Starting phenix.refine
on Mon Jul 20 16:42:05 2026 by afonine
===============================================================================

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

  Found miller_array, /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/1R6J.mtz
  Found model, /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/1R6J.pdb
  Found phil, /net/anaconda/raid1/afonine/work/discamb/varible_weights913//p.eff

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

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

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

No user-defined map coefficients or files defined; will use default map
outputs instead.
Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    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_weights913/1R6J/1R6J.pdb"
    }
    default_model = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/1R6J.pdb"
    miller_array {
      file = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/1R6J.mtz"
    }
    default_miller_array = "/net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/1R6J.mtz"
  }
  refinement {
    output {
      write_geo_vs_map = True
    }
    electron_density_maps {
      map_coefficients {
        map_type = 2mFo-DFc
        mtz_label_amplitudes = 2FOFCWT
        mtz_label_phases = PH2FOFCWT
        fill_missing_f_obs = True
      }
      map_coefficients {
        map_type = 2mFo-DFc
        mtz_label_amplitudes = 2FOFCWT_no_fill
        mtz_label_phases = PH2FOFCWT_no_fill
      }
      map_coefficients {
        map_type = mFo-DFc
        mtz_label_amplitudes = FOFCWT
        mtz_label_phases = PHFOFCWT
      }
      map_coefficients {
        map_type = anomalous
        mtz_label_amplitudes = ANOM
        mtz_label_phases = PANOM
      }
      map {
        map_type = 2mFo-DFc
        fill_missing_f_obs = True
      }
      map {
        map_type = 2mFo-DFc
      }
      map {
        map_type = mFo-DFc
      }
    }
    refine {
      strategy = *individual_sites individual_sites_real_space rigid_body \
                 *individual_adp group_adp tls *occupancies group_anomalous \
                 den
    }
    main {
      number_of_macro_cycles = 10
      max_number_of_iterations = 50
      scattering_table = *wk1995 it1992 n_gaussian electron neutron
    }
    hydrogens {
      refine = *individual riding Auto
    }
    pdb_interpretation {
      restraints_library {
        cdl = False
      }
      nonbonded_weight = 16
    }
    target_weights {
      optimize_xyz_weight = true
      wu = 0.1
    }
  }
  output {
    prefix = unscale
    overwrite = True
  }


Starting job
===============================================================================
  Monomer Library directory:
    "/net/anaconda/raid1/afonine/phenix/modules/chem_data/mon_lib"
  Total number of atoms: 1735
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1497
      Number of conformers: 4
      Conformer: "A"
        Number of residues, atoms: 82, 1231
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 79}
      Conformer: "B"
        Number of residues, atoms: 82, 1225
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 79}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 975
      Conformer: "C"
        Number of residues, atoms: 73, 986
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
          Unresolved chain links: 5
          Unresolved chain link angles: 15
          Unresolved chain link dihedrals: 15
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 18
          bond proxies already assigned to first conformer: 975
      Conformer: "D"
        Number of residues, atoms: 71, 974
          Classifications: {'peptide': 71}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
          Unresolved chain links: 2
          Chain breaks: 1
          Unresolved chain link angles: 6
          Unresolved chain link dihedrals: 6
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 16
          bond proxies already assigned to first conformer: 975
    Chain: "A"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 238, 238
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1, 'water': 237}
          Link IDs: {None: 237}
  Residues with excluded nonbonded symmetry interactions: 233
    residue:
      pdb=" N  AGLY A 192 " occ=0.82
      ... (12 atoms not shown)
      pdb=" HA3BGLY A 192 " occ=0.18
    residue:
      pdb=" N  AALA A 193 " occ=0.82
      ... (18 atoms not shown)
      pdb=" HB3BALA A 193 " occ=0.18
    residue:
      pdb=" N  AMET A 194 " occ=0.82
      ... (32 atoms not shown)
      pdb=" HE3BMET A 194 " occ=0.18
    residue:
      pdb=" N  AASP A 195 " occ=0.82
      ... (19 atoms not shown)
      pdb=" OD2CASP A 195 " occ=0.41
    residue:
      pdb=" N  APRO A 196 " occ=0.82
      ... (26 atoms not shown)
      pdb=" HD3BPRO A 196 " occ=0.18
    residue:
      pdb=" N  AARG A 197 " occ=0.82
      ... (46 atoms not shown)
      pdb="HH22BARG A 197 " occ=0.18
    residue:
      pdb=" N  ATHR A 198 " occ=0.82
      ... (26 atoms not shown)
      pdb="HG23BTHR A 198 " occ=0.18
    residue:
      pdb=" N  AHIS A 202 " occ=0.84
      ... (43 atoms not shown)
      pdb=" HE2CHIS A 202 " occ=0.42
    residue:
      pdb=" N  AASP A 204 " occ=0.81
      ... (22 atoms not shown)
      pdb=" HB3BASP A 204 " occ=0.19
    residue:
      pdb=" N  ASER A 205 " occ=0.81
      ... (22 atoms not shown)
      pdb=" OG DSER A 205 " occ=0.20
    residue:
      pdb=" N  ATHR A 206 " occ=0.81
      ... (26 atoms not shown)
      pdb="HG23BTHR A 206 " occ=0.19
    residue:
      pdb=" N  AGLY A 207 " occ=0.81
      ... (12 atoms not shown)
      pdb=" HA3BGLY A 207 " occ=0.19
    ... (remaining 221 not shown)
  Time building chain proxies: 0.78, per 1000 atoms: 0.45
  Number of scatterers: 1735
  At special positions: 0
  Unit cell: (25.876, 39.544, 32.276, 90, 109.64, 90)
  Space group: P 1 21 1 (No. 4)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S       6     16.00
     O     385      8.00
     N     129      7.00
     C     443      6.00
     H     771      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.15
  Time building geometry restraints manager: 0.19 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: 770
        1.04 -     1.24: 89
        1.24 -     1.44: 230
        1.44 -     1.64: 407
        1.64 -     1.85: 10
  Bond restraints: 1506
  Sorted by residual:
  bond pdb=" CG  MET A 270 "
       pdb=" SD BMET A 270 "
    ideal  model  delta    sigma   weight residual
    1.803  1.624  0.179 2.50e-02 1.60e+03 5.13e+01
  bond pdb=" C  BGLY A 207 "
       pdb=" N   HIS A 208 "
    ideal  model  delta    sigma   weight residual
    1.329  1.408 -0.079 1.40e-02 5.10e+03 3.16e+01
  bond pdb=" CA  THR A 268 "
       pdb=" CB BTHR A 268 "
    ideal  model  delta    sigma   weight residual
    1.540  1.417  0.123 2.70e-02 1.37e+03 2.08e+01
  bond pdb=" ND1AHIS A 236 "
       pdb=" CE1AHIS A 236 "
    ideal  model  delta    sigma   weight residual
    1.321  1.362 -0.041 1.00e-02 1.00e+04 1.67e+01
  bond pdb=" CB  SER A 259 "
       pdb=" OG BSER A 259 "
    ideal  model  delta    sigma   weight residual
    1.417  1.343  0.074 2.00e-02 2.50e+03 1.35e+01
  ... (remaining 1501 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 2558
        2.87 -     5.74: 158
        5.74 -     8.62: 18
        8.62 -    11.49: 8
       11.49 -    14.36: 3
  Bond angle restraints: 2745
  Sorted by residual:
  angle pdb=" CA BHIS A 202 "
        pdb=" CB BHIS A 202 "
        pdb=" CG BHIS A 202 "
      ideal   model   delta    sigma   weight residual
     113.80  122.24   -8.44 1.00e+00 1.00e+00 7.12e+01
  angle pdb=" C   THR A 268 "
        pdb=" CA  THR A 268 "
        pdb=" CB BTHR A 268 "
      ideal   model   delta    sigma   weight residual
     109.10  123.46  -14.36 2.20e+00 2.07e-01 4.26e+01
  angle pdb=" CA  ASN A 245 "
        pdb=" CB  ASN A 245 "
        pdb=" CG BASN A 245 "
      ideal   model   delta    sigma   weight residual
     112.60  118.85   -6.25 1.00e+00 1.00e+00 3.91e+01
  angle pdb=" CG  MET A 270 "
        pdb=" SD BMET A 270 "
        pdb=" CE BMET A 270 "
      ideal   model   delta    sigma   weight residual
     100.90  113.50  -12.60 2.20e+00 2.07e-01 3.28e+01
  angle pdb=" C  BGLY A 207 "
        pdb=" N   HIS A 208 "
        pdb=" CA  HIS A 208 "
      ideal   model   delta    sigma   weight residual
     121.70  111.56   10.14 1.80e+00 3.09e-01 3.18e+01
  ... (remaining 2740 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.65: 501
       34.65 -    69.30: 29
       69.30 -   103.95: 2
      103.95 -   138.60: 0
      138.60 -   173.24: 1
  Dihedral angle restraints: 533
    sinusoidal: 399
      harmonic: 134
  Sorted by residual:
  dihedral pdb=" CG CHIS A 202 "
           pdb=" CD2CHIS A 202 "
           pdb=" NE2CHIS A 202 "
           pdb=" HE2CHIS A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.46   26.54     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CB  GLU A 235 "
           pdb=" CG  GLU A 235 "
           pdb=" CD AGLU A 235 "
           pdb=" OE1AGLU A 235 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  173.24 -173.24     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CG CHIS A 202 "
           pdb=" ND1CHIS A 202 "
           pdb=" CE1CHIS A 202 "
           pdb=" HE1CHIS A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.00   20.00     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.154: 97
       0.154 -    0.307: 20
       0.307 -    0.459: 1
       0.459 -    0.612: 0
       0.612 -    0.765: 1
  Chirality restraints: 119
  Sorted by residual:
  chirality pdb=" CA  THR A 268 "
            pdb=" N   THR A 268 "
            pdb=" C   THR A 268 "
            pdb=" CB BTHR A 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.76    0.77 2.00e-01 2.50e+01 1.46e+01
  chirality pdb=" CA  THR A 268 "
            pdb=" N   THR A 268 "
            pdb=" C   THR A 268 "
            pdb=" CB ATHR A 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.83   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  ILE A 218 "
            pdb=" N   ILE A 218 "
            pdb=" C   ILE A 218 "
            pdb=" CB BILE A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 116 not shown)

  Planarity restraints: 230
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG CHIS A 202 "    0.075 2.00e-02 2.50e+03   2.56e-01 1.47e+03
        pdb=" ND1CHIS A 202 "    0.083 2.00e-02 2.50e+03
        pdb=" CD2CHIS A 202 "   -0.088 2.00e-02 2.50e+03
        pdb=" CE1CHIS A 202 "   -0.140 2.00e-02 2.50e+03
        pdb=" NE2CHIS A 202 "    0.157 2.00e-02 2.50e+03
        pdb=" HD1CHIS A 202 "    0.218 2.00e-02 2.50e+03
        pdb=" HD2CHIS A 202 "   -0.314 2.00e-02 2.50e+03
        pdb=" HE1CHIS A 202 "   -0.430 2.00e-02 2.50e+03
        pdb=" HE2CHIS A 202 "    0.439 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 273 "   -0.158 2.00e-02 2.50e+03   6.49e-02 1.26e+02
        pdb=" CG  PHE A 273 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 273 "    0.037 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 273 "    0.038 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 273 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 273 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 273 "   -0.038 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 273 "    0.062 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 273 "    0.066 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 273 "    0.026 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 273 "    0.024 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 273 "   -0.104 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 203 "    0.026 2.00e-02 2.50e+03   5.33e-02 2.84e+01
        pdb=" C   LYS A 203 "   -0.092 2.00e-02 2.50e+03
        pdb=" O   LYS A 203 "    0.036 2.00e-02 2.50e+03
        pdb=" N  BASP A 204 "    0.030 2.00e-02 2.50e+03
  ... (remaining 227 not shown)

  Histogram of nonbonded interaction distances:
        0.36 -     1.20: 34
        1.20 -     2.05: 192
        2.05 -     2.90: 5088
        2.90 -     3.75: 9852
        3.75 -     4.60: 17814
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 32980
  Sorted by model distance:
  nonbonded pdb=" HE1BHIS A 202 "
            pdb=" O   HOH A 386 "
     model   vdw sym.op.
     0.355 2.450 -x+1,y-1/2,-z+1
  nonbonded pdb=" CE1BHIS A 202 "
            pdb=" O   HOH A 386 "
     model   vdw sym.op.
     0.596 3.150 -x+1,y-1/2,-z+1
  nonbonded pdb=" HB3BALA A 193 "
            pdb=" O   HOH A 352 "
     model   vdw sym.op.
     0.670 2.620 -x,y+1/2,-z
  nonbonded pdb=" O   HOH A 435 "
            pdb=" O   HOH A 473 "
     model   vdw
     0.751 2.800
  nonbonded pdb=" O   HOH A 319 "
            pdb=" O   HOH A 505 "
     model   vdw
     0.767 2.800
  ... (remaining 32975 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: 6
  Type Number    sf(0)   Gaussians
   Cl      1     17.00       5+c
   S       6     16.00       5+c
   O     385      8.00       5+c
   N     129      7.00       5+c
   C     443      6.00       5+c
   H     771      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            =  1735
n_use_u_iso      =  771
n_use_u_aniso    =  964
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 =  1735

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

Refinement flags and selection counts:
  individual_sites       =  True (1735 atoms)
  torsion_angles         = False (0 atoms)
  rigid_body             = False (0 atoms in 0 groups)
  individual_adp         =  True (iso = 771 aniso = 964)
  group_adp              = False (0 atoms in 0 groups)
  tls                    = False (0 atoms in 0 groups)
  occupancies            =  True (775 atoms)
  group_anomalous        = False

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

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

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


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

Total:
  count: 771
  occupancy sum: 660.35 (% of total atoms  46.59)
Rotatable:
  count: 235
  occupancy sum: 201.45 (% of total atoms  14.21)

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


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

|--(resolution: 0.73 - 16.57 A, n_refl.=70743 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.1306 r_free= 0.1268 coordinate error (max.-lik. estimate): 0.01 A |
|                                                                             |
| normalized target function (ml) (work): -0.000020                           |
| target function (ml) not normalized (work): -1.404655                       |
| target function (ml) not normalized (free): 68.371536                       |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1:   16.57 -    1.57 1.00   8372  203 0.0817 0.0816      1.2897      1.1741|
|  2:    1.57 -    1.25 1.00   8283  170 0.0828 0.0884     0.46013     0.46476|
|  3:    1.25 -    1.09 1.00   8289  157 0.1260 0.1265   -0.025375    0.099823|
|  4:    1.09 -    0.99 1.00   8244  145 0.1733 0.1751    -0.19667    -0.15089|
|  5:    0.99 -    0.92 0.97   8014  161 0.2058 0.2043     -0.2771    -0.36113|
|  6:    0.92 -    0.87 0.97   7992  172 0.2238 0.2292    -0.37182    -0.36464|
|  7:    0.87 -    0.82 0.97   8006  139 0.2280 0.2111    -0.44281    -0.43956|
|  8:    0.82 -    0.79 0.89   7362  133 0.2180 0.2102    -0.36148    -0.28714|
|  9:    0.79 -    0.76 0.47   3907   75 0.1998 0.1779    -0.28331    -0.23071|
| 10:    0.76 -    0.73 0.11    897   22 0.2405 0.2626    -0.30374    -0.24197|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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:   16.57 -    1.57  8372   203  0.95   8.63   0.95     0.07          1.55|
|  2:    1.57 -    1.25  8283   170  0.95  10.34   1.07     0.08          0.63|
|  3:    1.25 -    1.09  8289   157  0.98   4.21   1.13     0.08          0.15|
|  4:    1.09 -    0.99  8244   145  0.98   4.79   1.20     0.09          0.10|
|  5:    0.99 -    0.92  8014   161  0.97   5.92   1.24     0.09          0.07|
|  6:    0.92 -    0.87  7992   172  0.97   7.03   1.26     0.09          0.06|
|  7:    0.87 -    0.82  8006   139  0.96   8.89   1.25     0.09          0.05|
|  8:    0.82 -    0.79  7362   133  0.95  11.65   1.19     0.09          0.06|
|  9:    0.79 -    0.76  3907    75  0.93  14.71   1.08     0.09          0.06|
| 10:    0.76 -    0.73   897    22  0.89  19.27   0.91     0.08          0.07|
|alpha:            min =        0.07 max =            0.09 mean =         0.09|
|beta:             min =        0.05 max =            1.55 mean =         0.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.96|
|phase err.(work): min =        0.00 max =           89.88 mean =         8.18|
|phase err.(test): min =        0.00 max =           88.98 mean =         8.13|
|-----------------------------------------------------------------------------|

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.016   0.179    735  Z= 0.821
    Angle     :  2.120  14.361    993  Z= 1.200
    Chirality :  0.131   0.765    119
    Planarity :  0.014   0.111    129
    Dihedral  : 17.533 173.244    271
    Min Nonbonded Distance : 0.596
  
  Molprobity Statistics.
    All-atom Clashscore : 4.78
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.25 %
      Favored  : 98.75 %
    Rotamer:
      Outliers :  6.59 %
      Allowed  :  1.10 %
      Favored  : 92.31 %
    Cbeta Deviations :  1.16 %
    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:  0.71 (0.88), residues: 95
    helix: -0.68 (0.95), residues: 19
    sheet:  0.00 (0.93), residues: 24
    loop :  1.45 (1.01), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   ARG   0.007   0.003   ARG A 229 
   PHE   0.090   0.023   PHE A 273 
   HIS   0.001   0.001   HIS A 208 
  
  
  
  Details of bonding type rmsd/Z
    covalent geometry    : bond        0.01611 /  0.82 (  735)
    covalent geometry    : angle       2.11985 /  1.20 (  993)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.72  83.77   6.68   1.55     0   964
   Protein:    2.72  33.73   5.33   1.55     0   726
   Water:      3.67  83.77  10.82    N/A     0   237
   Other:      5.60   5.60   5.60    N/A     0     1
   Chain  A:   2.72  83.77   6.68    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.72 - 10.82       864
    10.82 - 18.93        65
    18.93 - 27.03        23
    27.03 - 35.14         7
    35.14 - 43.24         2
    43.24 - 51.35         0
    51.35 - 59.45         1
    59.45 - 67.56         0
    67.56 - 75.66         1
    75.66 - 83.77         1

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.08   number of occupancies < 0.1 = 12     |
|-----------------------------------------------------------------------------|

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



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

|--(resolution: 0.73 - 16.57 A, n_refl.=70743 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.1306 r_free= 0.1268 coordinate error (max.-lik. estimate): 0.01 A |
|                                                                             |
| normalized target function (ml) (work): -0.000020                           |
| target function (ml) not normalized (work): -1.404655                       |
| target function (ml) not normalized (free): 68.371536                       |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1306 0.1307 0.1267 n_refl.: 70743
       re-set all scales: r(all,work,free)=0.1306 0.1307 0.1267 n_refl.: 70743
         remove outliers: r(all,work,free)=0.1306 0.1307 0.1267 n_refl.: 70743
overall B=-0.42 to atoms: r(all,work,free)=0.1017 0.1018 0.0997 n_refl.: 70743
bulk-solvent and scaling: r(all,work,free)=0.0757 0.0757 0.0768 n_refl.: 70743
         remove outliers: r(all,work,free)=0.0754 0.0754 0.0768 n_refl.: 70707

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1903

 ======================== 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
 16.574-7.016    98.04    98     2 0.1862   144.742   134.509 0.685 1.000 0.097
  6.993-5.565   100.00    96     3 0.1345   103.104   102.349 0.782 1.001 0.000
  5.554-4.399    99.51   197     6 0.0832   158.739   158.227 0.827 1.000 0.000
  4.392-3.482    99.76   403     7 0.0714   174.578   173.820 0.897 1.001 0.000
  3.480-2.756   100.00   799    22 0.0671   142.928   142.401 0.918 1.001 0.000
  2.754-2.182   100.00  1582    41 0.0659   109.790   109.433 0.914 1.002 0.000
  2.181-1.727    99.79  3187    71 0.0608    81.925    81.668 0.928 1.003 0.000
  1.727-1.367    99.86  6400   145 0.0590    52.279    52.012 0.956 1.004 0.000
  1.367-1.082    99.66 12832   245 0.0531    40.465    40.287 1.001 1.006 0.000
  1.082-0.857    97.60 25319   505 0.0782    22.294    22.255 1.060 1.009 0.000
  0.857-0.731    58.84 18417   330 0.1651    11.866    11.675 0.971 1.012 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9549   b_overall=-0.2195 

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

  using refinement target ls_wunit_k1 


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

r_work=0.0755 r_free=0.0770
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0755 r_free=0.0770

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.803125             wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 93.802412             wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

Real-space grid search fit H (or D) atoms:
  start:  r_work=0.0755 r_free=0.0770
  H omit: r_work=0.0794 r_free=0.0813
  final:  r_work=0.0753 r_free=0.0767
====================== Weight optimization ====================================
start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  1.000000
final b_rmsd: 0.0054 a_rmsd: 1.1874 r_work: 0.1095 r_free: 0.1171 wc:  1.000000

start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  0.500000
final b_rmsd: 0.0072 a_rmsd: 1.3059 r_work: 0.0982 r_free: 0.1064 wc:  0.500000

start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  0.250000
final b_rmsd: 0.0085 a_rmsd: 1.4144 r_work: 0.0897 r_free: 0.0973 wc:  0.250000

start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  0.125000
final b_rmsd: 0.0112 a_rmsd: 1.5742 r_work: 0.0835 r_free: 0.0900 wc:  0.125000

start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  0.062500
final b_rmsd: 0.0139 a_rmsd: 1.7032 r_work: 0.0795 r_free: 0.0852 wc:  0.062500

start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  0.031250
final b_rmsd: 0.0157 a_rmsd: 1.7834 r_work: 0.0764 r_free: 0.0821 wc:  0.031250

start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  0.015625
final b_rmsd: 0.0175 a_rmsd: 1.8739 r_work: 0.0753 r_free: 0.0814 wc:  0.015625

start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  0.007812
final b_rmsd: 0.0187 a_rmsd: 1.9725 r_work: 0.0745 r_free: 0.0808 wc:  0.007812

start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  0.003906
final b_rmsd: 0.0213 a_rmsd: 2.0731 r_work: 0.0741 r_free: 0.0810 wc:  0.003906

start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  0.001953
final b_rmsd: 0.0277 a_rmsd: 2.2286 r_work: 0.0740 r_free: 0.0817 wc:  0.001953

start b_rmsd: 0.0161 a_rmsd: 2.1198 r_work: 0.0753 r_free: 0.0767 wc:  0.000977
final b_rmsd: 0.0342 a_rmsd: 2.4452 r_work: 0.0739 r_free: 0.0818 wc:  0.000977
revert b_rmsd: 0.0277 a_rmsd: 2.2286 r_work: 0.0740 r_free: 0.0817 wc:  0.001953

====================== 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
 0.0735 0.0809 0.0074  0.025   2.2    2.0   0.0   6.6    2   5.402

Number of minimizer iterations: 50 (52 function evaluations)
end of opt. b_rmsd: 0.0246 a_rmsd: 2.2326 r_work: 0.0735 r_free: 0.0809 wc:  0.001953

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.35  8.09   0.74  1.080   5.724 93.802    0.005
 7.13  8.49   1.36  1.278   5.987 93.802    0.005

Number of minimizer iterations: 25 (29 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.22  82.78   6.30   1.20     0   964
   Protein:    2.22  30.38   4.95   1.20     0   726
   Water:      3.29  82.78  10.46    N/A     0   237
   Other:      5.22   5.22   5.22    N/A     0     1
   Chain  A:   2.22  82.78   6.30    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.22 - 10.27       857
    10.27 - 18.33        71
    18.33 - 26.39        26
    26.39 - 34.44         6
    34.44 - 42.50         0
    42.50 - 50.55         1
    50.55 - 58.61         1
    58.61 - 66.67         0
    66.67 - 74.72         1
    74.72 - 82.78         1


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

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00499147  r_work = 0.0714  r_free = 0.0849     |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00457218  r_work = 0.0713  r_free = 0.0853     |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0713 r_free = 0.0853    target_work(ls_wunit_k1) = 0.005         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       63 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0747 r_free = 0.0851    target_work(ls_wunit_k1) = 0.005         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (15 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70707 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0747 r_free= 0.0851 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.005096                   |
| target function (ls_wunit_k1) not normalized (work): 353.317820             |
| target function (ls_wunit_k1) not normalized (free): 10.753025              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0749 0.0747 0.0851 n_refl.: 70707
       re-set all scales: r(all,work,free)=0.0998 0.0996 0.1063 n_refl.: 70707
         remove outliers: r(all,work,free)=0.0998 0.0996 0.1063 n_refl.: 70707
overall B=-0.05 to atoms: r(all,work,free)=0.0971 0.0970 0.1041 n_refl.: 70707
bulk-solvent and scaling: r(all,work,free)=0.0745 0.0742 0.0849 n_refl.: 70707
         remove outliers: r(all,work,free)=0.0745 0.0742 0.0849 n_refl.: 70706

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1360

 ======================== 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
 16.574-7.016    98.04    98     2 0.1341   144.742   139.766 0.752 0.944 0.098
  6.993-5.565   100.00    96     3 0.1016   103.104   103.045 0.848 0.945 0.005
  5.554-4.399    99.51   197     6 0.0561   158.739   158.138 0.883 0.944 0.000
  4.392-3.482    99.76   403     7 0.0479   174.578   174.261 0.950 0.944 0.000
  3.480-2.756   100.00   799    22 0.0490   142.928   142.573 0.973 0.945 0.000
  2.754-2.182   100.00  1582    41 0.0517   109.790   109.459 0.971 0.945 0.000
  2.181-1.727    99.79  3187    71 0.0517    81.925    81.778 0.983 0.946 0.000
  1.727-1.367    99.86  6400   145 0.0583    52.279    52.055 1.005 0.947 0.000
  1.367-1.082    99.66 12832   245 0.0586    40.465    40.253 1.051 0.949 0.000
  1.082-0.857    97.60 25318   505 0.0870    22.295    22.172 1.109 0.952 0.000
  0.857-0.731    58.84 18417   330 0.1668    11.866    11.683 1.016 0.954 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1633 

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

  using refinement target ls_wunit_k1 


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

r_work=0.0742 r_free=0.0849
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0742 r_free=0.0849

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.160838             wxc_scale = 0.500            wc = 0.002         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 51.843111             wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

Real-space grid search fit H (or D) atoms:
  start:  r_work=0.0742 r_free=0.0849
  H omit: r_work=0.0796 r_free=0.0882
  final:  r_work=0.0744 r_free=0.0849
====================== Weight optimization ====================================

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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0725 0.0854 0.0129  0.029   2.2    3.4   0.0   6.6    4   5.580

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
 7.25  8.54   1.29  1.278   5.940 51.843    0.005
 7.01  8.38   1.37  1.262   5.905 51.843    0.004

Number of minimizer iterations: 25 (31 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.01  82.27   6.28   1.15     0   964
   Protein:    2.01  27.63   4.89   1.15     0   726
   Water:      3.59  82.27  10.55    N/A     0   237
   Other:      5.05   5.05   5.05    N/A     0     1
   Chain  A:   2.01  82.27   6.28    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.01 - 10.04       850
    10.04 - 18.07        79
    18.07 - 26.09        25
    26.09 - 34.12         6
    34.12 - 42.14         0
    42.14 - 50.17         1
    50.17 - 58.20         1
    58.20 - 66.22         0
    66.22 - 74.25         1
    74.25 - 82.27         1


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

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00444833  r_work = 0.0701  r_free = 0.0838     |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00428135  r_work = 0.0700  r_free = 0.0855     |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0700 r_free = 0.0855    target_work(ls_wunit_k1) = 0.004         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       59 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0702 r_free = 0.0845    target_work(ls_wunit_k1) = 0.004         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (16 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70706 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0702 r_free= 0.0845 coordinate error (max.-lik. estimate): 0.03 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.004355                   |
| target function (ls_wunit_k1) not normalized (work): 301.946338             |
| target function (ls_wunit_k1) not normalized (free): 10.708317              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0705 0.0702 0.0845 n_refl.: 70706
       re-set all scales: r(all,work,free)=0.0944 0.0942 0.1042 n_refl.: 70706
         remove outliers: r(all,work,free)=0.0944 0.0942 0.1042 n_refl.: 70706
overall B=-0.00 to atoms: r(all,work,free)=0.0944 0.0942 0.1041 n_refl.: 70706
bulk-solvent and scaling: r(all,work,free)=0.0705 0.0702 0.0845 n_refl.: 70706
         remove outliers: r(all,work,free)=0.0704 0.0701 0.0845 n_refl.: 70701

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1468

 ======================== 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
 16.574-7.016    98.04    98     2 0.1228   144.742   140.381 0.752 0.946 0.088
  6.993-5.565   100.00    96     3 0.0911   103.104   103.416 0.851 0.947 0.036
  5.554-4.399    99.51   197     6 0.0507   158.739   158.341 0.884 0.946 0.027
  4.392-3.482    99.76   403     7 0.0425   174.578   174.447 0.948 0.947 0.020
  3.480-2.756   100.00   799    22 0.0437   142.928   142.642 0.970 0.947 0.000
  2.754-2.182   100.00  1582    41 0.0456   109.790   109.499 0.969 0.947 0.000
  2.181-1.727    99.79  3187    71 0.0456    81.925    81.857 0.981 0.948 0.000
  1.727-1.367    99.86  6400   145 0.0530    52.279    52.079 1.003 0.949 0.000
  1.367-1.082    99.66 12832   245 0.0548    40.465    40.264 1.050 0.950 0.000
  1.082-0.857    97.60 25318   505 0.0842    22.295    22.177 1.111 0.953 0.000
  0.857-0.731    58.82 18412   330 0.1663    11.868    11.681 1.017 0.955 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9580   b_overall=-0.1702 

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

  using refinement target ml 


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

r_work=0.0701 r_free=0.0845
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0701 r_free=0.0845

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.818329              wxc_scale = 0.500            wc = 0.002         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.927039              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

Real-space grid search fit H (or D) atoms:
  start:  r_work=0.0701 r_free=0.0845
  H omit: r_work=0.0760 r_free=0.0875
  final:  r_work=0.0703 r_free=0.0841
====================== Weight optimization ====================================

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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0703 0.0829 0.0126  0.030   2.4    4.1   0.0   6.6    4   0.909

Number of minimizer iterations: 50 (54 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.03  8.29   1.26  1.262   5.905  0.927    2.504
 7.07  8.24   1.17  1.234   5.864  0.927    2.472

Number of minimizer iterations: 25 (30 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.81  82.24   6.21   1.08     0   964
   Protein:    1.81  26.21   4.86   1.08     0   726
   Water:      3.65  82.24  10.36    N/A     0   237
   Other:      4.86   4.86   4.86    N/A     0     1
   Chain  A:   1.81  82.24   6.21    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.81 - 9.86        850
     9.86 - 17.90        82
    17.90 - 25.94        23
    25.94 - 33.99         5
    33.99 - 42.03         0
    42.03 - 50.07         1
    50.07 - 58.11         1
    58.11 - 66.16         0
    66.16 - 74.20         1
    74.20 - 82.24         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.47198  r_work = 0.0707  r_free = 0.0823                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.47475  r_work = 0.0701  r_free = 0.0829                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0701 r_free = 0.0829             target_work(ml) = 2.475         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       65 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0703 r_free = 0.0827             target_work(ml) = 2.473         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 13 (20 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70701 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0703 r_free= 0.0827 coordinate error (max.-lik. estimate): 0.03 A |
|                                                                             |
| normalized target function (ml) (work): 2.473012                            |
| target function (ml) not normalized (work): 171439.065552                   |
| target function (ml) not normalized (free): 3620.054573                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0706 0.0703 0.0827 n_refl.: 70701
       re-set all scales: r(all,work,free)=0.0985 0.0983 0.1041 n_refl.: 70701
         remove outliers: r(all,work,free)=0.0985 0.0983 0.1041 n_refl.: 70701
overall B=-0.05 to atoms: r(all,work,free)=0.0955 0.0954 0.1018 n_refl.: 70701
bulk-solvent and scaling: r(all,work,free)=0.0702 0.0699 0.0823 n_refl.: 70701
         remove outliers: r(all,work,free)=0.0702 0.0699 0.0820 n_refl.: 70698

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1654

 ======================== 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
 16.574-7.016    98.04    98     2 0.1322   144.742   140.104 0.761 0.944 0.115
  6.993-5.565   100.00    96     3 0.1056   103.104   102.616 0.857 0.945 0.048
  5.554-4.399    99.51   197     6 0.0598   158.739   158.178 0.891 0.944 0.023
  4.392-3.482    99.76   403     7 0.0518   174.578   174.418 0.955 0.944 0.012
  3.480-2.756   100.00   799    22 0.0559   142.928   142.316 0.972 0.944 0.000
  2.754-2.182   100.00  1582    41 0.0606   109.790   109.269 0.970 0.944 0.000
  2.181-1.727    99.79  3187    71 0.0594    81.925    81.689 0.982 0.944 0.000
  1.727-1.367    99.86  6400   145 0.0623    52.279    51.982 1.006 0.945 0.000
  1.367-1.082    99.66 12832   245 0.0540    40.465    40.239 1.053 0.945 0.000
  1.082-0.857    97.60 25318   504 0.0695    22.296    22.191 1.122 0.946 0.000
  0.857-0.731    58.82 18410   330 0.1494    11.869    11.722 1.025 0.945 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1674 

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

  using refinement target ml 


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

r_work=0.0699 r_free=0.0820
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0699 r_free=0.0820

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.827798              wxc_scale = 0.500            wc = 0.002         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.809890              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

Real-space grid search fit H (or D) atoms:
  start:  r_work=0.0699 r_free=0.0820
  H omit: r_work=0.0751 r_free=0.0853
  final:  r_work=0.0700 r_free=0.0820
====================== Weight optimization ====================================

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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0702 0.0823 0.0122  0.030   2.4    3.4   0.0   6.6    4   0.914

Number of minimizer iterations: 19 (21 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.02  8.23   1.22  1.234   5.816  0.810    2.471
 7.04  8.22   1.17  1.209   5.790  0.810    2.468

Number of minimizer iterations: 25 (29 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.28  82.15   6.13   1.03     0   964
   Protein:    1.28  24.24   4.80   1.03     0   726
   Water:      3.59  82.15  10.19    N/A     0   237
   Other:      4.79   4.79   4.79    N/A     0     1
   Chain  A:   1.28  82.15   6.13    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.28 - 9.36        841
     9.36 - 17.45        91
    17.45 - 25.54        24
    25.54 - 33.63         4
    33.63 - 41.71         0
    41.71 - 49.80         1
    49.80 - 57.89         1
    57.89 - 65.98         0
    65.98 - 74.06         1
    74.06 - 82.15         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.46813  r_work = 0.0704  r_free = 0.0822                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46818  r_work = 0.0700  r_free = 0.0828                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0700 r_free = 0.0828             target_work(ml) = 2.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       62 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0703 r_free = 0.0823             target_work(ml) = 2.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 14 (21 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70698 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0703 r_free= 0.0823 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.467500                            |
| target function (ml) not normalized (work): 171052.041356                   |
| target function (ml) not normalized (free): 3601.162994                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0705 0.0703 0.0823 n_refl.: 70698
       re-set all scales: r(all,work,free)=0.0970 0.0969 0.1026 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0970 0.0969 0.1026 n_refl.: 70698
overall B=-0.04 to atoms: r(all,work,free)=0.0946 0.0945 0.1007 n_refl.: 70698
bulk-solvent and scaling: r(all,work,free)=0.0704 0.0701 0.0820 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0704 0.0701 0.0818 n_refl.: 70697

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1373

 ======================== 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
 16.574-7.016    98.04    98     2 0.1323   144.742   140.306 0.762 0.943 0.088
  6.993-5.565   100.00    96     3 0.1085   103.104   102.678 0.855 0.943 0.000
  5.554-4.399    99.51   197     6 0.0613   158.739   158.189 0.891 0.943 0.000
  4.392-3.482    99.76   403     7 0.0532   174.578   174.381 0.956 0.943 0.000
  3.480-2.756   100.00   799    22 0.0577   142.928   142.265 0.972 0.943 0.000
  2.754-2.182   100.00  1582    41 0.0624   109.790   109.212 0.970 0.943 0.000
  2.181-1.727    99.79  3187    71 0.0607    81.925    81.675 0.981 0.944 0.000
  1.727-1.367    99.86  6400   145 0.0636    52.279    51.972 1.004 0.944 0.000
  1.367-1.082    99.66 12832   245 0.0541    40.465    40.245 1.048 0.945 0.000
  1.082-0.857    97.60 25318   504 0.0683    22.296    22.199 1.115 0.946 0.000
  0.857-0.731    58.81 18410   329 0.1478    11.870    11.724 1.015 0.945 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1417 

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

  using refinement target ml 


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

r_work=0.0701 r_free=0.0818
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0701 r_free=0.0818

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.960810              wxc_scale = 0.500            wc = 0.002         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.779135              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

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

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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0702 0.0819 0.0118  0.030   2.4    3.4   0.0   6.6    4   0.980

Number of minimizer iterations: 9 (11 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.02  8.19   1.18  1.209   5.749  0.779    2.467
 7.06  8.24   1.18  1.208   5.728  0.779    2.467

Number of minimizer iterations: 25 (30 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.04  82.07   6.06   1.00     0   964
   Protein:    1.04  22.61   4.76   1.00     0   726
   Water:      3.49  82.07  10.06    N/A     0   237
   Other:      4.72   4.72   4.72    N/A     0     1
   Chain  A:   1.04  82.07   6.06    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.04 - 9.14        836
     9.14 - 17.24        96
    17.24 - 25.34        24
    25.34 - 33.45         4
    33.45 - 41.55         0
    41.55 - 49.65         1
    49.65 - 57.76         1
    57.76 - 65.86         0
    65.86 - 73.96         1
    73.96 - 82.07         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.46682  r_work = 0.0706  r_free = 0.0824                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46671  r_work = 0.0701  r_free = 0.0829                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0701 r_free = 0.0829             target_work(ml) = 2.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       59 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0705 r_free = 0.0825             target_work(ml) = 2.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (16 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70697 (all), 1.94  % free)------------|
|                                                                             |
| r_work= 0.0705 r_free= 0.0825 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.466613                            |
| target function (ml) not normalized (work): 170990.512256                   |
| target function (ml) not normalized (free): 3589.464424                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0707 0.0705 0.0825 n_refl.: 70697
       re-set all scales: r(all,work,free)=0.0959 0.0958 0.1018 n_refl.: 70697
         remove outliers: r(all,work,free)=0.0959 0.0958 0.1018 n_refl.: 70697
overall B=-0.04 to atoms: r(all,work,free)=0.0939 0.0938 0.1002 n_refl.: 70697
bulk-solvent and scaling: r(all,work,free)=0.0706 0.0703 0.0823 n_refl.: 70697
         remove outliers: r(all,work,free)=0.0706 0.0703 0.0823 n_refl.: 70696

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0956

 ======================== 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
 16.574-7.016    98.04    98     2 0.1318   144.742   139.730 0.762 0.938 0.092
  6.993-5.565   100.00    96     3 0.1095   103.104   102.665 0.859 0.939 0.000
  5.554-4.399    99.51   197     6 0.0618   158.739   158.045 0.895 0.938 0.000
  4.392-3.482    99.76   403     7 0.0536   174.578   174.209 0.960 0.939 0.000
  3.480-2.756   100.00   799    22 0.0582   142.928   142.352 0.977 0.939 0.000
  2.754-2.182   100.00  1582    41 0.0631   109.790   109.277 0.973 0.940 0.000
  2.181-1.727    99.79  3187    71 0.0615    81.925    81.695 0.983 0.941 0.000
  1.727-1.367    99.86  6400   145 0.0644    52.279    51.966 1.004 0.942 0.000
  1.367-1.082    99.66 12832   245 0.0545    40.465    40.238 1.045 0.944 0.000
  1.082-0.857    97.60 25318   504 0.0679    22.296    22.195 1.107 0.948 0.000
  0.857-0.731    58.81 18409   329 0.1468    11.870    11.731 1.003 0.950 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1231 

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

  using refinement target ml 


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

r_work=0.0703 r_free=0.0824
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0703 r_free=0.0824

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.777286              wxc_scale = 0.500            wc = 0.002         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.733533              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

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

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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0703 0.0824 0.0120  0.030   2.4    3.4   0.0   6.6    4   0.889

Number of minimizer iterations: 5 (7 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.03  8.24   1.20  1.208   5.693  0.734    2.467
 7.05  8.25   1.20  1.204   5.678  0.734    2.467

Number of minimizer iterations: 25 (30 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.05  81.99   6.01   0.97     0   964
   Protein:    1.05  21.09   4.72   0.97     0   726
   Water:      3.43  81.99   9.97    N/A     0   237
   Other:      4.68   4.68   4.68    N/A     0     1
   Chain  A:   1.05  81.99   6.01    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.05 - 9.15        842
     9.15 - 17.24        92
    17.24 - 25.33        22
    25.33 - 33.43         4
    33.43 - 41.52         0
    41.52 - 49.61         1
    49.61 - 57.71         1
    57.71 - 65.80         0
    65.80 - 73.89         1
    73.89 - 81.99         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.46716  r_work = 0.0705  r_free = 0.0825                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46728  r_work = 0.0700  r_free = 0.0830                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0700 r_free = 0.0830             target_work(ml) = 2.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       59 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0704 r_free = 0.0825             target_work(ml) = 2.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (16 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70696 (all), 1.94  % free)------------|
|                                                                             |
| r_work= 0.0704 r_free= 0.0825 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.466593                            |
| target function (ml) not normalized (work): 170986.712906                   |
| target function (ml) not normalized (free): 3590.526358                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0706 0.0704 0.0825 n_refl.: 70696
       re-set all scales: r(all,work,free)=0.0947 0.0946 0.1007 n_refl.: 70696
         remove outliers: r(all,work,free)=0.0947 0.0946 0.1007 n_refl.: 70696
overall B=-0.00 to atoms: r(all,work,free)=0.0947 0.0946 0.1007 n_refl.: 70696
bulk-solvent and scaling: r(all,work,free)=0.0705 0.0703 0.0825 n_refl.: 70696
         remove outliers: r(all,work,free)=0.0705 0.0703 0.0825 n_refl.: 70696

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1043

 ======================== 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
 16.574-7.016    98.04    98     2 0.1325   144.742   139.599 0.762 0.938 0.139
  6.993-5.565   100.00    96     3 0.1109   103.104   102.728 0.860 0.939 0.063
  5.554-4.399    99.51   197     6 0.0619   158.739   158.065 0.895 0.938 0.030
  4.392-3.482    99.76   403     7 0.0534   174.578   174.197 0.960 0.939 0.016
  3.480-2.756   100.00   799    22 0.0584   142.928   142.356 0.978 0.939 0.000
  2.754-2.182   100.00  1582    41 0.0631   109.790   109.275 0.974 0.940 0.000
  2.181-1.727    99.79  3187    71 0.0614    81.925    81.701 0.984 0.941 0.000
  1.727-1.367    99.86  6400   145 0.0644    52.279    51.966 1.004 0.942 0.000
  1.367-1.082    99.66 12832   245 0.0543    40.465    40.239 1.046 0.945 0.000
  1.082-0.857    97.60 25318   504 0.0678    22.296    22.197 1.109 0.949 0.000
  0.857-0.731    58.81 18409   329 0.1465    11.870    11.733 1.006 0.951 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1332 

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

  using refinement target ml 


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

r_work=0.0703 r_free=0.0825
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0703 r_free=0.0825

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.773073              wxc_scale = 0.500            wc = 0.002         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.644333              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

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

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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0703 0.0824 0.0121  0.030   2.4    4.1   0.0   6.6    4   0.887

Number of minimizer iterations: 7 (8 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.03  8.24   1.21  1.204   5.678  0.644    2.467
 7.06  8.29   1.23  1.201   5.667  0.644    2.469

Number of minimizer iterations: 25 (30 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.04  81.95   6.00   0.95     0   964
   Protein:    1.04  20.03   4.72   0.95     0   726
   Water:      3.41  81.95   9.93    N/A     0   237
   Other:      4.65   4.65   4.65    N/A     0     1
   Chain  A:   1.04  81.95   6.00    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.04 - 9.13        841
     9.13 - 17.22        95
    17.22 - 25.31        20
    25.31 - 33.41         4
    33.41 - 41.50         0
    41.50 - 49.59         1
    49.59 - 57.68         1
    57.68 - 65.77         0
    65.77 - 73.86         1
    73.86 - 81.95         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.4687  r_work = 0.0706  r_free = 0.0829                  |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46911  r_work = 0.0702  r_free = 0.0833                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0702 r_free = 0.0833             target_work(ml) = 2.469         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0705 r_free = 0.0830             target_work(ml) = 2.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (16 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70696 (all), 1.94  % free)------------|
|                                                                             |
| r_work= 0.0705 r_free= 0.0830 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.468478                            |
| target function (ml) not normalized (work): 171117.392477                   |
| target function (ml) not normalized (free): 3594.885707                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0708 0.0705 0.0830 n_refl.: 70696
       re-set all scales: r(all,work,free)=0.0957 0.0956 0.1016 n_refl.: 70696
         remove outliers: r(all,work,free)=0.0957 0.0956 0.1016 n_refl.: 70696
overall B=-0.00 to atoms: r(all,work,free)=0.0957 0.0956 0.1016 n_refl.: 70696
bulk-solvent and scaling: r(all,work,free)=0.0707 0.0704 0.0827 n_refl.: 70696
         remove outliers: r(all,work,free)=0.0707 0.0704 0.0827 n_refl.: 70696

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1109

 ======================== 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
 16.574-7.016    98.04    98     2 0.1324   144.742   139.664 0.759 0.937 0.088
  6.993-5.565   100.00    96     3 0.1110   103.104   102.662 0.857 0.938 0.000
  5.554-4.399    99.51   197     6 0.0623   158.739   158.037 0.894 0.937 0.000
  4.392-3.482    99.76   403     7 0.0538   174.578   174.188 0.960 0.938 0.000
  3.480-2.756   100.00   799    22 0.0587   142.928   142.348 0.979 0.938 0.000
  2.754-2.182   100.00  1582    41 0.0636   109.790   109.266 0.975 0.939 0.000
  2.181-1.727    99.79  3187    71 0.0620    81.925    81.693 0.984 0.940 0.000
  1.727-1.367    99.86  6400   145 0.0648    52.279    51.966 1.005 0.942 0.000
  1.367-1.082    99.66 12832   245 0.0545    40.465    40.237 1.048 0.945 0.000
  1.082-0.857    97.60 25318   504 0.0677    22.296    22.198 1.111 0.949 0.000
  0.857-0.731    58.81 18409   329 0.1462    11.870    11.733 1.009 0.951 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1413 

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

  using refinement target ml 


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

r_work=0.0704 r_free=0.0827
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0704 r_free=0.0827

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.854236              wxc_scale = 0.500            wc = 0.002         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.745277              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

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

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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0704 0.0827 0.0123  0.030   2.4    4.1   0.0   6.6    4   0.927

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
 7.04  8.27   1.23  1.201   5.667  0.745    2.468
 7.04  8.27   1.23  1.211   5.658  0.745    2.466

Number of minimizer iterations: 25 (30 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.03  81.92   6.00   0.94     0   964
   Protein:    1.03  19.04   4.73   0.94     0   726
   Water:      3.40  81.92   9.89    N/A     0   237
   Other:      4.64   4.64   4.64    N/A     0     1
   Chain  A:   1.03  81.92   6.00    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.03 - 9.12        840
     9.12 - 17.20        97
    17.20 - 25.29        19
    25.29 - 33.38         4
    33.38 - 41.47         0
    41.47 - 49.56         1
    49.56 - 57.65         1
    57.65 - 65.74         0
    65.74 - 73.83         1
    73.83 - 81.92         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.46624  r_work = 0.0704  r_free = 0.0827                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46723  r_work = 0.0700  r_free = 0.0832                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0700 r_free = 0.0832             target_work(ml) = 2.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0704 r_free = 0.0827             target_work(ml) = 2.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (16 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70696 (all), 1.94  % free)------------|
|                                                                             |
| r_work= 0.0704 r_free= 0.0827 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.465884                            |
| target function (ml) not normalized (work): 170937.511711                   |
| target function (ml) not normalized (free): 3591.030449                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0706 0.0704 0.0827 n_refl.: 70696
       re-set all scales: r(all,work,free)=0.0965 0.0964 0.1022 n_refl.: 70696
         remove outliers: r(all,work,free)=0.0965 0.0964 0.1022 n_refl.: 70696
overall B=-0.00 to atoms: r(all,work,free)=0.0965 0.0964 0.1022 n_refl.: 70696
bulk-solvent and scaling: r(all,work,free)=0.0705 0.0702 0.0825 n_refl.: 70696
         remove outliers: r(all,work,free)=0.0705 0.0702 0.0825 n_refl.: 70696

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1364

 ======================== 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
 16.574-7.016    98.04    98     2 0.1323   144.742   139.661 0.755 0.940 0.088
  6.993-5.565   100.00    96     3 0.1119   103.104   102.645 0.853 0.941 0.000
  5.554-4.399    99.51   197     6 0.0625   158.739   158.035 0.891 0.940 0.000
  4.392-3.482    99.76   403     7 0.0539   174.578   174.168 0.957 0.941 0.000
  3.480-2.756   100.00   799    22 0.0587   142.928   142.344 0.976 0.941 0.000
  2.754-2.182   100.00  1582    41 0.0635   109.790   109.263 0.972 0.942 0.000
  2.181-1.727    99.79  3187    71 0.0617    81.925    81.694 0.982 0.942 0.000
  1.727-1.367    99.86  6400   145 0.0646    52.279    51.966 1.004 0.944 0.000
  1.367-1.082    99.66 12832   245 0.0543    40.465    40.239 1.048 0.946 0.000
  1.082-0.857    97.60 25318   504 0.0675    22.296    22.198 1.115 0.949 0.000
  0.857-0.731    58.81 18409   329 0.1459    11.870    11.736 1.015 0.948 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1495 

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

  using refinement target ml 


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

r_work=0.0702 r_free=0.0826
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0702 r_free=0.0826

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.874444              wxc_scale = 0.500            wc = 0.002         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.685782              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

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

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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0702 0.0826 0.0124  0.030   2.4    3.4   0.0   6.6    4   0.937

Number of minimizer iterations: 4 (6 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.02  8.26   1.24  1.211   5.658  0.686    2.466
 7.04  8.27   1.23  1.207   5.659  0.686    2.467

Number of minimizer iterations: 13 (18 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    0.97  81.91   6.00   0.93     0   964
   Protein:    0.97  18.91   4.73   0.93     0   726
   Water:      3.39  81.91   9.88    N/A     0   237
   Other:      4.64   4.64   4.64    N/A     0     1
   Chain  A:   0.97  81.91   6.00    N/A     0   964
   Histogram:
       Values      Number of atoms
     0.97 - 9.06        840
     9.06 - 17.16        97
    17.16 - 25.25        19
    25.25 - 33.35         4
    33.35 - 41.44         0
    41.44 - 49.53         1
    49.53 - 57.63         1
    57.63 - 65.72         0
    65.72 - 73.82         1
    73.82 - 81.91         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.46655  r_work = 0.0704  r_free = 0.0827                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46726  r_work = 0.0700  r_free = 0.0832                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0700 r_free = 0.0832             target_work(ml) = 2.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0704 r_free = 0.0827             target_work(ml) = 2.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (18 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70696 (all), 1.94  % free)------------|
|                                                                             |
| r_work= 0.0704 r_free= 0.0827 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.466441                            |
| target function (ml) not normalized (work): 170976.158446                   |
| target function (ml) not normalized (free): 3592.350675                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0707 0.0704 0.0827 n_refl.: 70696
       re-set all scales: r(all,work,free)=0.0976 0.0975 0.1030 n_refl.: 70696
         remove outliers: r(all,work,free)=0.0976 0.0975 0.1030 n_refl.: 70696
overall B=-0.00 to atoms: r(all,work,free)=0.0976 0.0974 0.1030 n_refl.: 70696
bulk-solvent and scaling: r(all,work,free)=0.0705 0.0703 0.0826 n_refl.: 70696
         remove outliers: r(all,work,free)=0.0705 0.0703 0.0826 n_refl.: 70696

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1268

 ======================== 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
 16.574-7.016    98.04    98     2 0.1323   144.742   139.672 0.756 0.936 0.079
  6.993-5.565   100.00    96     3 0.1123   103.104   102.657 0.855 0.937 0.000
  5.554-4.399    99.51   197     6 0.0626   158.739   158.019 0.894 0.937 0.000
  4.392-3.482    99.76   403     7 0.0541   174.578   174.183 0.961 0.937 0.000
  3.480-2.756   100.00   799    22 0.0587   142.928   142.343 0.980 0.938 0.000
  2.754-2.182   100.00  1582    41 0.0636   109.790   109.264 0.976 0.939 0.000
  2.181-1.727    99.79  3187    71 0.0618    81.925    81.698 0.986 0.940 0.000
  1.727-1.367    99.86  6400   145 0.0647    52.279    51.967 1.006 0.942 0.000
  1.367-1.082    99.66 12832   245 0.0543    40.465    40.239 1.051 0.946 0.000
  1.082-0.857    97.60 25318   504 0.0675    22.296    22.200 1.116 0.951 0.000
  0.857-0.731    58.81 18409   329 0.1460    11.870    11.733 1.015 0.953 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1606 

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

  using refinement target ml 


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

r_work=0.0703 r_free=0.0826
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0703 r_free=0.0826

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.845303              wxc_scale = 0.500            wc = 0.002         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.694180              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

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

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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0703 0.0826 0.0123  0.030   2.4    3.4   0.0   6.6    4   0.923

Number of minimizer iterations: 3 (9 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.03  8.26   1.23  1.207   5.659  0.694    2.467
 7.05  8.28   1.24  1.207   5.657  0.694    2.468

Number of minimizer iterations: 20 (25 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    0.90  81.89   6.00   0.93     0   964
   Protein:    0.90  18.50   4.74   0.93     0   726
   Water:      3.39  81.89   9.87    N/A     0   237
   Other:      4.63   4.63   4.63    N/A     0     1
   Chain  A:   0.90  81.89   6.00    N/A     0   964
   Histogram:
       Values      Number of atoms
     0.90 - 9.00        839
     9.00 - 17.10        99
    17.10 - 25.20        18
    25.20 - 33.30         4
    33.30 - 41.40         0
    41.40 - 49.50         1
    49.50 - 57.60         1
    57.60 - 65.70         0
    65.70 - 73.80         1
    73.80 - 81.89         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.46761  r_work = 0.0705  r_free = 0.0829                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46799  r_work = 0.0700  r_free = 0.0832                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0700 r_free = 0.0832             target_work(ml) = 2.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0704 r_free = 0.0829             target_work(ml) = 2.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 13 (21 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70696 (all), 1.94  % free)------------|
|                                                                             |
| r_work= 0.0704 r_free= 0.0829 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.467370                            |
| target function (ml) not normalized (work): 171040.583803                   |
| target function (ml) not normalized (free): 3593.000509                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1:   16.57 -    1.57 1.00   8371  203 0.0640 0.0745      3.5808       3.691|
|  2:    1.57 -    1.25 1.00   8283  170 0.0621 0.0742       3.021       3.042|
|  3:    1.25 -    1.09 1.00   8289  157 0.0518 0.0644      2.5032      2.6382|
|  4:    1.09 -    0.99 1.00   8244  145 0.0552 0.0746      2.2827      2.4471|
|  5:    0.99 -    0.92 0.97   8007  161 0.0686 0.0837      2.1574      2.2592|
|  6:    0.92 -    0.87 0.97   7984  171 0.0813 0.0946       2.079      2.1896|
|  7:    0.87 -    0.82 0.97   8004  139 0.1118 0.1266      2.0895      2.1498|
|  8:    0.82 -    0.79 0.89   7349  132 0.1319 0.1458      2.0752      2.1736|
|  9:    0.79 -    0.76 0.47   3894   75 0.1989 0.2447      2.2082      2.4333|
| 10:    0.76 -    0.73 0.11    896   22 0.3639 0.3416      2.2622      2.3257|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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:   16.57 -    1.57  8371   203  0.96   7.84   1.00     1.04        243.97|
|  2:    1.57 -    1.25  8283   170  0.95   9.85   1.00     1.04        106.99|
|  3:    1.25 -    1.09  8289   157  0.98   5.00   1.01     1.04         32.17|
|  4:    1.09 -    0.99  8244   145  0.98   5.46   1.00     1.04         20.58|
|  5:    0.99 -    0.92  8007   161  0.97   6.98   1.01     1.04         15.15|
|  6:    0.92 -    0.87  7984   171  0.96   7.97   1.00     1.04         11.86|
|  7:    0.87 -    0.82  8004   139  0.96   9.71   1.04     1.04         10.27|
|  8:    0.82 -    0.79  7349   132  0.95  11.90   1.00     1.04          9.75|
|  9:    0.79 -    0.76  3894    75  0.93  14.56   0.89     0.98         10.62|
| 10:    0.76 -    0.73   896    22  0.89  19.32   0.74     0.86         12.21|
|alpha:            min =        0.86 max =            1.04 mean =         1.03|
|beta:             min =        9.75 max =          243.97 mean =        54.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.96|
|phase err.(work): min =        0.00 max =           89.98 mean =         8.55|
|phase err.(test): min =        0.00 max =           86.47 mean =         8.50|
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0707 0.0704 0.0829 n_refl.: 70696
       re-set all scales: r(all,work,free)=0.0986 0.0985 0.1039 n_refl.: 70696
         remove outliers: r(all,work,free)=0.0986 0.0985 0.1039 n_refl.: 70696
overall B=-0.00 to atoms: r(all,work,free)=0.0986 0.0985 0.1039 n_refl.: 70696
bulk-solvent and scaling: r(all,work,free)=0.0706 0.0703 0.0827 n_refl.: 70696
         remove outliers: r(all,work,free)=0.0706 0.0703 0.0827 n_refl.: 70696

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1503

 ======================== 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
 16.574-7.016    98.04    98     2 0.1327   144.742   139.651 0.753 0.939 0.075
  6.993-5.565   100.00    96     3 0.1127   103.104   102.629 0.852 0.940 0.000
  5.554-4.399    99.51   197     6 0.0627   158.739   158.001 0.891 0.939 0.000
  4.392-3.482    99.76   403     7 0.0541   174.578   174.166 0.958 0.940 0.000
  3.480-2.756   100.00   799    22 0.0588   142.928   142.335 0.977 0.940 0.000
  2.754-2.182   100.00  1582    41 0.0637   109.790   109.262 0.974 0.941 0.000
  2.181-1.727    99.79  3187    71 0.0618    81.925    81.693 0.984 0.942 0.000
  1.727-1.367    99.86  6400   145 0.0648    52.279    51.966 1.005 0.944 0.000
  1.367-1.082    99.66 12832   245 0.0544    40.465    40.239 1.051 0.947 0.000
  1.082-0.857    97.60 25318   504 0.0676    22.296    22.199 1.119 0.951 0.000
  0.857-0.731    58.81 18409   329 0.1457    11.870    11.736 1.021 0.951 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1679 

================= 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    : 0.1306 0.1268 0.016  2.120   2.7  83.8   6.7 237      0.000
       1_bss: 0.0755 0.0770 0.016  2.120   2.3  83.4   6.3 237      0.000
 1_settarget: 0.0755 0.0770 0.016  2.120   2.3  83.4   6.3 237      0.000
       1_nqh: 0.0755 0.0770 0.016  2.120   2.3  83.4   6.3 237      0.000
    1_weight: 0.0755 0.0770 0.016  2.120   2.3  83.4   6.3 237      0.000
     1_fitrh: 0.0753 0.0767 0.016  2.120   2.3  83.4   6.3 237      0.149
    1_xyzrec: 0.0735 0.0809 0.025  2.233   2.3  83.4   6.3 237      0.206
       1_adp: 0.0714 0.0849 0.025  2.233   2.2  82.8   6.3 237      0.206
      1_occh: 0.0713 0.0853 0.025  2.233   2.2  82.8   6.3 237      0.206
       1_occ: 0.0747 0.0851 0.025  2.233   2.2  82.8   6.3 237      0.206
       2_bss: 0.0742 0.0849 0.025  2.233   2.2  82.7   6.3 237      0.206
 2_settarget: 0.0742 0.0849 0.025  2.233   2.2  82.7   6.3 237      0.206
       2_nqh: 0.0742 0.0849 0.025  2.233   2.2  82.7   6.3 237      0.206
    2_weight: 0.0742 0.0849 0.025  2.233   2.2  82.7   6.3 237      0.206
     2_fitrh: 0.0744 0.0849 0.025  2.233   2.2  82.7   6.3 237      0.202
    2_xyzrec: 0.0725 0.0854 0.029  2.247   2.2  82.7   6.3 237      0.206
       2_adp: 0.0701 0.0838 0.029  2.247   2.0  82.3   6.3 237      0.206
      2_occh: 0.0700 0.0855 0.029  2.247   2.0  82.3   6.3 237      0.206
       2_occ: 0.0702 0.0845 0.029  2.247   2.0  82.3   6.3 237      0.206
       3_bss: 0.0701 0.0845 0.029  2.247   2.0  82.3   6.3 237      0.206
 3_settarget: 0.0701 0.0845 0.029  2.247   2.0  82.3   6.3 237      0.206
       3_nqh: 0.0701 0.0845 0.029  2.247   2.0  82.3   6.3 237      0.206
    3_weight: 0.0701 0.0845 0.029  2.247   2.0  82.3   6.3 237      0.206
     3_fitrh: 0.0703 0.0841 0.029  2.247   2.0  82.3   6.3 237      0.217
    3_xyzrec: 0.0703 0.0829 0.030  2.399   2.0  82.3   6.3 237      0.213
       3_adp: 0.0707 0.0823 0.030  2.399   1.8  82.2   6.2 237      0.213
      3_occh: 0.0701 0.0829 0.030  2.399   1.8  82.2   6.2 237      0.213
       3_occ: 0.0703 0.0827 0.030  2.399   1.8  82.2   6.2 237      0.213
       4_bss: 0.0699 0.0820 0.030  2.399   1.8  82.2   6.2 237      0.213
 4_settarget: 0.0699 0.0820 0.030  2.399   1.8  82.2   6.2 237      0.213
       4_nqh: 0.0699 0.0820 0.030  2.399   1.8  82.2   6.2 237      0.213
    4_weight: 0.0699 0.0820 0.030  2.399   1.8  82.2   6.2 237      0.213
     4_fitrh: 0.0700 0.0820 0.030  2.399   1.8  82.2   6.2 237      0.211
    4_xyzrec: 0.0702 0.0823 0.030  2.411   1.8  82.2   6.2 237      0.211
       4_adp: 0.0704 0.0822 0.030  2.411   1.3  82.2   6.1 237      0.211
      4_occh: 0.0700 0.0828 0.030  2.411   1.3  82.2   6.1 237      0.211
       4_occ: 0.0703 0.0823 0.030  2.411   1.3  82.2   6.1 237      0.211
       5_bss: 0.0701 0.0818 0.030  2.411   1.2  82.1   6.1 237      0.211
 5_settarget: 0.0701 0.0818 0.030  2.411   1.2  82.1   6.1 237      0.211
       5_nqh: 0.0701 0.0818 0.030  2.411   1.2  82.1   6.1 237      0.211
    5_weight: 0.0701 0.0818 0.030  2.411   1.2  82.1   6.1 237      0.211
     5_fitrh: 0.0701 0.0818 0.030  2.411   1.2  82.1   6.1 237      0.211
    5_xyzrec: 0.0702 0.0819 0.030  2.415   1.2  82.1   6.1 237      0.211
       5_adp: 0.0706 0.0824 0.030  2.415   1.0  82.1   6.1 237      0.211
      5_occh: 0.0701 0.0829 0.030  2.415   1.0  82.1   6.1 237      0.211
       5_occ: 0.0705 0.0825 0.030  2.415   1.0  82.1   6.1 237      0.211
       6_bss: 0.0703 0.0824 0.030  2.415   1.0  82.0   6.0 237      0.211
 6_settarget: 0.0703 0.0824 0.030  2.415   1.0  82.0   6.0 237      0.211
       6_nqh: 0.0703 0.0824 0.030  2.415   1.0  82.0   6.0 237      0.211
    6_weight: 0.0703 0.0824 0.030  2.415   1.0  82.0   6.0 237      0.211
     6_fitrh: 0.0703 0.0824 0.030  2.415   1.0  82.0   6.0 237      0.211
    6_xyzrec: 0.0703 0.0824 0.030  2.413   1.0  82.0   6.0 237      0.211
       6_adp: 0.0705 0.0825 0.030  2.413   1.1  82.0   6.0 237      0.211
      6_occh: 0.0700 0.0830 0.030  2.413   1.1  82.0   6.0 237      0.211
       6_occ: 0.0704 0.0825 0.030  2.413   1.1  82.0   6.0 237      0.211
       7_bss: 0.0703 0.0825 0.030  2.413   1.1  82.0   6.0 237      0.211
 7_settarget: 0.0703 0.0825 0.030  2.413   1.1  82.0   6.0 237      0.211
       7_nqh: 0.0703 0.0825 0.030  2.413   1.1  82.0   6.0 237      0.211
    7_weight: 0.0703 0.0825 0.030  2.413   1.1  82.0   6.0 237      0.211
     7_fitrh: 0.0703 0.0825 0.030  2.413   1.1  82.0   6.0 237      0.211
    7_xyzrec: 0.0703 0.0824 0.030  2.415   1.1  82.0   6.0 237      0.211
       7_adp: 0.0706 0.0829 0.030  2.415   1.0  82.0   6.0 237      0.211
      7_occh: 0.0702 0.0833 0.030  2.415   1.0  82.0   6.0 237      0.211
       7_occ: 0.0705 0.0830 0.030  2.415   1.0  82.0   6.0 237      0.211
       8_bss: 0.0704 0.0827 0.030  2.415   1.0  82.0   6.0 237      0.211
 8_settarget: 0.0704 0.0827 0.030  2.415   1.0  82.0   6.0 237      0.211
       8_nqh: 0.0704 0.0827 0.030  2.415   1.0  82.0   6.0 237      0.211
    8_weight: 0.0704 0.0827 0.030  2.415   1.0  82.0   6.0 237      0.211
     8_fitrh: 0.0704 0.0827 0.030  2.415   1.0  82.0   6.0 237      0.211
    8_xyzrec: 0.0704 0.0827 0.030  2.415   1.0  82.0   6.0 237      0.211
       8_adp: 0.0704 0.0827 0.030  2.415   1.0  81.9   6.0 237      0.211
      8_occh: 0.0700 0.0832 0.030  2.415   1.0  81.9   6.0 237      0.211
       8_occ: 0.0704 0.0827 0.030  2.415   1.0  81.9   6.0 237      0.211
       9_bss: 0.0702 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
 9_settarget: 0.0702 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
       9_nqh: 0.0702 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
    9_weight: 0.0702 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
     9_fitrh: 0.0702 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
    9_xyzrec: 0.0702 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
       9_adp: 0.0704 0.0827 0.030  2.415   1.0  81.9   6.0 237      0.211
      9_occh: 0.0700 0.0832 0.030  2.415   1.0  81.9   6.0 237      0.211
       9_occ: 0.0704 0.0827 0.030  2.415   1.0  81.9   6.0 237      0.211
      10_bss: 0.0703 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
10_settarget: 0.0703 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
      10_nqh: 0.0703 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
   10_weight: 0.0703 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
    10_fitrh: 0.0703 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
   10_xyzrec: 0.0703 0.0826 0.030  2.415   1.0  81.9   6.0 237      0.211
      10_adp: 0.0705 0.0829 0.030  2.415   0.9  81.9   6.0 237      0.211
     10_occh: 0.0700 0.0832 0.030  2.415   0.9  81.9   6.0 237      0.211
      10_occ: 0.0704 0.0829 0.030  2.415   0.9  81.9   6.0 237      0.211
         end: 0.0703 0.0827 0.030  2.415   0.9  81.9   6.0 237      0.211
------------------------------------------------------------------------

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


Writing refined structure to CIF file:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/unscale_001.cif
Writing default parameters for subsequent refinement:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/unscale_002.def

Timing summary:
  Write initial files (write_before_run_outputs): 1.1500
  Refinement macro-cycles (run)                 : 1694.6400
  Write final files (write_after_run_outputs)   : 45.9900
  Total                                         : 1741.7800
Total CPU time: 29.30 minutes

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

# Date 2026-07-20 Time 17:12:09 PDT -0700 (1784592729.38 s)

Start R-work = 0.0755, R-free = 0.0770
Final R-work = 0.0703, R-free = 0.0827

===============================================================================
Job complete
usr+sys time: 1758.20 seconds
wall clock time: 30 minutes 7.81 seconds (1807.81 seconds total)
