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=false
    output.prefix=default
    optimize_xyz_weight=false

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


Starting job
===============================================================================
  Monomer Library directory:
    "/net/anaconda/raid1/afonine/phenix/modules/chem_data/mon_lib"
  Total number of atoms: 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: 0.79, per 1000 atoms: 0.46
  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: 0.14
  Time building geometry restraints manager: 0.19 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 770
        1.04 -     1.24: 89
        1.24 -     1.44: 230
        1.44 -     1.64: 407
        1.64 -     1.85: 10
  Bond restraints: 1506
  Sorted by residual:
  bond pdb=" CG  MET A 270 "
       pdb=" SD BMET A 270 "
    ideal  model  delta    sigma   weight residual
    1.803  1.624  0.179 2.50e-02 1.60e+03 5.13e+01
  bond pdb=" C  BGLY A 207 "
       pdb=" N   HIS A 208 "
    ideal  model  delta    sigma   weight residual
    1.329  1.408 -0.079 1.40e-02 5.10e+03 3.16e+01
  bond pdb=" CA  THR A 268 "
       pdb=" CB BTHR A 268 "
    ideal  model  delta    sigma   weight residual
    1.540  1.417  0.123 2.70e-02 1.37e+03 2.08e+01
  bond pdb=" ND1AHIS A 236 "
       pdb=" CE1AHIS A 236 "
    ideal  model  delta    sigma   weight residual
    1.321  1.362 -0.041 1.00e-02 1.00e+04 1.67e+01
  bond pdb=" CB  SER A 259 "
       pdb=" OG BSER A 259 "
    ideal  model  delta    sigma   weight residual
    1.417  1.343  0.074 2.00e-02 2.50e+03 1.35e+01
  ... (remaining 1501 not shown)

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

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

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

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

  Histogram of nonbonded interaction distances:
        0.36 -     1.20: 34
        1.20 -     2.05: 192
        2.05 -     2.90: 5088
        2.90 -     3.75: 9852
        3.75 -     4.60: 17814
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 32980
  Sorted by model distance:
  nonbonded pdb=" HE1BHIS A 202 "
            pdb=" O   HOH A 386 "
     model   vdw sym.op.
     0.355 2.450 -x+1,y-1/2,-z+1
  nonbonded pdb=" CE1BHIS A 202 "
            pdb=" O   HOH A 386 "
     model   vdw sym.op.
     0.596 3.150 -x+1,y-1/2,-z+1
  nonbonded pdb=" HB3BALA A 193 "
            pdb=" O   HOH A 352 "
     model   vdw sym.op.
     0.670 2.620 -x,y+1/2,-z
  nonbonded pdb=" O   HOH A 435 "
            pdb=" O   HOH A 473 "
     model   vdw
     0.751 2.800
  nonbonded pdb=" O   HOH A 319 "
            pdb=" O   HOH A 505 "
     model   vdw
     0.767 2.800
  ... (remaining 32975 not shown)

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

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


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

Number of scattering types: 6
  Type Number    sf(0)   Gaussians
   Cl      1     17.00       5+c
   S       6     16.00       5+c
   O     385      8.00       5+c
   N     129      7.00       5+c
   C     443      6.00       5+c
   H     771      1.00       5
  sf(0) = scattering factor at diffraction angle 0.

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


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

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

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

n_use            =  1735
n_use_u_iso      =  771
n_use_u_aniso    =  964
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
total number of scatterers =  1735

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

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

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

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

#phil __ON__
refinement {
  output {
    write_geo_vs_map = True
  }
  electron_density_maps {
    map_coefficients {
      map_type = "2mFo-DFc"
      mtz_label_amplitudes = "2FOFCWT"
      mtz_label_phases = "PH2FOFCWT"
      fill_missing_f_obs = True
    }
    map_coefficients {
      map_type = "2mFo-DFc"
      mtz_label_amplitudes = "2FOFCWT_no_fill"
      mtz_label_phases = "PH2FOFCWT_no_fill"
    }
    map_coefficients {
      map_type = "mFo-DFc"
      mtz_label_amplitudes = "FOFCWT"
      mtz_label_phases = "PHFOFCWT"
    }
    map_coefficients {
      map_type = "anomalous"
      mtz_label_amplitudes = "ANOM"
      mtz_label_phases = "PANOM"
    }
    map {
      map_type = "2mFo-DFc"
      fill_missing_f_obs = True
    }
    map {
      map_type = "2mFo-DFc"
    }
    map {
      map_type = "mFo-DFc"
    }
  }
  refine {
    strategy = *individual_sites individual_sites_real_space rigid_body \
               *individual_adp group_adp tls *occupancies group_anomalous den
  }
  main {
    number_of_macro_cycles = 10
    max_number_of_iterations = 50
    scattering_table = *wk1995 it1992 n_gaussian electron neutron
  }
  hydrogens {
    refine = *individual riding Auto
  }
  pdb_interpretation {
    restraints_library {
      cdl = False
    }
    c_beta_restraints = False
    nonbonded_weight = 16
  }
  target_weights {
    wu = 0.1
  }
}
output {
  prefix = "default"
  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

====================== 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
 0.1095 0.1171 0.0075  0.005   1.2   16.4   0.0   6.6    0   5.402

Number of minimizer iterations: 50 (53 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
10.95 11.71   0.75  1.080   5.724 93.802    0.013
 9.95 11.39   1.44  1.646   6.482 93.802    0.010

Number of minimizer iterations: 25 (27 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.24  83.17   6.96   1.27     0   964
   Protein:    2.24  30.17   5.09   1.27     0   726
   Water:      3.05  83.17  12.68    N/A     0   237
   Other:      5.32   5.32   5.32    N/A     0     1
   Chain  A:   2.24  83.17   6.96    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.24 - 10.34       818
    10.34 - 18.43        89
    18.43 - 26.52        44
    26.52 - 34.62         8
    34.62 - 42.71         0
    42.71 - 50.80         2
    50.80 - 58.90         1
    58.90 - 66.99         0
    66.99 - 75.08         1
    75.08 - 83.17         1


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

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0101891  r_work = 0.0995  r_free = 0.1139      |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00927074  r_work = 0.0988  r_free = 0.1157     |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0988 r_free = 0.1157    target_work(ls_wunit_k1) = 0.009         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       73 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.1005 r_free = 0.1132    target_work(ls_wunit_k1) = 0.010         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 13 (19 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70707 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.1005 r_free= 0.1132 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.009573                   |
| target function (ls_wunit_k1) not normalized (work): 663.681088             |
| target function (ls_wunit_k1) not normalized (free): 19.924210              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.1008 0.1005 0.1132 n_refl.: 70707
       re-set all scales: r(all,work,free)=0.1210 0.1208 0.1292 n_refl.: 70707
         remove outliers: r(all,work,free)=0.1210 0.1208 0.1292 n_refl.: 70707
overall B=-0.00 to atoms: r(all,work,free)=0.1210 0.1208 0.1292 n_refl.: 70707
bulk-solvent and scaling: r(all,work,free)=0.1004 0.1001 0.1133 n_refl.: 70707
         remove outliers: r(all,work,free)=0.1004 0.1001 0.1133 n_refl.: 70707

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.1690

 ======================== 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 0.1357   144.742   138.989 0.756 0.937 0.094
  6.993-5.565   100.00    96     3 0.1141   103.104   102.368 0.845 0.937 0.024
  5.554-4.399    99.51   197     6 0.0736   158.739   158.345 0.891 0.937 0.000
  4.392-3.482    99.76   403     7 0.0670   174.578   174.178 0.961 0.937 0.000
  3.480-2.756   100.00   799    22 0.0703   142.928   142.107 0.986 0.938 0.000
  2.754-2.182   100.00  1582    41 0.0827   109.790   109.193 0.980 0.939 0.000
  2.181-1.727    99.79  3187    71 0.0820    81.925    81.541 0.992 0.940 0.000
  1.727-1.367    99.86  6400   145 0.0872    52.279    51.921 1.015 0.942 0.000
  1.367-1.082    99.66 12832   245 0.0842    40.465    40.161 1.067 0.946 0.000
  1.082-0.857    97.60 25319   505 0.1134    22.294    22.093 1.127 0.951 0.000
  0.857-0.731    58.84 18417   330 0.1857    11.866    11.638 1.037 0.956 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.2211 

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

  using refinement target ls_wunit_k1 


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

r_work=0.1001 r_free=0.1133
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.1001 r_free=0.1133

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.075799             wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 60.902963             wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

Real-space grid search fit H (or D) atoms:
  start:  r_work=0.1001 r_free=0.1133
  H omit: r_work=0.1035 r_free=0.1154
  final:  r_work=0.1002 r_free=0.1135

====================== 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
 0.1009 0.1152 0.0142  0.005   1.1   15.7   0.0   4.4    0   5.538

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
10.09 11.52   1.42  1.646   6.482 60.903    0.010
 9.67 10.95   1.28  1.633   6.516 60.903    0.009

Number of minimizer iterations: 25 (28 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.59  83.13   7.12   1.22     0   964
   Protein:    2.59  27.92   5.09   1.22     0   726
   Water:      3.75  83.13  13.33    N/A     0   237
   Other:      5.00   5.00   5.00    N/A     0     1
   Chain  A:   2.59  83.13   7.12    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.59 - 10.64       816
    10.64 - 18.69        88
    18.69 - 26.75        38
    26.75 - 34.80        17
    34.80 - 42.86         0
    42.86 - 50.91         2
    50.91 - 58.97         1
    58.97 - 67.02         0
    67.02 - 75.07         1
    75.07 - 83.13         1


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

|- start----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00904849  r_work = 0.0967  r_free = 0.1095     |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ls_wunit_k1) = 0.00858867  r_work = 0.0962  r_free = 0.1113     |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0962 r_free = 0.1113    target_work(ls_wunit_k1) = 0.009         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       97 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0966 r_free = 0.1104    target_work(ls_wunit_k1) = 0.009         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       52 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 16 (33 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70707 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0966 r_free= 0.1104 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.008687                   |
| target function (ls_wunit_k1) not normalized (work): 602.290726             |
| target function (ls_wunit_k1) not normalized (free): 18.764625              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0969 0.0966 0.1104 n_refl.: 70707
       re-set all scales: r(all,work,free)=0.1192 0.1190 0.1294 n_refl.: 70707
         remove outliers: r(all,work,free)=0.1192 0.1190 0.1294 n_refl.: 70707
overall B=-0.00 to atoms: r(all,work,free)=0.1192 0.1190 0.1294 n_refl.: 70707
bulk-solvent and scaling: r(all,work,free)=0.0968 0.0965 0.1104 n_refl.: 70707
         remove outliers: r(all,work,free)=0.0968 0.0965 0.1104 n_refl.: 70706

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.2362

 ======================== 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 0.1174   144.742   140.509 0.758 0.947 0.109
  6.993-5.565   100.00    96     3 0.1024   103.104   102.726 0.840 0.948 0.100
  5.554-4.399    99.51   197     6 0.0701   158.739   158.167 0.884 0.947 0.020
  4.392-3.482    99.76   403     7 0.0606   174.578   174.432 0.950 0.947 0.000
  3.480-2.756   100.00   799    22 0.0649   142.928   142.313 0.976 0.947 0.000
  2.754-2.182   100.00  1582    41 0.0788   109.790   109.391 0.971 0.947 0.000
  2.181-1.727    99.79  3187    71 0.0796    81.925    81.590 0.983 0.947 0.000
  1.727-1.367    99.86  6400   145 0.0841    52.279    51.906 1.011 0.947 0.000
  1.367-1.082    99.66 12832   245 0.0807    40.465    40.178 1.067 0.948 0.000
  1.082-0.857    97.60 25319   505 0.1093    22.294    22.105 1.138 0.948 0.000
  0.857-0.731    58.83 18416   330 0.1846    11.867    11.639 1.052 0.948 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9581   b_overall=-0.2370 

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

  using refinement target ml 


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

r_work=0.0965 r_free=0.1104
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0965 r_free=0.1104

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.634782              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 1.231866              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

Real-space grid search fit H (or D) atoms:
  start:  r_work=0.0965 r_free=0.1104
  H omit: r_work=0.1001 r_free=0.1124
  final:  r_work=0.0966 r_free=0.1105

====================== 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
 0.0912 0.1038 0.0125  0.007   1.3   10.9   0.0   4.4    0   0.817

Number of minimizer iterations: 50 (53 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 9.12 10.38   1.25  1.633   6.516  1.232    2.704
 8.98 10.01   1.03  1.591   6.495  1.232    2.648

Number of minimizer iterations: 25 (30 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.30  83.11   7.05   1.11     0   964
   Protein:    2.30  26.63   5.05   1.11     0   726
   Water:      3.63  83.11  13.19    N/A     0   237
   Other:      4.80   4.80   4.80    N/A     0     1
   Chain  A:   2.30  83.11   7.05    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.30 - 10.38       817
    10.38 - 18.46        86
    18.46 - 26.54        39
    26.54 - 34.62        17
    34.62 - 42.70         0
    42.70 - 50.79         2
    50.79 - 58.87         1
    58.87 - 66.95         0
    66.95 - 75.03         1
    75.03 - 83.11         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.64808  r_work = 0.0898  r_free = 0.1001                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.64793  r_work = 0.0888  r_free = 0.1010                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0888 r_free = 0.1010             target_work(ml) = 2.648         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      100 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0893 r_free = 0.1008             target_work(ml) = 2.648         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 12 (18 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70706 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0893 r_free= 0.1008 coordinate error (max.-lik. estimate): 0.03 A |
|                                                                             |
| normalized target function (ml) (work): 2.647803                            |
| target function (ml) not normalized (work): 183569.542412                   |
| target function (ml) not normalized (free): 3835.435836                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0895 0.0893 0.1008 n_refl.: 70706
       re-set all scales: r(all,work,free)=0.1180 0.1179 0.1236 n_refl.: 70706
         remove outliers: r(all,work,free)=0.1180 0.1179 0.1236 n_refl.: 70706
overall B=-0.00 to atoms: r(all,work,free)=0.1180 0.1179 0.1236 n_refl.: 70706
bulk-solvent and scaling: r(all,work,free)=0.0891 0.0888 0.1004 n_refl.: 70706
         remove outliers: r(all,work,free)=0.0891 0.0888 0.1004 n_refl.: 70705

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.2929

 ======================== 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 0.1256   144.742   139.694 0.766 0.940 0.120
  6.993-5.565   100.00    96     3 0.1196   103.104   102.497 0.846 0.941 0.120
  5.554-4.399    99.51   197     6 0.0769   158.739   158.000 0.891 0.940 0.060
  4.392-3.482    99.76   403     7 0.0683   174.578   174.080 0.962 0.940 0.005
  3.480-2.756   100.00   799    22 0.0740   142.928   142.117 0.983 0.940 0.000
  2.754-2.182   100.00  1582    41 0.0885   109.790   109.197 0.979 0.941 0.000
  2.181-1.727    99.79  3187    71 0.0891    81.925    81.450 0.991 0.941 0.000
  1.727-1.367    99.86  6400   145 0.0858    52.279    51.838 1.019 0.942 0.000
  1.367-1.082    99.66 12832   245 0.0720    40.465    40.177 1.079 0.942 0.000
  1.082-0.857    97.60 25319   505 0.0843    22.294    22.146 1.162 0.944 0.000
  0.857-0.731    58.83 18415   330 0.1575    11.867    11.703 1.078 0.944 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9549   b_overall=-0.3010 

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

  using refinement target ml 


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

r_work=0.0888 r_free=0.1004
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0888 r_free=0.1004

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.476456              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 1.012252              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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

Real-space grid search fit H (or D) atoms:
  start:  r_work=0.0888 r_free=0.1004
  H omit: r_work=0.0924 r_free=0.1025
  final:  r_work=0.0890 r_free=0.1003

====================== 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
 0.0885 0.1006 0.0121  0.008   1.3   12.3   0.0   4.4    0   0.738

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
 8.85 10.06   1.21  1.591   6.494  1.012    2.644
 8.89 10.12   1.23  1.543   6.478  1.012    2.641

Number of minimizer iterations: 25 (29 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.14  83.09   7.01   1.05     0   964
   Protein:    2.14  25.03   5.04   1.05     0   726
   Water:      3.63  83.09  13.07    N/A     0   237
   Other:      4.78   4.78   4.78    N/A     0     1
   Chain  A:   2.14  83.09   7.01    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.14 - 10.24       814
    10.24 - 18.33        90
    18.33 - 26.43        38
    26.43 - 34.52        17
    34.52 - 42.62         0
    42.62 - 50.71         2
    50.71 - 58.81         1
    58.81 - 66.90         0
    66.90 - 75.00         1
    75.00 - 83.09         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.64131  r_work = 0.0889  r_free = 0.1011                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.6395  r_work = 0.0878  r_free = 0.1011                  |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0878 r_free = 0.1011             target_work(ml) = 2.640         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      101 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0885 r_free = 0.1012             target_work(ml) = 2.640         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 12 (19 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70705 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0885 r_free= 0.1012 coordinate error (max.-lik. estimate): 0.03 A |
|                                                                             |
| normalized target function (ml) (work): 2.639734                            |
| target function (ml) not normalized (work): 183007.481236                   |
| target function (ml) not normalized (free): 3833.474309                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0887 0.0885 0.1012 n_refl.: 70705
       re-set all scales: r(all,work,free)=0.1198 0.1198 0.1243 n_refl.: 70705
         remove outliers: r(all,work,free)=0.1198 0.1198 0.1243 n_refl.: 70705
overall B=-0.00 to atoms: r(all,work,free)=0.1198 0.1197 0.1243 n_refl.: 70705
bulk-solvent and scaling: r(all,work,free)=0.0885 0.0883 0.1011 n_refl.: 70705
         remove outliers: r(all,work,free)=0.0885 0.0883 0.1011 n_refl.: 70705

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.3188

 ======================== 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 0.1308   144.742   139.181 0.762 0.939 0.130
  6.993-5.565   100.00    96     3 0.1291   103.104   102.145 0.843 0.940 0.084
  5.554-4.399    99.51   197     6 0.0789   158.739   157.975 0.889 0.939 0.043
  4.392-3.482    99.76   403     7 0.0697   174.578   174.054 0.964 0.940 0.000
  3.480-2.756   100.00   799    22 0.0761   142.928   142.104 0.984 0.940 0.000
  2.754-2.182   100.00  1582    41 0.0897   109.790   109.192 0.980 0.940 0.000
  2.181-1.727    99.79  3187    71 0.0899    81.925    81.443 0.993 0.941 0.000
  1.727-1.367    99.86  6400   145 0.0861    52.279    51.837 1.022 0.941 0.000
  1.367-1.082    99.66 12832   245 0.0712    40.465    40.183 1.083 0.943 0.000
  1.082-0.857    97.60 25319   505 0.0818    22.294    22.155 1.171 0.945 0.000
  0.857-0.731    58.83 18415   330 0.1547    11.867    11.716 1.089 0.944 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9549   b_overall=-0.3289 

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

  using refinement target ml 


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

r_work=0.0883 r_free=0.1011
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0883 r_free=0.1011

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.451792              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.958931              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0883 0.1013 0.0130  0.008   1.3   12.3   0.0   4.4    0   0.726

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
 8.83 10.13   1.30  1.543   6.478  0.959    2.641
 8.86 10.15   1.29  1.521   6.474  0.959    2.639

Number of minimizer iterations: 23 (26 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.10  83.07   7.00   1.02     0   964
   Protein:    2.10  23.85   5.05   1.02     0   726
   Water:      3.63  83.07  13.00    N/A     0   237
   Other:      4.76   4.76   4.76    N/A     0     1
   Chain  A:   2.10  83.07   7.00    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.10 - 10.20       815
    10.20 - 18.29        90
    18.29 - 26.39        38
    26.39 - 34.49        16
    34.49 - 42.59         0
    42.59 - 50.68         2
    50.68 - 58.78         1
    58.78 - 66.88         0
    66.88 - 74.97         1
    74.97 - 83.07         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.63883  r_work = 0.0886  r_free = 0.1015                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.63709  r_work = 0.0877  r_free = 0.1010                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0877 r_free = 0.1010             target_work(ml) = 2.637         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       95 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0885 r_free = 0.1016             target_work(ml) = 2.639         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (17 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70705 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0885 r_free= 0.1016 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.639150                            |
| target function (ml) not normalized (work): 182967.004631                   |
| target function (ml) not normalized (free): 3834.659146                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0887 0.0885 0.1016 n_refl.: 70705
       re-set all scales: r(all,work,free)=0.1220 0.1219 0.1261 n_refl.: 70705
         remove outliers: r(all,work,free)=0.1220 0.1219 0.1261 n_refl.: 70705
overall B=-0.00 to atoms: r(all,work,free)=0.1220 0.1219 0.1261 n_refl.: 70705
bulk-solvent and scaling: r(all,work,free)=0.0894 0.0892 0.1019 n_refl.: 70705
         remove outliers: r(all,work,free)=0.0894 0.0892 0.1019 n_refl.: 70705

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.4473

 ======================== 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 0.1311   144.742   139.381 0.683 1.008 0.114
  6.993-5.565   100.00    96     3 0.1305   103.104   102.330 0.757 1.008 0.110
  5.554-4.399    99.51   197     6 0.0792   158.739   158.163 0.799 1.007 0.038
  4.392-3.482    99.76   403     7 0.0702   174.578   174.305 0.869 1.007 0.000
  3.480-2.756   100.00   799    22 0.0767   142.928   142.335 0.889 1.006 0.000
  2.754-2.182   100.00  1582    41 0.0902   109.790   109.308 0.886 1.006 0.000
  2.181-1.727    99.79  3187    71 0.0906    81.925    81.554 0.901 1.004 0.000
  1.727-1.367    99.86  6400   145 0.0864    52.279    51.860 0.930 1.002 0.000
  1.367-1.082    99.66 12832   245 0.0706    40.465    40.162 0.991 0.999 0.000
  1.082-0.857    97.60 25319   505 0.0829    22.294    22.181 1.090 0.993 0.000
  0.857-0.731    58.83 18415   330 0.1604    11.867    11.651 1.014 0.985 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9167   b_overall=-0.3806 

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

  using refinement target ml 


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

r_work=0.0892 r_free=0.1019
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0892 r_free=0.1019

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.485972              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.923464              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0891 0.1019 0.0128  0.008   1.3   11.6   0.0   4.4    0   0.743

Number of minimizer iterations: 7 (9 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 8.91 10.19   1.28  1.521   6.474  0.923    2.651
 8.93 10.21   1.28  1.500   6.478  0.923    2.649

Number of minimizer iterations: 24 (28 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.10  83.05   7.01   1.00     0   964
   Protein:    2.10  22.74   5.06   1.00     0   726
   Water:      3.62  83.05  12.96    N/A     0   237
   Other:      4.73   4.73   4.73    N/A     0     1
   Chain  A:   2.10  83.05   7.01    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.10 - 10.19       816
    10.19 - 18.29        89
    18.29 - 26.38        38
    26.38 - 34.48        16
    34.48 - 42.57         0
    42.57 - 50.67         2
    50.67 - 58.76         1
    58.76 - 66.86         0
    66.86 - 74.95         1
    74.95 - 83.05         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.64881  r_work = 0.0893  r_free = 0.1021                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.64632  r_work = 0.0883  r_free = 0.1014                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0883 r_free = 0.1014             target_work(ml) = 2.646         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       99 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0892 r_free = 0.1019             target_work(ml) = 2.648         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (17 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70705 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0892 r_free= 0.1019 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.648099                            |
| target function (ml) not normalized (work): 183587.374984                   |
| target function (ml) not normalized (free): 3840.938226                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0894 0.0892 0.1019 n_refl.: 70705
       re-set all scales: r(all,work,free)=0.1241 0.1240 0.1274 n_refl.: 70705
         remove outliers: r(all,work,free)=0.1241 0.1240 0.1274 n_refl.: 70705
overall B=-0.00 to atoms: r(all,work,free)=0.1241 0.1240 0.1274 n_refl.: 70705
bulk-solvent and scaling: r(all,work,free)=0.0893 0.0890 0.1017 n_refl.: 70705
         remove outliers: r(all,work,free)=0.0893 0.0890 0.1017 n_refl.: 70705

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.4571

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

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

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 16.574-7.016    98.04    98     2 0.1318   144.742   139.256 0.679 1.007 0.100
  6.993-5.565   100.00    96     3 0.1318   103.104   102.188 0.752 1.007 0.068
  5.554-4.399    99.51   197     6 0.0805   158.739   158.113 0.798 1.006 0.040
  4.392-3.482    99.76   403     7 0.0708   174.578   174.229 0.869 1.006 0.000
  3.480-2.756   100.00   799    22 0.0769   142.928   142.301 0.889 1.006 0.000
  2.754-2.182   100.00  1582    41 0.0905   109.790   109.282 0.886 1.005 0.000
  2.181-1.727    99.79  3187    71 0.0904    81.925    81.543 0.901 1.005 0.000
  1.727-1.367    99.86  6400   145 0.0862    52.279    51.859 0.931 1.003 0.000
  1.367-1.082    99.66 12832   245 0.0704    40.465    40.168 0.993 1.001 0.000
  1.082-0.857    97.60 25319   505 0.0824    22.294    22.177 1.094 0.997 0.000
  0.857-0.731    58.83 18415   330 0.1600    11.867    11.657 1.017 0.989 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9167   b_overall=-0.4018 

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

  using refinement target ml 


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

r_work=0.0890 r_free=0.1017
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0890 r_free=0.1017

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.521341              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.797218              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0889 0.1016 0.0127  0.008   1.3   10.9   0.0   4.4    0   0.761

Number of minimizer iterations: 7 (8 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 8.89 10.16   1.27  1.500   6.478  0.797    2.648
 8.92 10.18   1.26  1.485   6.487  0.797    2.648

Number of minimizer iterations: 11 (14 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.11  83.05   7.02   0.99     0   964
   Protein:    2.11  22.53   5.09   0.99     0   726
   Water:      3.62  83.05  12.94    N/A     0   237
   Other:      4.73   4.73   4.73    N/A     0     1
   Chain  A:   2.11  83.05   7.02    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.11 - 10.21       818
    10.21 - 18.30        87
    18.30 - 26.39        38
    26.39 - 34.49        16
    34.49 - 42.58         0
    42.58 - 50.67         2
    50.67 - 58.77         1
    58.77 - 66.86         0
    66.86 - 74.95         1
    74.95 - 83.05         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.64764  r_work = 0.0892  r_free = 0.1018                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.64572  r_work = 0.0883  r_free = 0.1013                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0883 r_free = 0.1013             target_work(ml) = 2.646         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      102 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0891 r_free = 0.1017             target_work(ml) = 2.648         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 12 (21 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70705 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0891 r_free= 0.1017 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.647528                            |
| target function (ml) not normalized (work): 183547.833511                   |
| target function (ml) not normalized (free): 3839.772081                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0894 0.0891 0.1017 n_refl.: 70705
       re-set all scales: r(all,work,free)=0.1262 0.1261 0.1290 n_refl.: 70705
         remove outliers: r(all,work,free)=0.1262 0.1261 0.1290 n_refl.: 70705
overall B=-0.00 to atoms: r(all,work,free)=0.1262 0.1261 0.1290 n_refl.: 70705
bulk-solvent and scaling: r(all,work,free)=0.0892 0.0889 0.1015 n_refl.: 70705
         remove outliers: r(all,work,free)=0.0892 0.0889 0.1015 n_refl.: 70705

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.4778

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

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

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 16.574-7.016    98.04    98     2 0.1327   144.742   139.185 0.705 1.006 0.093
  6.993-5.565   100.00    96     3 0.1326   103.104   102.173 0.782 1.007 0.080
  5.554-4.399    99.51   197     6 0.0812   158.739   158.090 0.830 1.006 0.038
  4.392-3.482    99.76   403     7 0.0712   174.578   174.206 0.905 1.006 0.000
  3.480-2.756   100.00   799    22 0.0772   142.928   142.286 0.927 1.006 0.000
  2.754-2.182   100.00  1582    41 0.0905   109.790   109.271 0.924 1.005 0.000
  2.181-1.727    99.79  3187    71 0.0904    81.925    81.538 0.940 1.005 0.000
  1.727-1.367    99.86  6400   145 0.0862    52.279    51.854 0.971 1.004 0.000
  1.367-1.082    99.66 12832   245 0.0703    40.465    40.168 1.039 1.002 0.000
  1.082-0.857    97.60 25319   505 0.0822    22.294    22.179 1.146 0.999 0.000
  0.857-0.731    58.83 18415   330 0.1594    11.867    11.660 1.069 0.992 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9549   b_overall=-0.4281 

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

  using refinement target ml 


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

r_work=0.0889 r_free=0.1015
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0889 r_free=0.1015

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.526449              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.904468              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0889 0.1015 0.0126  0.008   1.3   10.9   0.0   4.4    0   0.763

Number of minimizer iterations: 2 (3 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 8.89 10.15   1.26  1.485   6.487  0.904    2.647
 8.91 10.15   1.24  1.483   6.492  0.904    2.645

Number of minimizer iterations: 20 (23 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.15  83.02   7.03   0.98     0   964
   Protein:    2.15  21.62   5.11   0.98     0   726
   Water:      3.61  83.02  12.91    N/A     0   237
   Other:      4.72   4.72   4.72    N/A     0     1
   Chain  A:   2.15  83.02   7.03    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.15 - 10.23       818
    10.23 - 18.32        88
    18.32 - 26.41        37
    26.41 - 34.50        16
    34.50 - 42.59         0
    42.59 - 50.67         2
    50.67 - 58.76         1
    58.76 - 66.85         0
    66.85 - 74.94         1
    74.94 - 83.02         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.64535  r_work = 0.0891  r_free = 0.1015                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.64354  r_work = 0.0881  r_free = 0.1010                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0881 r_free = 0.1010             target_work(ml) = 2.644         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       99 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0890 r_free = 0.1014             target_work(ml) = 2.645         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (17 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70705 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0890 r_free= 0.1014 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.645386                            |
| target function (ml) not normalized (work): 183399.296249                   |
| target function (ml) not normalized (free): 3837.255703                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0893 0.0890 0.1014 n_refl.: 70705
       re-set all scales: r(all,work,free)=0.1283 0.1282 0.1307 n_refl.: 70705
         remove outliers: r(all,work,free)=0.1283 0.1282 0.1307 n_refl.: 70705
overall B=-0.00 to atoms: r(all,work,free)=0.1283 0.1282 0.1307 n_refl.: 70705
bulk-solvent and scaling: r(all,work,free)=0.0891 0.0889 0.1013 n_refl.: 70705
         remove outliers: r(all,work,free)=0.0891 0.0889 0.1013 n_refl.: 70705

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.4840

 ======================== 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   139.103 0.755 1.004 0.083
  6.993-5.565   100.00    96     3 0.1331   103.104   102.158 0.839 1.005 0.070
  5.554-4.399    99.51   197     6 0.0818   158.739   158.024 0.893 1.004 0.036
  4.392-3.482    99.76   403     7 0.0716   174.578   174.180 0.974 1.004 0.000
  3.480-2.756   100.00   799    22 0.0774   142.928   142.272 0.998 1.004 0.000
  2.754-2.182   100.00  1582    41 0.0908   109.790   109.258 0.995 1.004 0.000
  2.181-1.727    99.79  3187    71 0.0904    81.925    81.531 1.012 1.004 0.000
  1.727-1.367    99.86  6400   145 0.0863    52.279    51.853 1.046 1.004 0.000
  1.367-1.082    99.66 12832   245 0.0702    40.465    40.169 1.119 1.004 0.000
  1.082-0.857    97.60 25319   505 0.0819    22.294    22.179 1.235 1.004 0.000
  0.857-0.731    58.83 18415   330 0.1592    11.867    11.663 1.153 0.998 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0265   b_overall=-0.4534 

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

  using refinement target ml 


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

r_work=0.0889 r_free=0.1013
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0889 r_free=0.1013

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.520017              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.820283              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0889 0.1013 0.0124  0.008   1.3   10.9   0.0   4.4    0   0.760

Number of minimizer iterations: 2 (4 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 8.89 10.13   1.24  1.483   6.492  0.820    2.646
 8.91 10.15   1.24  1.473   6.501  0.820    2.646

Number of minimizer iterations: 8 (11 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.16  83.02   7.04   0.97     0   964
   Protein:    2.16  21.52   5.13   0.97     0   726
   Water:      3.61  83.02  12.91    N/A     0   237
   Other:      4.74   4.74   4.74    N/A     0     1
   Chain  A:   2.16  83.02   7.04    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.16 - 10.25       819
    10.25 - 18.33        87
    18.33 - 26.42        37
    26.42 - 34.51        16
    34.51 - 42.59         0
    42.59 - 50.68         2
    50.68 - 58.76         1
    58.76 - 66.85         0
    66.85 - 74.94         1
    74.94 - 83.02         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.6456  r_work = 0.0891  r_free = 0.1015                  |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.64392  r_work = 0.0882  r_free = 0.1012                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0882 r_free = 0.1012             target_work(ml) = 2.644         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      101 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0891 r_free = 0.1014             target_work(ml) = 2.646         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (19 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70705 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0891 r_free= 0.1014 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.645526                            |
| target function (ml) not normalized (work): 183409.043145                   |
| target function (ml) not normalized (free): 3838.044966                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0893 0.0891 0.1014 n_refl.: 70705
       re-set all scales: r(all,work,free)=0.1303 0.1303 0.1323 n_refl.: 70705
         remove outliers: r(all,work,free)=0.1303 0.1303 0.1323 n_refl.: 70705
overall B=-0.00 to atoms: r(all,work,free)=0.1303 0.1303 0.1323 n_refl.: 70705
bulk-solvent and scaling: r(all,work,free)=0.0891 0.0889 0.1013 n_refl.: 70705
         remove outliers: r(all,work,free)=0.0891 0.0889 0.1013 n_refl.: 70705

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.5020

 ======================== 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 0.1345   144.742   139.016 0.784 1.004 0.094
  6.993-5.565   100.00    96     3 0.1335   103.104   102.173 0.871 1.004 0.090
  5.554-4.399    99.51   197     6 0.0824   158.739   158.027 0.928 1.004 0.034
  4.392-3.482    99.76   403     7 0.0719   174.578   174.162 1.014 1.004 0.000
  3.480-2.756   100.00   799    22 0.0775   142.928   142.267 1.039 1.004 0.000
  2.754-2.182   100.00  1582    41 0.0908   109.790   109.250 1.036 1.004 0.000
  2.181-1.727    99.79  3187    71 0.0904    81.925    81.527 1.054 1.004 0.000
  1.727-1.367    99.86  6400   145 0.0863    52.279    51.852 1.090 1.005 0.000
  1.367-1.082    99.66 12832   245 0.0702    40.465    40.169 1.167 1.005 0.000
  1.082-0.857    97.60 25319   505 0.0819    22.294    22.180 1.291 1.006 0.000
  0.857-0.731    58.83 18415   330 0.1587    11.867    11.664 1.209 1.001 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0675   b_overall=-0.4769 

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

  using refinement target ml 


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

r_work=0.0889 r_free=0.1013
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

r_work=0.0889 r_free=0.1013

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.508507              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.825258              wxu_scale = 1.000            wu = 0.100         |
|-----------------------------------------------------------------------------|


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


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

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

 R-FACTORS             RMSD           CLASH  RAMA  ROTA CBET WEIGHT
 work   free   delta   bonds   angl
 0.0889 0.1013 0.0124  0.008   1.3   10.9   0.0   4.4    0   0.754

Number of minimizer iterations: 1 (1 function evaluations)

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
 8.89 10.13   1.24  1.473   6.501  0.825    2.646
 8.91 10.15   1.24  1.464   6.509  0.825    2.646

Number of minimizer iterations: 15 (18 function evaluations)

 Individual atomic B
                min    max   mean <Bi,j>   iso aniso
   Overall:    2.19  83.01   7.06   0.96     0   964
   Protein:    2.19  21.16   5.15   0.96     0   726
   Water:      3.63  83.01  12.90    N/A     0   237
   Other:      4.74   4.74   4.74    N/A     0     1
   Chain  A:   2.19  83.01   7.06    N/A     0   964
   Histogram:
       Values      Number of atoms
     2.19 - 10.28       820
    10.28 - 18.36        86
    18.36 - 26.44        37
    26.44 - 34.52        16
    34.52 - 42.60         0
    42.60 - 50.69         2
    50.69 - 58.77         1
    58.77 - 66.85         1
    66.85 - 74.93         0
    74.93 - 83.01         1


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

|- start----------------------------------------------------------------------|
| target_work(ml) = 2.64605  r_work = 0.0891  r_free = 0.1015                 |
|-----------------------------------------------------------------------------|
|- final----------------------------------------------------------------------|
| target_work(ml) = 2.64409  r_work = 0.0881  r_free = 0.1012                 |
|-----------------------------------------------------------------------------|

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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.0881 r_free = 0.1012             target_work(ml) = 2.644         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      101 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.0891 r_free = 0.1015             target_work(ml) = 2.646         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (19 function evaluations)

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

|--(resolution: 0.73 - 16.57 A, n_refl.=70705 (all), 1.95  % free)------------|
|                                                                             |
| r_work= 0.0891 r_free= 0.1015 coordinate error (max.-lik. estimate): 0.04 A |
|                                                                             |
| normalized target function (ml) (work): 2.646260                            |
| target function (ml) not normalized (work): 183459.914344                   |
| target function (ml) not normalized (free): 3839.967160                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| 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 0.0883 0.0998      3.8602      3.9484|
|  2:    1.57 -    1.25 1.00   8283  170 0.0820 0.0889      3.2745      3.2574|
|  3:    1.25 -    1.09 1.00   8289  157 0.0663 0.0762      2.7243      2.8394|
|  4:    1.09 -    0.99 1.00   8244  145 0.0707 0.0910      2.4822       2.638|
|  5:    0.99 -    0.92 0.97   8008  161 0.0818 0.0965      2.3249      2.4039|
|  6:    0.92 -    0.87 0.97   7984  172 0.0946 0.1103      2.2301      2.4056|
|  7:    0.87 -    0.82 0.97   8004  139 0.1302 0.1444      2.2398      2.2619|
|  8:    0.82 -    0.79 0.89   7352  133 0.1413 0.1597      2.1559      2.2977|
|  9:    0.79 -    0.76 0.47   3897   75 0.2070 0.2505      2.2426      2.4357|
| 10:    0.76 -    0.73 0.11    896   22 0.3799 0.3799       2.275      2.4053|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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  0.94  11.26   1.00     0.93        416.34|
|  2:    1.57 -    1.25  8283   170  0.92  13.81   1.00     0.94        178.34|
|  3:    1.25 -    1.09  8289   157  0.97   7.08   1.00     0.94         48.78|
|  4:    1.09 -    0.99  8244   145  0.96   7.60   1.01     0.94         30.16|
|  5:    0.99 -    0.92  8008   161  0.96   9.15   1.01     0.94         21.30|
|  6:    0.92 -    0.87  7984   172  0.95  10.18   0.99     0.93         16.49|
|  7:    0.87 -    0.82  8004   139  0.94  12.52   1.05     0.93         14.36|
|  8:    0.82 -    0.79  7352   133  0.93  14.65   1.01     0.92         13.24|
|  9:    0.79 -    0.76  3897    75  0.91  16.83   0.88     0.87         13.38|
| 10:    0.76 -    0.73   896    22  0.88  20.42   0.73     0.77         13.68|
|alpha:            min =        0.77 max =            0.94 mean =         0.93|
|beta:             min =       13.24 max =          416.34 mean =        89.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.94|
|phase err.(work): min =        0.00 max =           89.97 mean =        11.20|
|phase err.(test): min =        0.00 max =           83.41 mean =        11.14|
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.0893 0.0891 0.1015 n_refl.: 70705
       re-set all scales: r(all,work,free)=0.1323 0.1323 0.1341 n_refl.: 70705
         remove outliers: r(all,work,free)=0.1323 0.1323 0.1341 n_refl.: 70705
overall B=-0.00 to atoms: r(all,work,free)=0.1323 0.1323 0.1341 n_refl.: 70705
bulk-solvent and scaling: r(all,work,free)=0.0891 0.0889 0.1013 n_refl.: 70705
         remove outliers: r(all,work,free)=0.0891 0.0889 0.1013 n_refl.: 70705

bulk-solvent scaling B-values (mode: fast):
  b_isotropic: -0.5286

 ======================== 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 0.1352   144.742   138.902 0.776 1.004 0.104
  6.993-5.565   100.00    96     3 0.1338   103.104   102.165 0.863 1.005 0.100
  5.554-4.399    99.51   197     6 0.0829   158.739   157.992 0.921 1.004 0.052
  4.392-3.482    99.76   403     7 0.0724   174.578   174.138 1.006 1.004 0.000
  3.480-2.756   100.00   799    22 0.0777   142.928   142.246 1.032 1.004 0.000
  2.754-2.182   100.00  1582    41 0.0910   109.790   109.240 1.029 1.005 0.000
  2.181-1.727    99.79  3187    71 0.0904    81.925    81.519 1.048 1.005 0.000
  1.727-1.367    99.86  6400   145 0.0863    52.279    51.849 1.085 1.005 0.000
  1.367-1.082    99.66 12832   245 0.0703    40.465    40.171 1.164 1.006 0.000
  1.082-0.857    97.60 25319   505 0.0818    22.294    22.180 1.290 1.007 0.000
  0.857-0.731    58.83 18415   330 0.1583    11.867    11.668 1.213 1.001 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0610   b_overall=-0.4978 

================= 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: 0.1095 0.1171 0.005  1.187   2.3  83.4   6.3 237      0.227
       1_adp: 0.0995 0.1139 0.005  1.187   2.2  83.2   7.0 237      0.227
      1_occh: 0.0988 0.1157 0.005  1.187   2.2  83.2   7.0 237      0.227
       1_occ: 0.1005 0.1132 0.005  1.187   2.2  83.2   7.0 237      0.227
       2_bss: 0.1001 0.1133 0.005  1.187   2.2  83.2   7.0 237      0.227
 2_settarget: 0.1001 0.1133 0.005  1.187   2.2  83.2   7.0 237      0.227
       2_nqh: 0.1001 0.1133 0.005  1.187   2.2  83.2   7.0 237      0.227
    2_weight: 0.1001 0.1133 0.005  1.187   2.2  83.2   7.0 237      0.227
     2_fitrh: 0.1002 0.1135 0.005  1.187   2.2  83.2   7.0 237      0.218
    2_xyzrec: 0.1009 0.1152 0.005  1.094   2.2  83.2   7.0 237      0.238
       2_adp: 0.0967 0.1095 0.005  1.094   2.6  83.1   7.1 237      0.238
      2_occh: 0.0962 0.1113 0.005  1.094   2.6  83.1   7.1 237      0.238
       2_occ: 0.0966 0.1104 0.005  1.094   2.6  83.1   7.1 237      0.238
       3_bss: 0.0965 0.1104 0.005  1.094   2.6  83.1   7.1 237      0.238
 3_settarget: 0.0965 0.1104 0.005  1.094   2.6  83.1   7.1 237      0.238
       3_nqh: 0.0965 0.1104 0.005  1.094   2.6  83.1   7.1 237      0.238
    3_weight: 0.0965 0.1104 0.005  1.094   2.6  83.1   7.1 237      0.238
     3_fitrh: 0.0966 0.1105 0.005  1.094   2.6  83.1   7.1 237      0.218
    3_xyzrec: 0.0912 0.1038 0.007  1.298   2.6  83.1   7.1 237      0.208
       3_adp: 0.0898 0.1001 0.007  1.298   2.3  83.1   7.0 237      0.208
      3_occh: 0.0888 0.1010 0.007  1.298   2.3  83.1   7.0 237      0.208
       3_occ: 0.0893 0.1008 0.007  1.298   2.3  83.1   7.0 237      0.208
       4_bss: 0.0888 0.1004 0.007  1.298   2.3  83.1   7.0 237      0.208
 4_settarget: 0.0888 0.1004 0.007  1.298   2.3  83.1   7.0 237      0.208
       4_nqh: 0.0888 0.1004 0.007  1.298   2.3  83.1   7.0 237      0.208
    4_weight: 0.0888 0.1004 0.007  1.298   2.3  83.1   7.0 237      0.208
     4_fitrh: 0.0890 0.1003 0.007  1.298   2.3  83.1   7.0 237      0.225
    4_xyzrec: 0.0885 0.1006 0.008  1.324   2.3  83.1   7.0 237      0.227
       4_adp: 0.0889 0.1011 0.008  1.324   2.1  83.1   7.0 237      0.227
      4_occh: 0.0878 0.1011 0.008  1.324   2.1  83.1   7.0 237      0.227
       4_occ: 0.0885 0.1012 0.008  1.324   2.1  83.1   7.0 237      0.227
       5_bss: 0.0883 0.1011 0.008  1.324   2.1  83.1   7.0 237      0.227
 5_settarget: 0.0883 0.1011 0.008  1.324   2.1  83.1   7.0 237      0.227
       5_nqh: 0.0883 0.1011 0.008  1.324   2.1  83.1   7.0 237      0.227
    5_weight: 0.0883 0.1011 0.008  1.324   2.1  83.1   7.0 237      0.227
     5_fitrh: 0.0883 0.1011 0.008  1.324   2.1  83.1   7.0 237      0.227
    5_xyzrec: 0.0883 0.1013 0.008  1.327   2.1  83.1   7.0 237      0.227
       5_adp: 0.0886 0.1015 0.008  1.327   2.1  83.1   7.0 237      0.227
      5_occh: 0.0877 0.1010 0.008  1.327   2.1  83.1   7.0 237      0.227
       5_occ: 0.0885 0.1016 0.008  1.327   2.1  83.1   7.0 237      0.227
       6_bss: 0.0892 0.1019 0.008  1.327   2.1  83.1   7.0 237      0.227
 6_settarget: 0.0892 0.1019 0.008  1.327   2.1  83.1   7.0 237      0.227
       6_nqh: 0.0892 0.1019 0.008  1.327   2.1  83.1   7.0 237      0.227
    6_weight: 0.0892 0.1019 0.008  1.327   2.1  83.1   7.0 237      0.227
     6_fitrh: 0.0892 0.1019 0.008  1.327   2.1  83.1   7.0 237      0.227
    6_xyzrec: 0.0891 0.1019 0.008  1.331   2.1  83.1   7.0 237      0.227
       6_adp: 0.0893 0.1021 0.008  1.331   2.1  83.0   7.0 237      0.227
      6_occh: 0.0883 0.1014 0.008  1.331   2.1  83.0   7.0 237      0.227
       6_occ: 0.0892 0.1019 0.008  1.331   2.1  83.0   7.0 237      0.227
       7_bss: 0.0890 0.1017 0.008  1.331   2.1  83.0   7.0 237      0.227
 7_settarget: 0.0890 0.1017 0.008  1.331   2.1  83.0   7.0 237      0.227
       7_nqh: 0.0890 0.1017 0.008  1.331   2.1  83.0   7.0 237      0.227
    7_weight: 0.0890 0.1017 0.008  1.331   2.1  83.0   7.0 237      0.227
     7_fitrh: 0.0890 0.1017 0.008  1.331   2.1  83.0   7.0 237      0.227
    7_xyzrec: 0.0889 0.1016 0.008  1.335   2.1  83.0   7.0 237      0.227
       7_adp: 0.0892 0.1018 0.008  1.335   2.1  83.0   7.0 237      0.227
      7_occh: 0.0883 0.1013 0.008  1.335   2.1  83.0   7.0 237      0.227
       7_occ: 0.0891 0.1017 0.008  1.335   2.1  83.0   7.0 237      0.227
       8_bss: 0.0889 0.1015 0.008  1.335   2.1  83.0   7.0 237      0.227
 8_settarget: 0.0889 0.1015 0.008  1.335   2.1  83.0   7.0 237      0.227
       8_nqh: 0.0889 0.1015 0.008  1.335   2.1  83.0   7.0 237      0.227
    8_weight: 0.0889 0.1015 0.008  1.335   2.1  83.0   7.0 237      0.227
     8_fitrh: 0.0889 0.1015 0.008  1.335   2.1  83.0   7.0 237      0.227
    8_xyzrec: 0.0889 0.1015 0.008  1.335   2.1  83.0   7.0 237      0.227
       8_adp: 0.0891 0.1015 0.008  1.335   2.1  83.0   7.0 237      0.227
      8_occh: 0.0881 0.1010 0.008  1.335   2.1  83.0   7.0 237      0.227
       8_occ: 0.0890 0.1014 0.008  1.335   2.1  83.0   7.0 237      0.227
       9_bss: 0.0889 0.1013 0.008  1.335   2.1  83.0   7.0 237      0.227
 9_settarget: 0.0889 0.1013 0.008  1.335   2.1  83.0   7.0 237      0.227
       9_nqh: 0.0889 0.1013 0.008  1.335   2.1  83.0   7.0 237      0.227
    9_weight: 0.0889 0.1013 0.008  1.335   2.1  83.0   7.0 237      0.227
     9_fitrh: 0.0889 0.1013 0.008  1.335   2.1  83.0   7.0 237      0.227
    9_xyzrec: 0.0889 0.1013 0.008  1.335   2.1  83.0   7.0 237      0.227
       9_adp: 0.0891 0.1015 0.008  1.335   2.2  83.0   7.0 237      0.227
      9_occh: 0.0882 0.1012 0.008  1.335   2.2  83.0   7.0 237      0.227
       9_occ: 0.0891 0.1014 0.008  1.335   2.2  83.0   7.0 237      0.227
      10_bss: 0.0889 0.1013 0.008  1.335   2.2  83.0   7.0 237      0.227
10_settarget: 0.0889 0.1013 0.008  1.335   2.2  83.0   7.0 237      0.227
      10_nqh: 0.0889 0.1013 0.008  1.335   2.2  83.0   7.0 237      0.227
   10_weight: 0.0889 0.1013 0.008  1.335   2.2  83.0   7.0 237      0.227
    10_fitrh: 0.0889 0.1013 0.008  1.335   2.2  83.0   7.0 237      0.227
   10_xyzrec: 0.0889 0.1013 0.008  1.335   2.2  83.0   7.0 237      0.227
      10_adp: 0.0891 0.1015 0.008  1.335   2.2  83.0   7.1 237      0.227
     10_occh: 0.0881 0.1012 0.008  1.335   2.2  83.0   7.1 237      0.227
      10_occ: 0.0891 0.1015 0.008  1.335   2.2  83.0   7.1 237      0.227
         end: 0.0889 0.1013 0.008  1.335   2.2  83.0   7.1 237      0.227
------------------------------------------------------------------------

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


Writing refined structure to CIF file:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/default_001.cif
Writing default parameters for subsequent refinement:
  /net/anaconda/raid1/afonine/work/discamb/varible_weights913/1R6J/default_002.def

Timing summary:
  Write initial files (write_before_run_outputs): 1.1500
  Refinement macro-cycles (run)                 : 1402.5900
  Write final files (write_after_run_outputs)   : 50.5200
  Total                                         : 1454.2600
Total CPU time: 24.50 minutes

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

# Date 2026-07-20 Time 17:07:03 PDT -0700 (1784592423.28 s)

Start R-work = 0.0755, R-free = 0.0770
Final R-work = 0.0889, R-free = 0.1013

===============================================================================
Job complete
usr+sys time: 1469.87 seconds
wall clock time: 25 minutes 1.70 seconds (1501.70 seconds total)
