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

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

  Found miller_array, /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/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=true
    output.prefix=scale
    optimize_xyz_weight=true

No user-defined map coefficients or files defined; will use default map
outputs instead.
Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    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 {
      local_restraints_scaling = true
      number_of_macro_cycles = 10
      max_number_of_iterations = 50
      scattering_table = *wk1995 it1992 n_gaussian electron neutron
    }
    hydrogens {
      refine = *individual riding Auto
    }
    pdb_interpretation {
      restraints_library {
        cdl = False
      }
      nonbonded_weight = 16
    }
    target_weights {
      optimize_xyz_weight = true
      wu = 0.1
    }
  }
  output {
    prefix = scale
    overwrite = True
  }


Starting job
===============================================================================
  Monomer Library directory:
    "/net/anaconda/raid1/afonine/phenix/modules/chem_data/mon_lib"
  Total number of atoms: 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: 0.81, per 1000 atoms: 0.47
  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: 0.16
  Time building geometry restraints manager: 0.21 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 {
    local_restraints_scaling = True
    number_of_macro_cycles = 10
    max_number_of_iterations = 50
    scattering_table = *wk1995 it1992 n_gaussian electron neutron
  }
  hydrogens {
    refine = *individual riding Auto
  }
  pdb_interpretation {
    restraints_library {
      cdl = False
    }
    c_beta_restraints = False
    nonbonded_weight = 16
  }
  target_weights {
    optimize_xyz_weight = True
    wu = 0.1
  }
}
output {
  prefix = "scale"
  serial = 1
  target_output_format = None *pdb mmcif
  overwrite = True
}
#phil __OFF__


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

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

====================== 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
 0.0762 0.0836 0.0074  0.023   2.1    5.5   0.0   6.6    1   5.402

Number of minimizer iterations: 50 (55 function evaluations)
end of opt. b_rmsd: 0.0235 a_rmsd: 2.1302 r_work: 0.0762 r_free: 0.0836 wc:  0.000977

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.62  8.36   0.74  1.080   5.724 93.802    0.006
 7.34  8.73   1.39  1.243   5.993 93.802    0.005

Number of minimizer iterations: 25 (34 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.20  82.85   6.32   1.23     0   964
   Protein:    2.20  30.55   4.97   1.23     0   726
   Water:      3.33  82.85  10.46    N/A     0   237
   Other:      5.26   5.26   5.26    N/A     0     1
   Chain  A:   2.20  82.85   6.32    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.20 - 10.27       857
    10.27 - 18.33        71
    18.33 - 26.40        25
    26.40 - 34.46         7
    34.46 - 42.53         0
    42.53 - 50.59         1
    50.59 - 58.66         1
    58.66 - 66.72         0
    66.72 - 74.79         1
    74.79 - 82.85         1


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

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00530974  r_work = 0.0734  r_free = 0.0872     |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00479965  r_work = 0.0730  r_free = 0.0871     |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0730 r_free = 0.0871    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 = 0.0763 r_free = 0.0872    target_work(ls_wunit_k1) = 0.005         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 12 (20 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70707 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0763 r_free= 0.0872 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.005329                   |
| target function (ls_wunit_k1) not normalized (work): 369.465818             |
| target function (ls_wunit_k1) not normalized (free): 10.852696              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0765 0.0763 0.0872 n_refl.: 70707
       re-set all scales: r(all,work,free)=0.1008 0.1007 0.1070 n_refl.: 70707
         remove outliers: r(all,work,free)=0.1008 0.1007 0.1070 n_refl.: 70707
overall B=-0.05 to atoms: r(all,work,free)=0.0981 0.0980 0.1048 n_refl.: 70707
bulk-solvent and scaling: r(all,work,free)=0.0761 0.0759 0.0870 n_refl.: 70707
         remove outliers: r(all,work,free)=0.0761 0.0758 0.0870 n_refl.: 70706

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1371

 ======================== 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 0.1350   144.742   139.564 0.749 0.944 0.070
  6.993-5.565   100.00    96     3 0.1021   103.104   103.103 0.848 0.945 0.000
  5.554-4.399    99.51   197     6 0.0577   158.739   158.189 0.884 0.944 0.000
  4.392-3.482    99.76   403     7 0.0505   174.578   174.201 0.951 0.945 0.010
  3.480-2.756   100.00   799    22 0.0503   142.928   142.569 0.974 0.945 0.005
  2.754-2.182   100.00  1582    41 0.0538   109.790   109.412 0.971 0.945 0.000
  2.181-1.727    99.79  3187    71 0.0526    81.925    81.741 0.983 0.946 0.000
  1.727-1.367    99.86  6400   145 0.0597    52.279    52.043 1.005 0.947 0.000
  1.367-1.082    99.66 12832   245 0.0603    40.465    40.252 1.050 0.949 0.000
  1.082-0.857    97.60 25319   505 0.0887    22.294    22.170 1.109 0.952 0.000
  0.857-0.731    58.83 18416   330 0.1687    11.867    11.678 1.017 0.954 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1637 

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

  using refinement target ls_wunit_k1 


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

r_work=0.0759 r_free=0.0870
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0759 r_free=0.0870

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.188701             wxc_scale = 0.500            wc = 0.001         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 51.886350             wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

Real-space grid search fit H (or D) atoms:
  start:  r_work=0.0759 r_free=0.0870
  H omit: r_work=0.0810 r_free=0.0901
  final:  r_work=0.0760 r_free=0.0866
====================== 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
 0.0747 0.0874 0.0127  0.027   1.8    5.5   0.0   6.6    3   5.594

Number of minimizer iterations: 50 (55 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.47  8.74   1.27  1.243   5.946 51.886    0.005
 7.22  8.59   1.37  1.242   5.910 51.886    0.005

Number of minimizer iterations: 25 (31 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.17  82.43   6.30   1.17     0   964
   Protein:    2.17  27.65   4.92   1.17     0   726
   Water:      3.63  82.43  10.55    N/A     0   237
   Other:      5.03   5.03   5.03    N/A     0     1
   Chain  A:   2.17  82.43   6.30    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.17 - 10.19       851
    10.19 - 18.22        77
    18.22 - 26.25        26
    26.25 - 34.27         6
    34.27 - 42.30         0
    42.30 - 50.33         1
    50.33 - 58.35         1
    58.35 - 66.38         0
    66.38 - 74.40         1
    74.40 - 82.43         1


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

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00475996  r_work = 0.0722  r_free = 0.0859     |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00455896  r_work = 0.0720  r_free = 0.0870     |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0720 r_free = 0.0870    target_work(ls_wunit_k1) = 0.005         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       74 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0723 r_free = 0.0866    target_work(ls_wunit_k1) = 0.005         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (15 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70706 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0723 r_free= 0.0866 coordinate error (max.-lik. estimate): 0.03 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.004654                   |
| target function (ls_wunit_k1) not normalized (work): 322.674873             |
| target function (ls_wunit_k1) not normalized (free): 10.911859              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0726 0.0723 0.0866 n_refl.: 70706
       re-set all scales: r(all,work,free)=0.0959 0.0957 0.1054 n_refl.: 70706
         remove outliers: r(all,work,free)=0.0959 0.0957 0.1054 n_refl.: 70706
overall B=-0.00 to atoms: r(all,work,free)=0.0959 0.0957 0.1054 n_refl.: 70706
bulk-solvent and scaling: r(all,work,free)=0.0725 0.0722 0.0865 n_refl.: 70706
         remove outliers: r(all,work,free)=0.0725 0.0722 0.0865 n_refl.: 70702

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1481

 ======================== 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 0.1252   144.742   140.299 0.749 0.945 0.044
  6.993-5.565   100.00    96     3 0.0930   103.104   103.337 0.849 0.946 0.000
  5.554-4.399    99.51   197     6 0.0529   158.739   158.385 0.884 0.945 0.000
  4.392-3.482    99.76   403     7 0.0454   174.578   174.403 0.950 0.946 0.000
  3.480-2.756   100.00   799    22 0.0461   142.928   142.624 0.972 0.946 0.000
  2.754-2.182   100.00  1582    41 0.0487   109.790   109.453 0.970 0.946 0.000
  2.181-1.727    99.79  3187    71 0.0477    81.925    81.820 0.981 0.947 0.000
  1.727-1.367    99.86  6400   145 0.0544    52.279    52.059 1.005 0.948 0.000
  1.367-1.082    99.66 12832   245 0.0568    40.465    40.260 1.051 0.950 0.000
  1.082-0.857    97.60 25318   505 0.0863    22.295    22.173 1.112 0.952 0.000
  0.857-0.731    58.83 18413   330 0.1683    11.868    11.676 1.019 0.954 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1709 

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

  using refinement target ml 


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

r_work=0.0722 r_free=0.0865
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0722 r_free=0.0865

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.933393              wxc_scale = 0.500            wc = 0.001         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.943668              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

Real-space grid search fit H (or D) atoms:
  start:  r_work=0.0722 r_free=0.0865
  H omit: r_work=0.0776 r_free=0.0899
  final:  r_work=0.0724 r_free=0.0869
====================== 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
 0.0714 0.0842 0.0128  0.025   1.7    4.8   0.0   6.6    1   0.967

Number of minimizer iterations: 47 (48 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.14  8.42   1.28  1.242   5.910  0.944    2.515
 7.14  8.29   1.15  1.213   5.870  0.944    2.478

Number of minimizer iterations: 25 (29 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.71  82.40   6.23   1.09     0   964
   Protein:    1.71  26.40   4.88   1.09     0   726
   Water:      3.66  82.40  10.38    N/A     0   237
   Other:      4.85   4.85   4.85    N/A     0     1
   Chain  A:   1.71  82.40   6.23    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.71 - 9.78        845
     9.78 - 17.85        84
    17.85 - 25.92        25
    25.92 - 33.99         6
    33.99 - 42.06         0
    42.06 - 50.13         1
    50.13 - 58.20         1
    58.20 - 66.27         0
    66.27 - 74.33         1
    74.33 - 82.40         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.47832  r_work = 0.0714  r_free = 0.0829                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.47799  r_work = 0.0708  r_free = 0.0834                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0708 r_free = 0.0834             target_work(ml) = 2.478         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       66 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0711 r_free = 0.0831             target_work(ml) = 2.477         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 15 (26 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70702 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0711 r_free= 0.0831 coordinate error (max.-lik. estimate): 0.03 A |
|                                                                             |
| normalized target function (ml) (work): 2.476854                            |
| target function (ml) not normalized (work): 171707.918993                   |
| target function (ml) not normalized (free): 3619.496866                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0713 0.0711 0.0831 n_refl.: 70702
       re-set all scales: r(all,work,free)=0.0985 0.0984 0.1043 n_refl.: 70702
         remove outliers: r(all,work,free)=0.0985 0.0984 0.1043 n_refl.: 70702
overall B=-0.05 to atoms: r(all,work,free)=0.0957 0.0956 0.1019 n_refl.: 70702
bulk-solvent and scaling: r(all,work,free)=0.0709 0.0707 0.0827 n_refl.: 70702
         remove outliers: r(all,work,free)=0.0709 0.0707 0.0824 n_refl.: 70698

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0985

 ======================== 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 0.1328   144.742   139.692 0.768 0.932 0.090
  6.993-5.565   100.00    96     3 0.1088   103.104   102.779 0.867 0.933 0.020
  5.554-4.399    99.51   197     6 0.0614   158.739   158.214 0.902 0.932 0.000
  4.392-3.482    99.76   403     7 0.0533   174.578   174.204 0.967 0.933 0.000
  3.480-2.756   100.00   799    22 0.0570   142.928   142.393 0.985 0.934 0.000
  2.754-2.182   100.00  1582    41 0.0624   109.790   109.278 0.981 0.935 0.000
  2.181-1.727    99.79  3187    71 0.0598    81.925    81.696 0.991 0.937 0.000
  1.727-1.367    99.86  6400   145 0.0625    52.279    51.977 1.012 0.940 0.000
  1.367-1.082    99.66 12832   245 0.0545    40.465    40.235 1.054 0.944 0.000
  1.082-0.857    97.60 25318   504 0.0703    22.296    22.192 1.115 0.951 0.000
  0.857-0.731    58.82 18410   330 0.1507    11.869    11.715 1.011 0.957 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1655 

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

  using refinement target ml 


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

r_work=0.0707 r_free=0.0824
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0707 r_free=0.0824

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.126675              wxc_scale = 0.500            wc = 0.001         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.761380              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

Real-space grid search fit H (or D) atoms:
  start:  r_work=0.0707 r_free=0.0824
  H omit: r_work=0.0756 r_free=0.0857
  final:  r_work=0.0707 r_free=0.0823
====================== 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
 0.0707 0.0821 0.0114  0.027   1.7    4.8   0.0   6.6    1   1.063

Number of minimizer iterations: 50 (57 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.07  8.21   1.14  1.213   5.822  0.761    2.471
 7.11  8.20   1.10  1.183   5.783  0.761    2.468

Number of minimizer iterations: 25 (29 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.18  82.32   6.14   1.03     0   964
   Protein:    1.18  24.39   4.81   1.03     0   726
   Water:      3.50  82.32  10.20    N/A     0   237
   Other:      4.77   4.77   4.77    N/A     0     1
   Chain  A:   1.18  82.32   6.14    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.18 - 9.29        837
     9.29 - 17.41        93
    17.41 - 25.52        26
    25.52 - 33.63         4
    33.63 - 41.75         0
    41.75 - 49.86         1
    49.86 - 57.97         1
    57.97 - 66.09         0
    66.09 - 74.20         1
    74.20 - 82.32         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.4677  r_work = 0.0711  r_free = 0.0821                  |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46904  r_work = 0.0706  r_free = 0.0830                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0706 r_free = 0.0830             target_work(ml) = 2.469         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       68 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0709 r_free = 0.0823             target_work(ml) = 2.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 12 (21 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70698 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0709 r_free= 0.0823 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.468037                            |
| target function (ml) not normalized (work): 171089.278707                   |
| target function (ml) not normalized (free): 3596.571702                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0712 0.0709 0.0823 n_refl.: 70698
       re-set all scales: r(all,work,free)=0.0973 0.0972 0.1023 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0973 0.0972 0.1023 n_refl.: 70698
overall B=-0.04 to atoms: r(all,work,free)=0.0950 0.0949 0.1004 n_refl.: 70698
bulk-solvent and scaling: r(all,work,free)=0.0710 0.0707 0.0820 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0710 0.0707 0.0820 n_refl.: 70698

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1147

 ======================== 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 0.1331   144.742   139.652 0.763 0.938 0.088
  6.993-5.565   100.00    96     3 0.1118   103.104   102.602 0.858 0.939 0.000
  5.554-4.399    99.51   197     6 0.0636   158.739   158.073 0.895 0.938 0.000
  4.392-3.482    99.76   403     7 0.0547   174.578   174.217 0.960 0.939 0.000
  3.480-2.756   100.00   799    22 0.0592   142.928   142.360 0.978 0.939 0.000
  2.754-2.182   100.00  1582    41 0.0643   109.790   109.253 0.974 0.940 0.000
  2.181-1.727    99.79  3187    71 0.0613    81.925    81.672 0.984 0.941 0.000
  1.727-1.367    99.86  6400   145 0.0639    52.279    51.957 1.006 0.942 0.000
  1.367-1.082    99.66 12832   245 0.0544    40.465    40.240 1.049 0.944 0.000
  1.082-0.857    97.60 25318   504 0.0687    22.296    22.195 1.113 0.947 0.000
  0.857-0.731    58.82 18410   330 0.1483    11.869    11.730 1.010 0.949 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1414 

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

  using refinement target ml 


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

r_work=0.0708 r_free=0.0820
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0708 r_free=0.0820

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.054470              wxc_scale = 0.500            wc = 0.001         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.780586              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
 0.0709 0.0820 0.0111  0.027   1.6    5.5   0.0   6.6    1   1.027

Number of minimizer iterations: 37 (38 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.09  8.20   1.11  1.183   5.743  0.781    2.468
 7.11  8.22   1.11  1.184   5.717  0.781    2.467

Number of minimizer iterations: 25 (30 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.14  82.23   6.07   1.01     0   964
   Protein:    1.14  22.73   4.77   1.01     0   726
   Water:      3.39  82.23  10.08    N/A     0   237
   Other:      4.72   4.72   4.72    N/A     0     1
   Chain  A:   1.14  82.23   6.07    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.14 - 9.25        837
     9.25 - 17.36        96
    17.36 - 25.47        23
    25.47 - 33.58         4
    33.58 - 41.69         0
    41.69 - 49.80         1
    49.80 - 57.91         1
    57.91 - 66.01         0
    66.01 - 74.12         1
    74.12 - 82.23         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.46685  r_work = 0.0712  r_free = 0.0823                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46709  r_work = 0.0707  r_free = 0.0831                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0707 r_free = 0.0831             target_work(ml) = 2.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       58 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0710 r_free = 0.0823             target_work(ml) = 2.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 12 (17 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70698 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0710 r_free= 0.0823 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.466229                            |
| target function (ml) not normalized (work): 170963.909042                   |
| target function (ml) not normalized (free): 3596.753195                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0713 0.0710 0.0823 n_refl.: 70698
       re-set all scales: r(all,work,free)=0.0963 0.0962 0.1014 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0963 0.0962 0.1014 n_refl.: 70698
overall B=-0.04 to atoms: r(all,work,free)=0.0944 0.0943 0.0998 n_refl.: 70698
bulk-solvent and scaling: r(all,work,free)=0.0711 0.0709 0.0821 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0711 0.0709 0.0821 n_refl.: 70698

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0938

 ======================== 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 0.1332   144.742   139.630 0.762 0.938 0.088
  6.993-5.565   100.00    96     3 0.1133   103.104   102.560 0.858 0.938 0.000
  5.554-4.399    99.51   197     6 0.0646   158.739   158.058 0.894 0.938 0.000
  4.392-3.482    99.76   403     7 0.0553   174.578   174.206 0.960 0.938 0.000
  3.480-2.756   100.00   799    22 0.0601   142.928   142.365 0.978 0.939 0.000
  2.754-2.182   100.00  1582    41 0.0654   109.790   109.248 0.973 0.939 0.000
  2.181-1.727    99.79  3187    71 0.0622    81.925    81.660 0.983 0.940 0.000
  1.727-1.367    99.86  6400   145 0.0644    52.279    51.954 1.004 0.942 0.000
  1.367-1.082    99.66 12832   245 0.0543    40.465    40.239 1.045 0.944 0.000
  1.082-0.857    97.60 25318   504 0.0680    22.296    22.197 1.107 0.948 0.000
  0.857-0.731    58.82 18410   330 0.1477    11.869    11.731 1.002 0.949 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1213 

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

  using refinement target ml 


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

r_work=0.0709 r_free=0.0821
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0709 r_free=0.0821

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.060970              wxc_scale = 0.500            wc = 0.001         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.744497              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
 0.0710 0.0821 0.0112  0.028   1.6    5.5   0.0   6.6    1   1.030

Number of minimizer iterations: 9 (10 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.10  8.21   1.12  1.184   5.682  0.744    2.467
 7.12  8.24   1.12  1.175   5.664  0.744    2.469

Number of minimizer iterations: 25 (32 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.01  82.16   6.02   0.98     0   964
   Protein:    1.01  21.37   4.73   0.98     0   726
   Water:      3.33  82.16   9.98    N/A     0   237
   Other:      4.65   4.65   4.65    N/A     0     1
   Chain  A:   1.01  82.16   6.02    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.01 - 9.13        838
     9.13 - 17.24        95
    17.24 - 25.36        23
    25.36 - 33.47         4
    33.47 - 41.59         0
    41.59 - 49.70         1
    49.70 - 57.81         1
    57.81 - 65.93         0
    65.93 - 74.04         1
    74.04 - 82.16         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.46876  r_work = 0.0712  r_free = 0.0824                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46932  r_work = 0.0707  r_free = 0.0833                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0707 r_free = 0.0833             target_work(ml) = 2.469         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       62 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0711 r_free = 0.0824             target_work(ml) = 2.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 12 (19 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70698 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0711 r_free= 0.0824 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.468187                            |
| target function (ml) not normalized (work): 171099.651034                   |
| target function (ml) not normalized (free): 3599.366374                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0713 0.0711 0.0824 n_refl.: 70698
       re-set all scales: r(all,work,free)=0.0955 0.0953 0.1008 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0955 0.0953 0.1008 n_refl.: 70698
overall B=-0.03 to atoms: r(all,work,free)=0.0939 0.0938 0.0995 n_refl.: 70698
bulk-solvent and scaling: r(all,work,free)=0.0712 0.0710 0.0823 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0712 0.0710 0.0823 n_refl.: 70698

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0744

 ======================== 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 0.1329   144.742   139.642 0.762 0.937 0.092
  6.993-5.565   100.00    96     3 0.1139   103.104   102.566 0.857 0.938 0.000
  5.554-4.399    99.51   197     6 0.0645   158.739   158.065 0.894 0.937 0.000
  4.392-3.482    99.76   403     7 0.0554   174.578   174.194 0.961 0.938 0.000
  3.480-2.756   100.00   799    22 0.0603   142.928   142.365 0.978 0.938 0.000
  2.754-2.182   100.00  1582    41 0.0657   109.790   109.246 0.973 0.939 0.000
  2.181-1.727    99.79  3187    71 0.0624    81.925    81.658 0.982 0.940 0.000
  1.727-1.367    99.86  6400   145 0.0647    52.279    51.952 1.002 0.942 0.000
  1.367-1.082    99.66 12832   245 0.0544    40.465    40.239 1.041 0.944 0.000
  1.082-0.857    97.60 25318   504 0.0681    22.296    22.198 1.101 0.948 0.000
  0.857-0.731    58.82 18410   330 0.1475    11.869    11.732 0.995 0.950 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.1036 

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

  using refinement target ml 


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

r_work=0.0710 r_free=0.0823
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0710 r_free=0.0823

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.977556              wxc_scale = 0.500            wc = 0.001         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.665796              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
 0.0712 0.0822 0.0111  0.025   1.7    7.5   0.0   6.6    2   0.989

Number of minimizer iterations: 47 (48 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.12  8.22   1.11  1.175   5.634  0.666    2.468
 7.13  8.24   1.11  1.178   5.610  0.666    2.469

Number of minimizer iterations: 25 (30 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    0.99  82.09   5.98   0.95     0   964
   Protein:    0.99  19.96   4.70   0.95     0   726
   Water:      3.31  82.09   9.89    N/A     0   237
   Other:      4.60   4.60   4.60    N/A     0     1
   Chain  A:   0.99  82.09   5.98    N/A     0   964
   Histogram:
       Values      Number of atoms
     0.99 - 9.10        838
     9.10 - 17.21        98
    17.21 - 25.32        20
    25.32 - 33.43         4
    33.43 - 41.54         0
    41.54 - 49.65         1
    49.65 - 57.76         1
    57.76 - 65.87         0
    65.87 - 73.98         1
    73.98 - 82.09         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.46868  r_work = 0.0714  r_free = 0.0824                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46928  r_work = 0.0708  r_free = 0.0832                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0708 r_free = 0.0832             target_work(ml) = 2.469         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       63 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0713 r_free = 0.0824             target_work(ml) = 2.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (18 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70698 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0713 r_free= 0.0824 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.468012                            |
| target function (ml) not normalized (work): 171087.550509                   |
| target function (ml) not normalized (free): 3598.284322                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0715 0.0713 0.0824 n_refl.: 70698
       re-set all scales: r(all,work,free)=0.0950 0.0949 0.1002 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0950 0.0949 0.1002 n_refl.: 70698
overall B=-0.02 to atoms: r(all,work,free)=0.0937 0.0936 0.0991 n_refl.: 70698
bulk-solvent and scaling: r(all,work,free)=0.0714 0.0712 0.0823 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0714 0.0712 0.0823 n_refl.: 70698

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0572

 ======================== 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 0.1337   144.742   139.592 0.766 0.937 0.084
  6.993-5.565   100.00    96     3 0.1141   103.104   102.546 0.863 0.937 0.000
  5.554-4.399    99.51   197     6 0.0649   158.739   158.059 0.901 0.937 0.000
  4.392-3.482    99.76   403     7 0.0564   174.578   174.152 0.967 0.937 0.000
  3.480-2.756   100.00   799    22 0.0611   142.928   142.344 0.984 0.938 0.000
  2.754-2.182   100.00  1582    41 0.0663   109.790   109.239 0.979 0.938 0.000
  2.181-1.727    99.79  3187    71 0.0633    81.925    81.652 0.987 0.940 0.000
  1.727-1.367    99.86  6400   145 0.0651    52.279    51.944 1.007 0.941 0.000
  1.367-1.082    99.66 12832   245 0.0544    40.465    40.240 1.046 0.944 0.000
  1.082-0.857    97.60 25318   504 0.0679    22.296    22.199 1.104 0.949 0.000
  0.857-0.731    58.82 18410   330 0.1473    11.869    11.733 0.995 0.950 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0874 

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

  using refinement target ml 


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

r_work=0.0712 r_free=0.0823
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0712 r_free=0.0823

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.021298              wxc_scale = 0.500            wc = 0.001         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.739129              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
 0.0713 0.0823 0.0111  0.024   1.6    6.8   0.0   6.6    1   1.011

Number of minimizer iterations: 33 (35 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.13  8.23   1.11  1.178   5.586  0.739    2.469
 7.13  8.23   1.10  1.188   5.566  0.739    2.467

Number of minimizer iterations: 25 (31 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.02  82.02   5.94   0.94     0   964
   Protein:    1.02  18.79   4.68   0.94     0   726
   Water:      3.26  82.02   9.83    N/A     0   237
   Other:      4.54   4.54   4.54    N/A     0     1
   Chain  A:   1.02  82.02   5.94    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.02 - 9.12        842
     9.12 - 17.22        96
    17.22 - 25.32        18
    25.32 - 33.42         4
    33.42 - 41.52         0
    41.52 - 49.62         1
    49.62 - 57.72         1
    57.72 - 65.82         0
    65.82 - 73.92         1
    73.92 - 82.02         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.46678  r_work = 0.0713  r_free = 0.0823                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46733  r_work = 0.0708  r_free = 0.0831                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0708 r_free = 0.0831             target_work(ml) = 2.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       66 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0712 r_free = 0.0823             target_work(ml) = 2.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 13 (23 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70698 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0712 r_free= 0.0823 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.466016                            |
| target function (ml) not normalized (work): 170949.142173                   |
| target function (ml) not normalized (free): 3596.791257                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0715 0.0712 0.0823 n_refl.: 70698
       re-set all scales: r(all,work,free)=0.0947 0.0946 0.0998 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0947 0.0946 0.0998 n_refl.: 70698
overall B=-0.02 to atoms: r(all,work,free)=0.0936 0.0935 0.0989 n_refl.: 70698
bulk-solvent and scaling: r(all,work,free)=0.0714 0.0711 0.0822 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0714 0.0711 0.0822 n_refl.: 70698

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0431

 ======================== 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 0.1339   144.742   139.590 0.765 0.936 0.079
  6.993-5.565   100.00    96     3 0.1152   103.104   102.535 0.862 0.937 0.000
  5.554-4.399    99.51   197     6 0.0651   158.739   158.064 0.900 0.936 0.000
  4.392-3.482    99.76   403     7 0.0563   174.578   174.136 0.967 0.937 0.000
  3.480-2.756   100.00   799    22 0.0613   142.928   142.345 0.984 0.937 0.000
  2.754-2.182   100.00  1582    41 0.0663   109.790   109.234 0.979 0.938 0.000
  2.181-1.727    99.79  3187    71 0.0634    81.925    81.653 0.986 0.939 0.000
  1.727-1.367    99.86  6400   145 0.0651    52.279    51.942 1.005 0.941 0.000
  1.367-1.082    99.66 12832   245 0.0543    40.465    40.240 1.043 0.945 0.000
  1.082-0.857    97.60 25318   504 0.0678    22.296    22.201 1.100 0.950 0.000
  0.857-0.731    58.82 18410   330 0.1469    11.869    11.734 0.990 0.951 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.0757 

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

  using refinement target ml 


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

r_work=0.0711 r_free=0.0822
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0711 r_free=0.0822

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.116909              wxc_scale = 0.500            wc = 0.001         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.699811              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
 0.0711 0.0821 0.0110  0.022   1.6    6.8   0.0   6.6    2   1.058

Number of minimizer iterations: 14 (20 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.11  8.21   1.10  1.188   5.545  0.700    2.467
 7.14  8.23   1.09  1.192   5.530  0.700    2.468

Number of minimizer iterations: 25 (30 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    1.00  81.96   5.91   0.93     0   964
   Protein:    1.00  17.92   4.66   0.93     0   726
   Water:      3.24  81.96   9.77    N/A     0   237
   Other:      4.50   4.50   4.50    N/A     0     1
   Chain  A:   1.00  81.96   5.91    N/A     0   964
   Histogram:
       Values      Number of atoms
     1.00 - 9.10        842
     9.10 - 17.20        97
    17.20 - 25.29        17
    25.29 - 33.39         4
    33.39 - 41.48         0
    41.48 - 49.58         1
    49.58 - 57.68         1
    57.68 - 65.77         0
    65.77 - 73.87         1
    73.87 - 81.96         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.4681  r_work = 0.0714  r_free = 0.0824                  |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46906  r_work = 0.0709  r_free = 0.0831                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0709 r_free = 0.0831             target_work(ml) = 2.469         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       62 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0713 r_free = 0.0824             target_work(ml) = 2.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 12 (21 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70698 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0713 r_free= 0.0824 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.467540                            |
| target function (ml) not normalized (work): 171054.832817                   |
| target function (ml) not normalized (free): 3598.327549                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0715 0.0713 0.0824 n_refl.: 70698
       re-set all scales: r(all,work,free)=0.0946 0.0945 0.0997 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0946 0.0945 0.0997 n_refl.: 70698
overall B=-0.02 to atoms: r(all,work,free)=0.0935 0.0934 0.0988 n_refl.: 70698
bulk-solvent and scaling: r(all,work,free)=0.0714 0.0712 0.0822 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0714 0.0712 0.0822 n_refl.: 70698

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0267

 ======================== 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 0.1337   144.742   139.600 0.796 0.935 0.079
  6.993-5.565   100.00    96     3 0.1155   103.104   102.541 0.898 0.936 0.000
  5.554-4.399    99.51   197     6 0.0650   158.739   158.075 0.938 0.936 0.000
  4.392-3.482    99.76   403     7 0.0563   174.578   174.131 1.007 0.936 0.000
  3.480-2.756   100.00   799    22 0.0615   142.928   142.339 1.025 0.937 0.000
  2.754-2.182   100.00  1582    41 0.0665   109.790   109.230 1.019 0.938 0.000
  2.181-1.727    99.79  3187    71 0.0636    81.925    81.652 1.027 0.939 0.000
  1.727-1.367    99.86  6400   145 0.0653    52.279    51.943 1.045 0.942 0.000
  1.367-1.082    99.66 12832   245 0.0543    40.465    40.240 1.084 0.945 0.000
  1.082-0.857    97.60 25318   504 0.0677    22.296    22.202 1.140 0.951 0.000
  0.857-0.731    58.82 18410   330 0.1469    11.869    11.734 1.025 0.952 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0047   b_overall=-0.0611 

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

  using refinement target ml 


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

r_work=0.0712 r_free=0.0822
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0712 r_free=0.0822

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.117312              wxc_scale = 0.500            wc = 0.001         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.702880              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
 0.0713 0.0823 0.0111  0.018   1.7    6.1   0.0   6.6    1   1.059

Number of minimizer iterations: 23 (27 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 7.13  8.23   1.11  1.192   5.508  0.703    2.468
 7.14  8.25   1.11  1.201   5.495  0.703    2.468

Number of minimizer iterations: 25 (30 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    0.98  81.91   5.89   0.92     0   964
   Protein:    0.98  17.14   4.64   0.92     0   726
   Water:      3.22  81.91   9.72    N/A     0   237
   Other:      4.48   4.48   4.48    N/A     0     1
   Chain  A:   0.98  81.91   5.89    N/A     0   964
   Histogram:
       Values      Number of atoms
     0.98 - 9.07        842
     9.07 - 17.17       100
    17.17 - 25.26        14
    25.26 - 33.35         4
    33.35 - 41.44         0
    41.44 - 49.54         1
    49.54 - 57.63         1
    57.63 - 65.72         0
    65.72 - 73.81         1
    73.81 - 81.91         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.4676  r_work = 0.0714  r_free = 0.0825                  |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.46885  r_work = 0.0709  r_free = 0.0833                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0709 r_free = 0.0833             target_work(ml) = 2.469         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       63 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0713 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: 12 (22 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70698 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0713 r_free= 0.0825 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.467388                            |
| target function (ml) not normalized (work): 171044.261375                   |
| target function (ml) not normalized (free): 3599.189998                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| 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 0.0662 0.0738      3.5886        3.67|
|  2:    1.57 -    1.25 1.00   8283  170 0.0623 0.0731      3.0086      3.0259|
|  3:    1.25 -    1.09 1.00   8289  157 0.0518 0.0643      2.4965      2.6352|
|  4:    1.09 -    0.99 1.00   8244  145 0.0551 0.0746      2.2776      2.4444|
|  5:    0.99 -    0.92 0.97   8007  161 0.0691 0.0816      2.1578      2.2521|
|  6:    0.92 -    0.87 0.97   7984  171 0.0813 0.0957      2.0787      2.1971|
|  7:    0.87 -    0.82 0.97   8004  139 0.1122 0.1262      2.0981      2.1564|
|  8:    0.82 -    0.79 0.89   7349  133 0.1332 0.1496      2.0843      2.2614|
|  9:    0.79 -    0.76 0.47   3895   75 0.1998 0.2474      2.2094      2.4224|
| 10:    0.76 -    0.73 0.11    896   22 0.3626 0.3464      2.2584      2.3247|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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   7.62   1.00     0.99        233.65|
|  2:    1.57 -    1.25  8283   170  0.95   9.58   1.00     0.99        102.99|
|  3:    1.25 -    1.09  8289   157  0.98   4.91   1.01     0.99         31.55|
|  4:    1.09 -    0.99  8244   145  0.98   5.39   1.00     0.99         20.29|
|  5:    0.99 -    0.92  8007   161  0.97   6.93   1.01     0.99         15.07|
|  6:    0.92 -    0.87  7984   171  0.96   7.97   1.00     0.99         11.84|
|  7:    0.87 -    0.82  8004   139  0.96   9.89   1.04     0.99         10.50|
|  8:    0.82 -    0.79  7349   133  0.94  12.23   1.00     0.98         10.13|
|  9:    0.79 -    0.76  3895    75  0.93  14.87   0.89     0.93         10.97|
| 10:    0.76 -    0.73   896    22  0.89  19.23   0.74     0.82         12.13|
|alpha:            min =        0.82 max =            0.99 mean =         0.98|
|beta:             min =       10.13 max =          233.65 mean =        52.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.96|
|phase err.(work): min =        0.00 max =           89.91 mean =         8.53|
|phase err.(test): min =        0.00 max =           85.38 mean =         8.50|
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0716 0.0713 0.0825 n_refl.: 70698
       re-set all scales: r(all,work,free)=0.0946 0.0945 0.0996 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0946 0.0945 0.0996 n_refl.: 70698
overall B=-0.00 to atoms: r(all,work,free)=0.0946 0.0945 0.0996 n_refl.: 70698
bulk-solvent and scaling: r(all,work,free)=0.0715 0.0712 0.0824 n_refl.: 70698
         remove outliers: r(all,work,free)=0.0715 0.0712 0.0824 n_refl.: 70698

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.0322

 ======================== 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 0.1336   144.742   139.594 0.796 0.935 0.079
  6.993-5.565   100.00    96     3 0.1152   103.104   102.574 0.897 0.936 0.000
  5.554-4.399    99.51   197     6 0.0652   158.739   158.048 0.938 0.935 0.000
  4.392-3.482    99.76   403     7 0.0566   174.578   174.115 1.008 0.936 0.000
  3.480-2.756   100.00   799    22 0.0617   142.928   142.332 1.026 0.936 0.000
  2.754-2.182   100.00  1582    41 0.0666   109.790   109.232 1.020 0.937 0.000
  2.181-1.727    99.79  3187    71 0.0638    81.925    81.652 1.027 0.939 0.000
  1.727-1.367    99.86  6400   145 0.0653    52.279    51.944 1.046 0.941 0.000
  1.367-1.082    99.66 12832   245 0.0543    40.465    40.240 1.085 0.945 0.000
  1.082-0.857    97.60 25318   504 0.0677    22.296    22.203 1.142 0.952 0.000
  0.857-0.731    58.82 18410   330 0.1467    11.869    11.734 1.027 0.953 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0047   b_overall=-0.0690 

================= 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: 0.0762 0.0836 0.023  2.130   2.3  83.4   6.3 237      0.201
       1_adp: 0.0734 0.0872 0.023  2.130   2.2  82.9   6.3 237      0.201
      1_occh: 0.0730 0.0871 0.023  2.130   2.2  82.9   6.3 237      0.201
       1_occ: 0.0763 0.0872 0.023  2.130   2.2  82.9   6.3 237      0.201
       2_bss: 0.0759 0.0870 0.023  2.130   2.2  82.8   6.3 237      0.201
 2_settarget: 0.0759 0.0870 0.023  2.130   2.2  82.8   6.3 237      0.201
       2_nqh: 0.0759 0.0870 0.023  2.130   2.2  82.8   6.3 237      0.201
    2_weight: 0.0759 0.0870 0.023  2.130   2.2  82.8   6.3 237      0.201
     2_fitrh: 0.0760 0.0866 0.023  2.130   2.2  82.8   6.3 237      0.198
    2_xyzrec: 0.0747 0.0874 0.027  1.762   2.2  82.8   6.3 237      0.199
       2_adp: 0.0722 0.0859 0.027  1.762   2.2  82.4   6.3 237      0.199
      2_occh: 0.0720 0.0870 0.027  1.762   2.2  82.4   6.3 237      0.199
       2_occ: 0.0723 0.0866 0.027  1.762   2.2  82.4   6.3 237      0.199
       3_bss: 0.0722 0.0865 0.027  1.762   2.2  82.4   6.3 237      0.199
 3_settarget: 0.0722 0.0865 0.027  1.762   2.2  82.4   6.3 237      0.199
       3_nqh: 0.0722 0.0865 0.027  1.762   2.2  82.4   6.3 237      0.199
    3_weight: 0.0722 0.0865 0.027  1.762   2.2  82.4   6.3 237      0.199
     3_fitrh: 0.0724 0.0869 0.027  1.762   2.2  82.4   6.3 237      0.205
    3_xyzrec: 0.0714 0.0842 0.025  1.671   2.2  82.4   6.3 237      0.201
       3_adp: 0.0714 0.0829 0.025  1.671   1.7  82.4   6.2 237      0.201
      3_occh: 0.0708 0.0834 0.025  1.671   1.7  82.4   6.2 237      0.201
       3_occ: 0.0711 0.0831 0.025  1.671   1.7  82.4   6.2 237      0.201
       4_bss: 0.0707 0.0824 0.025  1.671   1.7  82.4   6.2 237      0.201
 4_settarget: 0.0707 0.0824 0.025  1.671   1.7  82.4   6.2 237      0.201
       4_nqh: 0.0707 0.0824 0.025  1.671   1.7  82.4   6.2 237      0.201
    4_weight: 0.0707 0.0824 0.025  1.671   1.7  82.4   6.2 237      0.201
     4_fitrh: 0.0707 0.0823 0.025  1.671   1.7  82.4   6.2 237      0.200
    4_xyzrec: 0.0707 0.0821 0.027  1.667   1.7  82.4   6.2 237      0.200
       4_adp: 0.0711 0.0821 0.027  1.667   1.2  82.3   6.1 237      0.200
      4_occh: 0.0706 0.0830 0.027  1.667   1.2  82.3   6.1 237      0.200
       4_occ: 0.0709 0.0823 0.027  1.667   1.2  82.3   6.1 237      0.200
       5_bss: 0.0708 0.0820 0.027  1.667   1.1  82.3   6.1 237      0.200
 5_settarget: 0.0708 0.0820 0.027  1.667   1.1  82.3   6.1 237      0.200
       5_nqh: 0.0708 0.0820 0.027  1.667   1.1  82.3   6.1 237      0.200
    5_weight: 0.0708 0.0820 0.027  1.667   1.1  82.3   6.1 237      0.200
     5_fitrh: 0.0708 0.0820 0.027  1.667   1.1  82.3   6.1 237      0.200
    5_xyzrec: 0.0709 0.0820 0.027  1.622   1.1  82.3   6.1 237      0.200
       5_adp: 0.0712 0.0823 0.027  1.622   1.1  82.2   6.1 237      0.200
      5_occh: 0.0707 0.0831 0.027  1.622   1.1  82.2   6.1 237      0.200
       5_occ: 0.0710 0.0823 0.027  1.622   1.1  82.2   6.1 237      0.200
       6_bss: 0.0709 0.0821 0.027  1.622   1.1  82.2   6.0 237      0.200
 6_settarget: 0.0709 0.0821 0.027  1.622   1.1  82.2   6.0 237      0.200
       6_nqh: 0.0709 0.0821 0.027  1.622   1.1  82.2   6.0 237      0.200
    6_weight: 0.0709 0.0821 0.027  1.622   1.1  82.2   6.0 237      0.200
     6_fitrh: 0.0709 0.0821 0.027  1.622   1.1  82.2   6.0 237      0.200
    6_xyzrec: 0.0710 0.0821 0.028  1.616   1.1  82.2   6.0 237      0.200
       6_adp: 0.0712 0.0824 0.028  1.616   1.0  82.2   6.0 237      0.200
      6_occh: 0.0707 0.0833 0.028  1.616   1.0  82.2   6.0 237      0.200
       6_occ: 0.0711 0.0824 0.028  1.616   1.0  82.2   6.0 237      0.200
       7_bss: 0.0710 0.0823 0.028  1.616   1.0  82.1   6.0 237      0.200
 7_settarget: 0.0710 0.0823 0.028  1.616   1.0  82.1   6.0 237      0.200
       7_nqh: 0.0710 0.0823 0.028  1.616   1.0  82.1   6.0 237      0.200
    7_weight: 0.0710 0.0823 0.028  1.616   1.0  82.1   6.0 237      0.200
     7_fitrh: 0.0710 0.0823 0.028  1.616   1.0  82.1   6.0 237      0.200
    7_xyzrec: 0.0712 0.0822 0.025  1.652   1.0  82.1   6.0 237      0.202
       7_adp: 0.0714 0.0824 0.025  1.652   1.0  82.1   6.0 237      0.202
      7_occh: 0.0708 0.0832 0.025  1.652   1.0  82.1   6.0 237      0.202
       7_occ: 0.0713 0.0824 0.025  1.652   1.0  82.1   6.0 237      0.202
       8_bss: 0.0712 0.0823 0.025  1.652   1.0  82.1   6.0 237      0.202
 8_settarget: 0.0712 0.0823 0.025  1.652   1.0  82.1   6.0 237      0.202
       8_nqh: 0.0712 0.0823 0.025  1.652   1.0  82.1   6.0 237      0.202
    8_weight: 0.0712 0.0823 0.025  1.652   1.0  82.1   6.0 237      0.202
     8_fitrh: 0.0712 0.0823 0.025  1.652   1.0  82.1   6.0 237      0.202
    8_xyzrec: 0.0713 0.0823 0.024  1.624   1.0  82.1   6.0 237      0.202
       8_adp: 0.0713 0.0823 0.024  1.624   1.0  82.0   5.9 237      0.202
      8_occh: 0.0708 0.0831 0.024  1.624   1.0  82.0   5.9 237      0.202
       8_occ: 0.0712 0.0823 0.024  1.624   1.0  82.0   5.9 237      0.202
       9_bss: 0.0711 0.0822 0.024  1.624   1.0  82.0   5.9 237      0.202
 9_settarget: 0.0711 0.0822 0.024  1.624   1.0  82.0   5.9 237      0.202
       9_nqh: 0.0711 0.0822 0.024  1.624   1.0  82.0   5.9 237      0.202
    9_weight: 0.0711 0.0822 0.024  1.624   1.0  82.0   5.9 237      0.202
     9_fitrh: 0.0711 0.0822 0.024  1.624   1.0  82.0   5.9 237      0.202
    9_xyzrec: 0.0711 0.0821 0.022  1.634   1.0  82.0   5.9 237      0.202
       9_adp: 0.0714 0.0824 0.022  1.634   1.0  82.0   5.9 237      0.202
      9_occh: 0.0709 0.0831 0.022  1.634   1.0  82.0   5.9 237      0.202
       9_occ: 0.0713 0.0824 0.022  1.634   1.0  82.0   5.9 237      0.202
      10_bss: 0.0712 0.0822 0.022  1.634   1.0  81.9   5.9 237      0.202
10_settarget: 0.0712 0.0822 0.022  1.634   1.0  81.9   5.9 237      0.202
      10_nqh: 0.0712 0.0822 0.022  1.634   1.0  81.9   5.9 237      0.202
   10_weight: 0.0712 0.0822 0.022  1.634   1.0  81.9   5.9 237      0.202
    10_fitrh: 0.0712 0.0822 0.022  1.634   1.0  81.9   5.9 237      0.202
   10_xyzrec: 0.0713 0.0823 0.018  1.689   1.0  81.9   5.9 237      0.202
      10_adp: 0.0714 0.0825 0.018  1.689   1.0  81.9   5.9 237      0.202
     10_occh: 0.0709 0.0833 0.018  1.689   1.0  81.9   5.9 237      0.202
      10_occ: 0.0713 0.0825 0.018  1.689   1.0  81.9   5.9 237      0.202
         end: 0.0712 0.0824 0.018  1.689   1.0  81.9   5.9 237      0.202
------------------------------------------------------------------------

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


Writing refined structure to CIF file:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/scale_001.cif
Writing default parameters for subsequent refinement:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/scale_002.def

Timing summary:
  Write initial files (write_before_run_outputs): 1.2100
  Refinement macro-cycles (run)                 : 1834.6700
  Write final files (write_after_run_outputs)   : 45.9200
  Total                                         : 1881.8000
Total CPU time: 31.63 minutes

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

# Date 2026-07-20 Time 17:14:29 PDT -0700 (1784592869.85 s)

Start R-work = 0.0755, R-free = 0.0770
Final R-work = 0.0712, R-free = 0.0824

===============================================================================
Job complete
usr+sys time: 1898.03 seconds
wall clock time: 32 minutes 28.29 seconds (1948.29 seconds total)
