adp: 0.1504 0.1642 0.007  1.186   4.0  54.2  12.6 129      0.153
      4_occh: 0.1498 0.1645 0.007  1.186   4.0  54.2  12.6 129      0.153
       4_occ: 0.1502 0.1641 0.007  1.186   4.0  54.2  12.6 129      0.153
       5_bss: 0.1501 0.1641 0.007  1.186   4.0  54.2  12.6 129      0.153
 5_settarget: 0.1501 0.1641 0.007  1.186   4.0  54.2  12.6 129      0.153
       5_nqh: 0.1501 0.1641 0.007  1.186   4.0  54.2  12.6 129      0.153
    5_weight: 0.1501 0.1641 0.007  1.186   4.0  54.2  12.6 129      0.153
     5_fitrh: 0.1501 0.1641 0.007  1.186   4.0  54.2  12.6 129      0.153
    5_xyzrec: 0.1502 0.1641 0.007  1.181   4.0  54.2  12.6 129      0.153
       5_adp: 0.1501 0.1639 0.007  1.181   4.0  54.2  12.6 129      0.153
      5_occh: 0.1497 0.1641 0.007  1.181   4.0  54.2  12.6 129      0.153
       5_occ: 0.1501 0.1636 0.007  1.181   4.0  54.2  12.6 129      0.153
       6_bss: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.6 129      0.153
 6_settarget: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.6 129      0.153
       6_nqh: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.6 129      0.153
    6_weight: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.6 129      0.153
     6_fitrh: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.6 129      0.153
    6_xyzrec: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.6 129      0.153
       6_adp: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.6 129      0.153
      6_occh: 0.1496 0.1638 0.007  1.181   3.9  54.1  12.6 129      0.153
       6_occ: 0.1501 0.1637 0.007  1.181   3.9  54.1  12.6 129      0.153
       7_bss: 0.1501 0.1637 0.007  1.181   3.9  54.1  12.5 129      0.153
 7_settarget: 0.1501 0.1637 0.007  1.181   3.9  54.1  12.5 129      0.153
       7_nqh: 0.1501 0.1637 0.007  1.181   3.9  54.1  12.5 129      0.153
    7_weight: 0.1501 0.1637 0.007  1.181   3.9  54.1  12.5 129      0.153
     7_fitrh: 0.1501 0.1637 0.007  1.181   3.9  54.1  12.5 129      0.153
    7_xyzrec: 0.1501 0.1637 0.007  1.181   3.9  54.1  12.5 129      0.153
       7_adp: 0.1501 0.1637 0.007  1.181   3.9  54.1  12.5 129      0.153
      7_occh: 0.1496 0.1639 0.007  1.181   3.9  54.1  12.5 129      0.153
       7_occ: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
       8_bss: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
 8_settarget: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
       8_nqh: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
    8_weight: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
     8_fitrh: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
    8_xyzrec: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
       8_adp: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
      8_occh: 0.1496 0.1639 0.007  1.181   3.9  54.1  12.5 129      0.153
       8_occ: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
       9_bss: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
 9_settarget: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
       9_nqh: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
    9_weight: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
     9_fitrh: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
    9_xyzrec: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
       9_adp: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
      9_occh: 0.1496 0.1639 0.007  1.181   3.9  54.1  12.5 129      0.153
       9_occ: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
      10_bss: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
10_settarget: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
      10_nqh: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
   10_weight: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
    10_fitrh: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
   10_xyzrec: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
      10_adp: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
     10_occh: 0.1496 0.1638 0.007  1.181   3.9  54.1  12.5 129      0.153
      10_occ: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
         end: 0.1501 0.1636 0.007  1.181   3.9  54.1  12.5 129      0.153
------------------------------------------------------------------------

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


Writing refined structure to CIF file:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/default_001.cif
Writing default parameters for subsequent refinement:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1AHO/default_002.def

Timing summary:
  Write initial files (write_before_run_outputs): 0.7600
  Refinement macro-cycles (run)                 : 410.3600
  Write final files (write_after_run_outputs)   : 19.9300
  Total                                         : 431.0500
Total CPU time: 7.38 minutes

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

# Date 2026-07-20 Time 16:49:52 PDT -0700 (1784591392.17 s)

Start R-work = 0.1523, R-free = 0.1485
Final R-work = 0.1501, R-free = 0.1636

===============================================================================
Job complete
usr+sys time: 442.97 seconds
wall clock time: 7 minutes 50.62 seconds (470.62 seconds total)
