3ds1_refine_001.log

# Date 2019-04-19 Time 09:17:49 CST +0800 (1555636669.82 s)
#phil __OFF__

Command line arguments: "3ds1.mtz" "3ds1.pdb" "ordered_solvent=true" "optimize_xyz=true" "optimize_adp=true" "--overwrite" "main.nproc=16"

HOST = pva_mbp
HOSTTYPE = unknown
MACHTYPE = x86_64
OSTYPE = darwin
VENDOR = apple
USER = pafonine
PID = 96383

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  Version: dev
  Release tag: svn+SVN
  User: pafonine
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------

Phenix developers include:
  Paul Adams, Pavel Afonine, Gabor Bunkoczi, Tom Burnley, Vincent Chen, 
  Youval Dar, Ian Davis, Eli Draizen, Nathaniel Echols, Richard Gildea, 
  Piet Gros, Ralf Grosse-Kunstleve, Jeffrey Headd, Bradley Hintze, Li-Wei Hung, 
  Tom Ioerger, Dorothee Liebschner, Airlie McCoy, Erik McKee, Nigel Moriarty, 
  Robert Oeffner, Billy Poon, Randy Read, Jane Richardson, David Richardson, 
  Jim Sacchettini, Nicholas Sauter, Oleg Sobolev, Laurent Storoni, 
  Tom Terwilliger, Christopher Williams, Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxWidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS,
    MUSCLE, KSDSSP, PULCHRA, ANTLRv3
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.ordered_solvent = true

  refinement.target_weights.optimize_xyz_weight = true

  refinement.target_weights.optimize_adp_weight = true

  refinement.main.nproc = 16

  No user-defined map coefficients or files defined; will use default map
  outputs instead.
Working crystal symmetry after inspecting all inputs:
  Unit cell: (42.894, 42.894, 90.813, 90, 90, 90)
  Space group: P 41 21 2 (No. 92)


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

F-obs:
  3ds1.mtz:FOBS,SIGFOBS

Miller array info: 3ds1.mtz:FOBS,SIGFOBS
Observation type: xray.amplitude
Type of data: double, size=11748
Type of sigmas: double, size=11748
Number of Miller indices: 11748
Anomalous flag: False
Unit cell: (42.894, 42.894, 90.813, 90, 90, 90)
Space group: P 41 21 2 (No. 92)
Systematic absences: 0
Centric reflections: 2233
Resolution range: 28.7685 1.60119
Completeness in resolution range: 0.996607
Completeness with d_max=infinity: 0.996353
Wavelength: 0.0000

Number of F-obs in resolution range:                   11748
Number of F-obs<0 (these reflections will be rejected): 0
Number of F-obs=0 (these reflections will be used in refinement): 0
Refinement resolution range: d_max =  28.7685
                             d_min =   1.6012

R-free flags:
  3ds1.mtz:R-free-flags

Miller array info: 3ds1.mtz:R-free-flags
Observation type: None
Type of data: int, size=11788
Type of sigmas: None
Number of Miller indices: 11788
Anomalous flag: False
Unit cell: (42.894, 42.894, 90.813, 90, 90, 90)
Space group: P 41 21 2 (No. 92)
Systematic absences: 0
Centric reflections: 2255
Resolution range: 28.7685 1.60119
Completeness in resolution range: 1
Completeness with d_max=infinity: 0.999746
Wavelength: 0.0000

Test (R-free flags) flag value: 0

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 28.7731 -  3.4479 [1280/1308]  1236    44   3.4%
  bin  2:  3.4479 -  2.7374 [1207/1207]  1146    61   5.1%
  bin  3:  2.7374 -  2.3915 [1173/1173]  1118    55   4.7%
  bin  4:  2.3915 -  2.1730 [1189/1189]  1123    66   5.6%
  bin  5:  2.1730 -  2.0173 [1159/1159]  1100    59   5.1%
  bin  6:  2.0173 -  1.8984 [1161/1161]  1118    43   3.7%
  bin  7:  1.8984 -  1.8033 [1159/1159]  1104    55   4.7%
  bin  8:  1.8033 -  1.7248 [1145/1145]  1083    62   5.4%
  bin  9:  1.7248 -  1.6584 [1148/1148]  1087    61   5.3%
  bin 10:  1.6584 -  1.6012 [1127/1139]  1074    53   4.7%
                                overall 11189   559   4.8%
  Monomer Library directory:
    "/Users/pafonine/phenix/modules/chem_data/mon_lib"
  Total number of atoms: 810
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 628
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 81, 622
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 4, 'TRANS': 75, 'PCIS': 1}
      Conformer: "B"
        Number of residues, atoms: 81, 622
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 4, 'TRANS': 75, 'PCIS': 1}
          bond proxies already assigned to first conformer: 626
    Chain: "T"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 95
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
    Chain: "A"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 80
          Classifications: {'water': 80}
          Link IDs: {None: 79}
    Chain: "T"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O   HOH A  88 " occ=0.50
  Time building chain proxies: 0.49, per 1000 atoms: 0.60
  Number of scatterers: 810
  At special positions: 0
  Unit cell: (42.894, 42.894, 90.813, 90, 90, 90)
  Space group: P 41 21 2 (No. 92)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       5     16.00
     O     226      8.00
     N     122      7.00
     C     457      6.00
    sf(0) = scattering factor at diffraction angle 0.


No array of experimental phases found.


 ******************************************************************
 INFO: Some parts of this job will make use of multiple processors:
 ******************************************************************

   nproc = 16

 Please ask your system administrator for advice about this, in particular if
 you run this job through a queuing system.


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


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

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S       5     15.96       2
   O     226      7.97       2
   N     122      6.97       2
   C     457      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


==================== Fixing bad ADP in input model (if any) ===================


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

All atoms refined with f_prime=0 and f_double_prime=0.
  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : False - 3.50
        Amimo acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.08
  Conformation dependent library (CDL) restraints added in 43.3 milliseconds
  
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  170

  Time building geometry restraints manager: 0.11 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 126
        1.30 -     1.43: 176
        1.43 -     1.56: 423
        1.56 -     1.68: 4
        1.68 -     1.81: 8
  Bond restraints: 737
  Sorted by residual:
  bond pdb=" C   GLU A 180 "
       pdb=" O   GLU A 180 "
    ideal  model  delta    sigma   weight residual
    1.236  1.175  0.062 1.15e-02 7.56e+03 2.89e+01
  bond pdb=" C   GLY A 222 "
       pdb=" O   GLY A 222 "
    ideal  model  delta    sigma   weight residual
    1.237  1.176  0.061 1.44e-02 4.82e+03 1.79e+01
  bond pdb=" C   GLY A 223 "
       pdb=" O   GLY A 223 "
    ideal  model  delta    sigma   weight residual
    1.235  1.183  0.052 1.35e-02 5.49e+03 1.50e+01
  bond pdb=" N   GLU A 180 "
       pdb=" CA  GLU A 180 "
    ideal  model  delta    sigma   weight residual
    1.459  1.414  0.046 1.19e-02 7.06e+03 1.48e+01
  bond pdb=" CB  THR A 188 "
       pdb=" OG1 THR A 188 "
    ideal  model  delta    sigma   weight residual
    1.433  1.373  0.060 1.60e-02 3.91e+03 1.40e+01
  ... (remaining 732 not shown)

  Histogram of bond angle deviations from ideal:
       97.96 -   105.13: 21
      105.13 -   112.31: 334
      112.31 -   119.49: 266
      119.49 -   126.67: 369
      126.67 -   133.85: 7
  Bond angle restraints: 997
  Sorted by residual:
  angle pdb=" N   GLY A 222 "
        pdb=" CA  GLY A 222 "
        pdb=" C   GLY A 222 "
      ideal   model   delta    sigma   weight residual
     114.92  110.35    4.57 1.30e+00 5.92e-01 1.23e+01
  angle pdb=" N   GLU A 180 "
        pdb=" CA  GLU A 180 "
        pdb=" CB  GLU A 180 "
      ideal   model   delta    sigma   weight residual
     110.01  105.22    4.79 1.45e+00 4.76e-01 1.09e+01
  angle pdb=" N   ALA A 209 "
        pdb=" CA  ALA A 209 "
        pdb=" C   ALA A 209 "
      ideal   model   delta    sigma   weight residual
     110.23  114.40   -4.17 1.45e+00 4.76e-01 8.26e+00
  angle pdb=" OG1 THR A 188 "
        pdb=" CB  THR A 188 "
        pdb=" CG2 THR A 188 "
      ideal   model   delta    sigma   weight residual
     109.30  103.85    5.45 2.00e+00 2.50e-01 7.42e+00
  angle pdb=" CA  ASN A 183 "
        pdb=" C   ASN A 183 "
        pdb=" N   TRP A 184 "
      ideal   model   delta    sigma   weight residual
     117.30  114.29    3.01 1.16e+00 7.43e-01 6.72e+00
  ... (remaining 992 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    16.44: 413
       16.44 -    32.86: 28
       32.86 -    49.29: 3
       49.29 -    65.72: 3
       65.72 -    82.15: 1
  Dihedral angle restraints: 448
    sinusoidal: 182
      harmonic: 266
  Sorted by residual:
  dihedral pdb=" CA  GLY A 222 "
           pdb=" C   GLY A 222 "
           pdb=" N   GLY A 223 "
           pdb=" CA  GLY A 223 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.08  -15.92     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  ARG A 162 "
           pdb=" CB  ARG A 162 "
           pdb=" CG  ARG A 162 "
           pdb=" CD  ARG A 162 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  110.58  -50.58     3      1.50e+01 4.44e-03 8.92e+00
  dihedral pdb=" C   VAL A 181 "
           pdb=" N   VAL A 181 "
           pdb=" CA  VAL A 181 "
           pdb=" CB  VAL A 181 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -129.23    7.23     0      2.50e+00 1.60e-01 8.37e+00
  ... (remaining 445 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 61
       0.058 -    0.117: 31
       0.117 -    0.175: 13
       0.175 -    0.233: 4
       0.233 -    0.291: 1
  Chirality restraints: 110
  Sorted by residual:
  chirality pdb=" CA  ASN A 193 "
            pdb=" N   ASN A 193 "
            pdb=" C   ASN A 193 "
            pdb=" CB  ASN A 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  LEU A 189 "
            pdb=" N   LEU A 189 "
            pdb=" C   LEU A 189 "
            pdb=" CB  LEU A 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  SER A 149 "
            pdb=" N   SER A 149 "
            pdb=" C   SER A 149 "
            pdb=" CB  SER A 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.82e-01
  ... (remaining 107 not shown)

  Planarity restraints: 130
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 164 "    0.018 2.00e-02 2.50e+03   1.19e-02 2.86e+00
        pdb=" CG  TYR A 164 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 164 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 164 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 164 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 164 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 164 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR A 164 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 169 "    0.019 2.00e-02 2.50e+03   1.11e-02 2.46e+00
        pdb=" CG  TYR A 169 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 169 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 169 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 169 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 169 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 169 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 169 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 159 "    0.006 2.00e-02 2.50e+03   1.17e-02 1.37e+00
        pdb=" CD  GLU A 159 "   -0.020 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 159 "    0.007 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 159 "    0.007 2.00e-02 2.50e+03
  ... (remaining 127 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 410
        2.90 -     3.40: 923
        3.40 -     3.90: 1832
        3.90 -     4.40: 2013
        4.40 -     4.90: 3114
  Nonbonded interactions: 8292
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 163 "
            pdb=" OD2 ASP T   5 "
     model   vdw sym.op.
     2.403 3.040 y-1/2,-x+1/2,z-1/4
  nonbonded pdb=" OD2 ASP T   5 "
            pdb=" OD2 ASP A 163 "
     model   vdw sym.op.
     2.403 3.040 -y+1/2,x+1/2,z+1/4
  nonbonded pdb=" OH  TYR T   9 "
            pdb=" O   HOH T  19 "
     model   vdw
     2.450 2.440
  nonbonded pdb=" O   HIS A 226 "
            pdb=" O   HOH A  13 "
     model   vdw
     2.492 2.440
  nonbonded pdb=" OE1 GLU T   4 "
            pdb=" O   HOH T  16 "
     model   vdw
     2.503 2.440
  ... (remaining 8287 not shown)

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

======================== Summary of geometry restraints =======================


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

n_use            =  810
n_use_u_iso      =  0
n_use_u_aniso    =  810
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 =  810

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

Refinement flags and selection counts:
  individual_sites       =  True (810 atoms)
  torsion_angles         = False (0 atoms)
  rigid_body             = False (0 atoms in 0 groups)
  individual_adp         =  True (iso = 0 aniso = 810)
  group_adp              = False (0 atoms in 0 groups)
  tls                    = False (0 atoms in 0 groups)
  occupancies            =  True (13 atoms)
  group_anomalous        = False

*******************************************************************************
Automatic adjustment:
  hydrogens.refine=riding
*******************************************************************************


==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use ncs_search.enabled=true to activate it.
Look at refinement.ncs for more NCS related parameters.

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

Writing effective parameters to file:
  /Users/pafonine/Desktop/QR2019April/low_high_res_pair/3ds1_refine_001.eff

Writing geometry restraints to file:
  /Users/pafonine/Desktop/QR2019April/low_high_res_pair/3ds1_refine_001.geo
CPU time processing inputs: 5.90


============================ 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 {
  crystal_symmetry {
    unit_cell = 42.89400101 42.89400101 90.81300354 90 90 90
    space_group = "P 41 21 2"
  }
  input {
    pdb {
      file_name = "3ds1.pdb"
    }
    xray_data {
      file_name = "3ds1.mtz"
      labels = "FOBS,SIGFOBS"
      r_free_flags {
        file_name = "3ds1.mtz"
        label = "R-free-flags"
        test_flag_value = 0
      }
    }
  }
  output {
    prefix = "3ds1_refine"
    serial = 1
  }
  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"
    }
  }
  main {
    ordered_solvent = True
    nproc = 16
  }
  hydrogens {
    refine = individual *riding Auto
  }
  target_weights {
    optimize_xyz_weight = True
    optimize_adp_weight = True
  }
}
#phil __OFF__


=============================== refinement start ==============================


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


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

|--(resolution: 1.60 - 28.77 A, n_refl.=11748 (all), 4.76  % free)------------|
|                                                                             |
| r_work= 0.2749 r_free= 0.3123 coordinate error (max.-lik. estimate): 0.14 A |
|                                                                             |
| normalized target function (ml) (work): 4.627053                            |
| target function (ml) not normalized (work): 51772.095185                    |
| target function (ml) not normalized (free): 2612.573658                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 28.7731 -  2.5413 0.99   2938  136 0.2876 0.3332      5.8182      5.7819|
|  2:  2.5413 -  2.0173 1.00   2785  149 0.2625 0.2668      4.9669      4.9928|
|  3:  2.0173 -  1.7623 1.00   2756  131 0.2533 0.3327      4.1087      4.2831|
|  4:  1.7623 -  1.6012 1.00   2710  143 0.2462 0.3052      3.5135      3.6449|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 28.7731 -  2.5413  2938   136  0.72  31.58   0.98     0.86      15337.19|
|  2:  2.5413 -  2.0173  2785   149  0.63  40.60   1.15     0.93       5835.25|
|  3:  2.0173 -  1.7623  2756   131  0.75  30.94   1.12     0.91        795.51|
|  4:  1.7623 -  1.6012  2710   143  0.78  28.43   1.00     0.80        217.96|
|alpha:            min =        0.80 max =            0.93 mean =         0.88|
|beta:             min =      217.96 max =        15337.19 mean =      5728.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.72|
|phase err.(work): min =        0.00 max =           90.00 mean =        32.90|
|phase err.(test): min =        0.00 max =           89.18 mean =        33.15|
|-----------------------------------------------------------------------------|

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


                min    max   mean <Bi,j>   iso aniso
   Overall:   11.42  54.27  23.75   1.83   810     0
   Protein:   11.42  43.21  22.62   1.83   723     0
   Water:     18.60  54.27  33.20    N/A    87     0
   Chain  A:  11.42  54.27  23.67    N/A   708     0
   Chain  T:  17.76  43.79  24.33    N/A   102     0
   Histogram:
       Values      Number of atoms
    11.42 - 15.70        49
    15.70 - 19.99       230
    19.99 - 24.27       216
    24.27 - 28.56       146
    28.56 - 32.84        73
    32.84 - 37.13        52
    37.13 - 41.41        25
    41.41 - 45.70        13
    45.70 - 49.98         5
    49.98 - 54.27         1

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.50   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 3 *************************

|--(resolution: 1.60 - 28.77 A, n_refl.=11748 (all), 4.76  % free)------------|
|                                                                             |
| r_work= 0.2749 r_free= 0.3123 coordinate error (max.-lik. estimate): 0.14 A |
|                                                                             |
| normalized target function (ml) (work): 4.627053                            |
| target function (ml) not normalized (work): 51772.095185                    |
| target function (ml) not normalized (free): 2612.573658                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.2763 0.2749 0.3123 n_refl.: 11748
       re-set all scales: r(all,work,free)=0.2763 0.2749 0.3123 n_refl.: 11748
         remove outliers: r(all,work,free)=0.2763 0.2749 0.3123 n_refl.: 11748
 overall B=1.17 to atoms: r(all,work,free)=0.2842 0.2830 0.3153 n_refl.: 11748
bulk-solvent and scaling: r(all,work,free)=0.2291 0.2268 0.2789 n_refl.: 11748
         remove outliers: r(all,work,free)=0.2291 0.2268 0.2789 n_refl.: 11748

======================== 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
 28.768-8.096    81.97    96     4 0.2350   292.180   280.266 0.995 0.946 0.325
  8.025-6.498    99.01    97     3 0.2760   224.188   217.081 0.939 0.947 0.338
  6.467-5.218    98.92   177     6 0.2390   254.841   243.325 1.003 0.947 0.337
  5.202-4.200    99.41   323    16 0.2066   323.484   313.469 1.044 0.948 0.302
  4.197-3.385    99.84   606    16 0.2008   290.333   283.240 1.045 0.948 0.196
  3.383-2.727   100.00  1105    62 0.2348   183.580   176.726 1.022 0.949 0.000
  2.726-2.198   100.00  2070   114 0.2257   116.304   112.041 1.046 0.949 0.000
  2.197-1.771   100.00  3892   188 0.2348    59.667    58.237 1.092 0.949 0.000
  1.771-1.601    99.60  2823   150 0.2475    27.833    26.786 0.981 0.949 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0016   b_overall=0.2673  

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

  using refinement target ls_wunit_k1 


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

r_work=0.2268 r_free=0.2789
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN

Total number of N/Q/H flips: 1

r_work=0.2269 r_free=0.2789

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.347056             wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.414868              wxu_scale = 1.000            wu = 1.000         |
|-----------------------------------------------------------------------------|


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

    R-FACTORS           RMSD     CLASH  RAMA  ROTA CBET WEIGHT    TARGETS
 work  free  delta  bonds  angl                                  data   restr
22.69 27.89   5.20  0.014   1.3    4.9   0.0   0.0    0   none  0.060  0.1710
23.78 28.14   4.35  0.003   0.6    3.5   0.0   0.0    0  0.125  0.064  0.0440
23.68 28.09   4.41  0.003   0.6    3.5   0.0   0.0    0  0.250  0.064  0.0441
23.65 28.08   4.43  0.003   0.6    3.5   0.0   0.0    0  0.500  0.063  0.0438
23.51 28.12   4.62  0.003   0.6    3.5   0.0   0.0    0  1.000  0.062  0.0441
23.25 28.07   4.82  0.003   0.6    3.5   0.0   0.0    0  2.000  0.059  0.0461
22.98 27.98   4.99  0.003   0.6    3.5   0.0   0.0    0  3.000  0.057  0.0483
22.86 28.07   5.20  0.004   0.6    3.5   0.0   0.0    0  4.000  0.056  0.0518
22.77 28.17   5.41  0.004   0.7    4.2   0.0   0.0    0  5.000  0.055  0.0531
22.80 28.35   5.56  0.005   0.7    4.2   0.0   0.0    0  6.000  0.054  0.0559
22.73 28.45   5.72  0.005   0.7    4.9   0.0   0.0    0  7.000  0.053  0.0597
22.59 28.39   5.80  0.005   0.7    4.9   0.0   0.0    0  8.000  0.052  0.0623
22.54 28.42   5.88  0.006   0.8    4.9   0.0   0.0    0  9.000  0.052  0.0648
22.53 28.54   6.00  0.006   0.8    4.9   0.0   1.3    0 10.000  0.052  0.0684
22.49 28.42   5.93  0.006   0.8    4.9   0.0   0.0    0  9.674  0.052  0.0668
Best XYZ weight:    3.000
Updating mask...
Accepted refinement result:
22.98 27.98   4.99  0.003   0.6    3.5   0.0   0.0    0  3.000  0.057  0.0483

Legend:
  - first line corresponds to starting state (before refinement)
  - R-factors reported in percent
  - delta is Rfree-Rwork in percent
  - CLASH is all-atom Molprobity clashscore
  - ROTA is percent of side-chain rotamer outliers
  - RAMA is percent of Ramachandran plot outliers
  - CBET is number of Cbeta deviations
  - WEIGHT is relative weight between X-ray (or neutron) target and restraints
  - TARGETS: the values of X-ray (or neutron) and restraints target functions

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
22.98 27.98   4.99  1.831  24.928  0.415    0.057
25.92 30.56   4.64  1.096  26.823  0.012    0.068
23.74 28.72   4.98  1.388  25.662  0.052    0.059
22.19 27.08   4.89  3.000  26.853  0.207    0.051
21.68 26.78   5.09  4.047  27.578  0.415    0.048
21.49 26.82   5.34  4.828  27.871  0.622    0.047
21.41 26.88   5.47  5.461  28.150  0.830    0.046
21.37 26.90   5.53  6.009  28.355  1.037    0.046
21.34 26.90   5.56  6.455  28.517  1.245    0.046
21.32 26.84   5.52  7.010  28.774  1.452    0.045
21.31 26.92   5.61  7.378  28.932  1.659    0.045
21.31 26.94   5.63  7.805  29.084  1.867    0.045
21.30 26.98   5.68  7.953  29.143  2.074    0.045
  max suggested <Bi-Bj> for this run:   10.00
  max allowed Rfree-Rwork gap:   5.0
  range of equivalent Rfree:   0.0
Best ADP weight:    0.207
Accepted refinement result:
22.19 27.08   4.89  3.000  26.853  0.207    0.051

                min    max   mean <Bi,j>   iso aniso
   Overall:   14.36  65.92  26.85   3.00   810     0
   Protein:   14.36  65.92  26.14   3.00   723     0
   Water:     18.97  50.44  32.77    N/A    87     0
   Chain  A:  14.36  65.92  26.93    N/A   708     0
   Chain  T:  19.13  40.55  26.29    N/A   102     0
   Histogram:
       Values      Number of atoms
    14.36 - 19.52       147
    19.52 - 24.67       220
    24.67 - 29.83       206
    29.83 - 34.99       120
    34.99 - 40.14        74
    40.14 - 45.30        26
    45.30 - 50.45         5
    50.45 - 55.61         3
    55.61 - 60.76         7
    60.76 - 65.92         2


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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2219 r_free = 0.2708    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2218 r_free = 0.2705    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 3 *************************

|--(resolution: 1.60 - 28.77 A, n_refl.=11748 (all), 4.76  % free)------------|
|                                                                             |
| r_work= 0.2218 r_free= 0.2705 coordinate error (max.-lik. estimate): 0.15 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.051324                   |
| target function (ls_wunit_k1) not normalized (work): 574.262999             |
| target function (ls_wunit_k1) not normalized (free): 46.511937              |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.2240 0.2218 0.2705 n_refl.: 11748
       re-set all scales: r(all,work,free)=0.2902 0.2894 0.3109 n_refl.: 11748
         remove outliers: r(all,work,free)=0.2902 0.2894 0.3109 n_refl.: 11748
overall B=-0.08 to atoms: r(all,work,free)=0.2894 0.2886 0.3104 n_refl.: 11748
bulk-solvent and scaling: r(all,work,free)=0.2238 0.2217 0.2703 n_refl.: 11748
         remove outliers: r(all,work,free)=0.2238 0.2217 0.2703 n_refl.: 11748

======================== 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
 28.768-8.096    81.97    96     4 0.2200   292.180   282.230 0.922 1.000 0.316
  8.025-6.498    99.01    97     3 0.2579   224.188   219.270 0.885 1.001 0.319
  6.467-5.218    98.92   177     6 0.2111   254.841   247.053 0.942 1.000 0.319
  5.202-4.200    99.41   323    16 0.1736   323.484   317.681 0.988 1.001 0.307
  4.197-3.385    99.84   606    16 0.1784   290.333   285.670 1.005 1.000 0.230
  3.383-2.727   100.00  1105    62 0.2154   183.580   178.297 0.987 0.999 0.000
  2.726-2.198   100.00  2070   114 0.2241   116.304   112.261 1.022 0.998 0.000
  2.197-1.771   100.00  3892   188 0.2558    59.667    58.116 1.085 0.996 0.000
  1.771-1.601    99.60  2823   150 0.2872    27.833    26.386 0.975 0.994 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0047   b_overall=-0.2308 

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

  using refinement target ml 


============================ Update CDL restraints ============================


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

r_work=0.2217 r_free=0.2703
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
r_work=0.2217 r_free=0.2703

================== Update (add/remove/refine) ordered solvent =================

Start model:
  number           = 87     
  b_iso_min        = 18.89   (limit = 1.00)
  b_iso_max        = 50.36   (limit = 80.00)
  b_iso_mean       = 32.69               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.50    (limit = 1.80)
  dist_sol_mol_max = 4.29    (limit = 6.00)
Filtered:
  number           = 80     
  b_iso_min        = 18.89   (limit = 1.00)
  b_iso_max        = 50.36   (limit = 80.00)
  b_iso_mean       = 32.54               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.50    (limit = 1.80)
  dist_sol_mol_max = 4.29    (limit = 6.00)
Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 84          
Filter by distance & map next to the model:
   mapped sites are within: 0.770 - 4.215
   number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 53 from: 84
   mapped sites are within: 1.810 - 4.215
Just added new:
  number           = 133    
  b_iso_min        = 18.89   (limit = 1.00)
  b_iso_max        = 50.36   (limit = 80.00)
  b_iso_mean       = 29.96               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.82    (limit = 1.80)
  dist_sol_mol_max = 4.48    (limit = 6.00)
Filtered:
  number           = 116    
  b_iso_min        = 18.89   (limit = 1.00)
  b_iso_max        = 50.36   (limit = 80.00)
  b_iso_mean       = 30.53               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.82    (limit = 1.80)
  dist_sol_mol_max = 4.29    (limit = 6.00)
Number of peaks found at 2mFobs-DFmodel map (map cutoff=1.00 sigma)= 721         
Filter by distance & map next to the model:
   mapped sites are within: 0.031 - 0.500
   number of sites selected in [dist_min= 0.01, dist_max= 0.50]: 551 from: 721
   mapped sites are within: 0.031 - 0.500
ADP refinement (water only), start r_work=0.2383 r_free=0.2788
ADP refinement (water only), final r_work=0.2173 r_free=0.2602
Before filtering:
  number           = 116    
  b_iso_min        = 19.42   (limit = 1.00)
  b_iso_max        = 172.88  (limit = 80.00)
  b_iso_mean       = 43.10               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.56    (limit = 1.80)
  dist_sol_mol_max = 4.33    (limit = 6.00)
Before RSCC filtering:  103
After RSCC filtering:  92
2mFo-DFmodel map selection:
  number           = 92     
  b_iso_min        = 19.42   (limit = 1.00)
  b_iso_max        = 55.88   (limit = 80.00)
  b_iso_mean       = 36.41               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.85    (limit = 1.80)
  dist_sol_mol_max = 4.33    (limit = 6.00)
Final:
  number           = 92     
  b_iso_min        = 19.42   (limit = 1.00)
  b_iso_max        = 55.88   (limit = 80.00)
  b_iso_mean       = 36.41               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.85    (limit = 1.80)
  dist_sol_mol_max = 4.33    (limit = 6.00)

========================= Local real-space refinement =========================

Before:
  r_work=0.2197 r_free=0.2658
  rotamer outliers:  0.00 %
outliers start: 0
outliers after map fit: 0
tune up
outliers final: 0
Did it for: 14
After:
  r_work=0.2253 r_free=0.2641
  rotamer outliers:  0.00 %

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.579301              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.073139              wxu_scale = 1.000            wu = 1.000         |
|-----------------------------------------------------------------------------|


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

    R-FACTORS           RMSD     CLASH  RAMA  ROTA CBET WEIGHT    TARGETS
 work  free  delta  bonds  angl                                  data   restr
22.53 26.41   3.87  0.003   0.7    7.6   0.0   0.0    0   none  4.525  0.5008
22.83 26.19   3.37  0.002   0.5    5.6   0.0   0.0    0  0.125  4.528  0.0286
22.54 25.93   3.39  0.003   0.5    6.9   0.0   0.0    0  0.250  4.517  0.0304
22.27 25.65   3.38  0.003   0.6    6.9   0.0   0.0    0  0.500  4.506  0.0336
22.06 25.65   3.58  0.004   0.6    5.6   0.0   0.0    0  1.000  4.499  0.0388
21.79 25.62   3.83  0.006   0.8    5.6   0.0   0.0    0  2.000  4.490  0.0506
21.60 25.62   4.02  0.008   0.9    4.9   0.0   0.0    0  3.000  4.484  0.0642
21.49 25.72   4.23  0.009   1.0    5.6   0.0   0.0    0  4.000  4.480  0.0741
21.41 25.78   4.37  0.010   1.1    5.6   0.0   0.0    0  5.000  4.478  0.0861
21.32 25.77   4.45  0.011   1.1    5.6   0.0   0.0    0  6.000  4.475  0.0972
21.25 25.74   4.49  0.012   1.2    5.6   0.0   0.0    0  7.000  4.473  0.1084
21.18 25.90   4.72  0.013   1.3    5.6   0.0   0.0    0  8.000  4.473  0.1200
21.14 25.97   4.83  0.014   1.3    4.9   0.0   0.0    0  9.000  4.473  0.1333
21.09 26.02   4.94  0.015   1.4    4.9   0.0   0.0    0 10.000  4.472  0.1446
21.64 25.59   3.95  0.007   0.9    4.9   0.0   0.0    0  2.790  4.484  0.0605
Best XYZ weight:    2.790
Updating mask...
Accepted refinement result:
21.64 25.59   3.95  0.007   0.9    4.9   0.0   0.0    0  2.790  4.484  0.0605

Legend:
  - first line corresponds to starting state (before refinement)
  - R-factors reported in percent
  - delta is Rfree-Rwork in percent
  - CLASH is all-atom Molprobity clashscore
  - ROTA is percent of side-chain rotamer outliers
  - RAMA is percent of Ramachandran plot outliers
  - CBET is number of Cbeta deviations
  - WEIGHT is relative weight between X-ray (or neutron) target and restraints
  - TARGETS: the values of X-ray (or neutron) and restraints target functions

===================== Post-minimization rotamer correction ====================

Before:
  r_work=0.2164 r_free=0.2559
  rotamer outliers:  0.00 %
outliers start: 0
tune up
outliers final: 0
Did it for: 0
After:
  r_work=0.2164 r_free=0.2559
  rotamer outliers:  0.00 %

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
21.64 25.59   3.95  3.000  27.227  0.073    4.484
24.87 28.12   3.25  1.938  28.717  0.002    4.561
22.61 26.12   3.52  1.971  27.445  0.009    4.499
21.64 25.61   3.96  2.634  27.106  0.037    4.462
21.32 25.45   4.13  3.093  27.252  0.073    4.451
21.19 25.43   4.24  3.499  27.429  0.110    4.447
21.11 25.43   4.33  3.786  27.554  0.146    4.446
21.06 25.44   4.39  4.081  27.694  0.183    4.444
21.03 25.44   4.41  4.340  27.831  0.219    4.444
21.00 25.44   4.45  4.488  27.891  0.256    4.443
20.98 25.46   4.47  4.588  27.935  0.293    4.443
20.97 25.46   4.49  4.918  28.115  0.329    4.442
20.96 25.47   4.51  5.019  28.165  0.366    4.443
  max suggested <Bi-Bj> for this run:   10.00
  max allowed Rfree-Rwork gap:   5.0
  range of equivalent Rfree:   0.0
Best ADP weight:    0.110
Accepted refinement result:
21.19 25.43   4.24  3.499  27.429  0.110    4.447

                min    max   mean <Bi,j>   iso aniso
   Overall:   13.70  60.84  27.43   3.50   815     0
   Protein:   13.70  60.84  26.32   3.50   723     0
   Water:     20.47  52.71  36.18    N/A    92     0
   Chain  A:  13.70  60.84  26.27    N/A   628     0
   Chain  S:  20.47  52.71  36.18    N/A    92     0
   Chain  T:  18.62  41.62  26.64    N/A    95     0
   Histogram:
       Values      Number of atoms
    13.70 - 18.42        98
    18.42 - 23.13       207
    23.13 - 27.84       193
    27.84 - 32.56       114
    32.56 - 37.27        92
    37.27 - 41.98        50
    41.98 - 46.70        32
    46.70 - 51.41        17
    51.41 - 56.12         7
    56.12 - 60.84         5


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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2119 r_free = 0.2543             target_work(ml) = 4.447         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2119 r_free = 0.2542             target_work(ml) = 4.447         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.60 - 28.77 A, n_refl.=11748 (all), 4.76  % free)------------|
|                                                                             |
| r_work= 0.2119 r_free= 0.2542 coordinate error (max.-lik. estimate): 0.15 A |
|                                                                             |
| normalized target function (ml) (work): 4.446903                            |
| target function (ml) not normalized (work): 49756.397278                    |
| target function (ml) not normalized (free): 2541.910272                     |
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.2138 0.2119 0.2542 n_refl.: 11748
       re-set all scales: r(all,work,free)=0.2882 0.2881 0.2890 n_refl.: 11748
         remove outliers: r(all,work,free)=0.2882 0.2881 0.2890 n_refl.: 11748
overall B=-0.10 to atoms: r(all,work,free)=0.2871 0.2871 0.2884 n_refl.: 11748
bulk-solvent and scaling: r(all,work,free)=0.2135 0.2116 0.2546 n_refl.: 11748
         remove outliers: r(all,work,free)=0.2135 0.2116 0.2546 n_refl.: 11748

======================== 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
 28.768-8.096    81.97    96     4 0.2072   292.180   284.064 0.894 1.001 0.318
  8.025-6.498    99.01    97     3 0.2489   224.188   221.360 0.824 1.001 0.314
  6.467-5.218    98.92   177     6 0.2098   254.841   248.523 0.900 1.001 0.313
  5.202-4.200    99.41   323    16 0.1653   323.484   316.644 0.939 1.001 0.292
  4.197-3.385    99.84   606    16 0.1805   290.333   284.746 0.964 1.000 0.250
  3.383-2.727   100.00  1105    62 0.2197   183.580   177.041 0.949 1.000 0.000
  2.726-2.198   100.00  2070   114 0.2195   116.304   112.004 0.990 0.998 0.000
  2.197-1.771   100.00  3892   188 0.2279    59.667    58.224 1.054 0.996 0.000
  1.771-1.601    99.60  2823   150 0.2416    27.833    26.678 0.943 0.994 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9645   b_overall=-0.3566 

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

  using refinement target ml 


============================ Update CDL restraints ============================


============================= Setup riding H model ============================

  Before: r_work=0.2116 r_free=0.2546
  After: r_work=0.2116 r_free=0.2546

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

r_work=0.2116 r_free=0.2546
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
r_work=0.2116 r_free=0.2546

================== Update (add/remove/refine) ordered solvent =================

Start model:
  number           = 92     
  b_iso_min        = 20.36   (limit = 1.00)
  b_iso_max        = 52.61   (limit = 80.00)
  b_iso_mean       = 36.08               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.77    (limit = 1.80)
  dist_sol_mol_max = 4.21    (limit = 6.00)
Filtered:
  number           = 90     
  b_iso_min        = 20.36   (limit = 1.00)
  b_iso_max        = 50.77   (limit = 80.00)
  b_iso_mean       = 35.74               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.18    (limit = 1.80)
  dist_sol_mol_max = 4.21    (limit = 6.00)
Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 95          
Filter by distance & map next to the model:
   mapped sites are within: 0.791 - 4.400
   number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 39 from: 95
   mapped sites are within: 1.815 - 4.400
Just added new:
  number           = 129    
  b_iso_min        = 20.36   (limit = 1.00)
  b_iso_max        = 50.77   (limit = 80.00)
  b_iso_mean       = 32.86               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.82    (limit = 1.80)
  dist_sol_mol_max = 4.40    (limit = 6.00)
Filtered:
  number           = 115    
  b_iso_min        = 20.36   (limit = 1.00)
  b_iso_max        = 50.77   (limit = 80.00)
  b_iso_mean       = 33.67               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.83    (limit = 1.80)
  dist_sol_mol_max = 4.40    (limit = 6.00)
Number of peaks found at 2mFobs-DFmodel map (map cutoff=1.00 sigma)= 701         
Filter by distance & map next to the model:
   mapped sites are within: 0.018 - 0.498
   number of sites selected in [dist_min= 0.01, dist_max= 0.50]: 534 from: 701
   mapped sites are within: 0.018 - 0.498
ADP refinement (water only), start r_work=0.2255 r_free=0.2614
ADP refinement (water only), final r_work=0.2083 r_free=0.2481
Before filtering:
  number           = 115    
  b_iso_min        = 19.04   (limit = 1.00)
  b_iso_max        = 102.15  (limit = 80.00)
  b_iso_mean       = 42.12               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 0.45    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.74    (limit = 1.80)
  dist_sol_mol_max = 4.40    (limit = 6.00)
Before RSCC filtering:  108
After RSCC filtering:  97
2mFo-DFmodel map selection:
  number           = 97     
  b_iso_min        = 19.04   (limit = 1.00)
  b_iso_max        = 60.30   (limit = 80.00)
  b_iso_mean       = 38.27               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.83    (limit = 1.80)
  dist_sol_mol_max = 4.40    (limit = 6.00)
Final:
  number           = 97     
  b_iso_min        = 19.04   (limit = 1.00)
  b_iso_max        = 60.30   (limit = 80.00)
  b_iso_mean       = 38.27               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.83    (limit = 1.80)
  dist_sol_mol_max = 4.40    (limit = 6.00)

========================= Local real-space refinement =========================

Before:
  r_work=0.2103 r_free=0.2527
  rotamer outliers:  0.00 %
outliers start: 0
outliers after map fit: 0
tune up
outliers final: 0
Did it for: 14
After:
  r_work=0.2136 r_free=0.2520
  rotamer outliers:  0.00 %

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.024015              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.107884              wxu_scale = 1.000            wu = 1.000         |
|-----------------------------------------------------------------------------|


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

    R-FACTORS           RMSD     CLASH  RAMA  ROTA CBET WEIGHT    TARGETS
 work  free  delta  bonds  angl                                  data   restr
21.36 25.20   3.84  0.007   0.9    6.9   0.0   0.0    0   none  4.460  0.0757
22.00 25.43   3.43  0.003   0.5    4.9   0.0   0.0    0  0.125  4.479  0.0288
21.74 25.29   3.56  0.003   0.5    4.9   0.0   0.0    0  0.250  4.468  0.0300
21.43 25.34   3.91  0.003   0.6    4.9   0.0   0.0    0  0.500  4.459  0.0326
21.17 25.41   4.24  0.004   0.6    4.9   0.0   0.0    0  1.000  4.453  0.0369
20.87 25.68   4.81  0.005   0.8    4.9   0.0   0.0    0  2.000  4.447  0.0477
20.73 25.80   5.08  0.007   0.9    4.9   0.0   0.0    0  3.000  4.443  0.0586
20.61 25.86   5.25  0.008   1.0    4.9   0.0   0.0    0  4.000  4.440  0.0691
20.54 25.97   5.43  0.010   1.1    4.9   0.0   0.0    0  5.000  4.439  0.0818
20.47 25.98   5.51  0.011   1.2    4.2   0.0   0.0    0  6.000  4.436  0.0931
20.41 26.00   5.59  0.012   1.2    4.2   0.0   0.0    0  7.000  4.434  0.1042
20.37 26.06   5.69  0.013   1.3    5.6   0.0   0.0    0  8.000  4.433  0.1151
20.33 26.06   5.74  0.014   1.4    5.6   0.0   0.0    0  9.000  4.432  0.1268
20.28 26.05   5.77  0.015   1.4    5.6   0.0   0.0    0 10.000  4.430  0.1394
20.78 25.68   4.90  0.006   0.8    4.9   0.0   0.0    0  2.512  4.443  0.0534
Best XYZ weight:    0.250
Updating mask...
Accepted refinement result:
21.74 25.29   3.56  0.003   0.5    4.9   0.0   0.0    0  0.250  4.468  0.0300

Legend:
  - first line corresponds to starting state (before refinement)
  - R-factors reported in percent
  - delta is Rfree-Rwork in percent
  - CLASH is all-atom Molprobity clashscore
  - ROTA is percent of side-chain rotamer outliers
  - RAMA is percent of Ramachandran plot outliers
  - CBET is number of Cbeta deviations
  - WEIGHT is relative weight between X-ray (or neutron) target and restraints
  - TARGETS: the values of X-ray (or neutron) and restraints target functions

===================== Post-minimization rotamer correction ====================

Before:
  r_work=0.2174 r_free=0.2529
  rotamer outliers:  0.00 %
outliers start: 0
tune up
outliers final: 0
Did it for: 0
After:
  r_work=0.2174 r_free=0.2529
  rotamer outliers:  0.00 %

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


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

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
21.74 25.29   3.56  3.499  27.641  0.108    4.468
24.29 27.15   2.86  1.962  28.721  0.003    4.555
22.68 25.81   3.13  2.140  27.846  0.013    4.502
21.96 25.52   3.56  2.979  27.621  0.054    4.476
21.68 25.38   3.70  3.743  27.833  0.108    4.467
21.57 25.42   3.85  4.228  28.023  0.162    4.465
21.50 25.43   3.93  4.739  28.225  0.216    4.463
21.47 25.39   3.92  5.043  28.345  0.270    4.461
21.45 25.44   3.99  5.181  28.388  0.324    4.462
21.42 25.43   4.01  5.591  28.541  0.378    4.460
21.42 25.44   4.02  5.632  28.549  0.432    4.461
21.40 25.44   4.04  5.929  28.648  0.485    4.460
21.40 25.43   4.03  6.099  28.704  0.539    4.460
  max suggested <Bi-Bj> for this run:   10.00
  max allowed Rfree-Rwork gap:   5.0
  range of equivalent Rfree:   0.0
Best ADP weight:    0.108
Accepted refinement result:
21.68 25.38   3.70  3.743  27.833  0.108    4.467

                min    max   mean <Bi,j>   iso aniso
   Overall:   13.33  59.25  27.83   3.74   820     0
   Protein:   13.33  59.25  26.58   3.74   723     0
   Water:     20.48  55.30  37.14    N/A    97     0
   Chain  A:  13.33  59.25  26.53    N/A   628     0
   Chain  S:  20.48  55.30  37.14    N/A    97     0
   Chain  T:  18.65  44.15  26.91    N/A    95     0
   Histogram:
       Values      Number of atoms
    13.33 - 17.93        75
    17.93 - 22.52       203
    22.52 - 27.11       178
    27.11 - 31.70       143
    31.70 - 36.29        73
    36.29 - 40.88        68
    40.88 - 45.48        37
    45.48 - 50.07        24
    50.07 - 54.66        12
    54.66 - 59.25         7


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

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2168 r_free = 0.2538             target_work(ml) = 4.467         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2168 r_free = 0.2540             target_work(ml) = 4.467         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

======================= ordered solvent: final clean up =======================

Start model:
  number           = 97     
  b_iso_min        = 20.48   (limit = 1.00)
  b_iso_max        = 55.30   (limit = 80.00)
  b_iso_mean       = 37.14               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.20    (limit = 1.80)
  dist_sol_mol_max = 4.39    (limit = 6.00)
Filtered:
  number           = 96     
  b_iso_min        = 20.48   (limit = 1.00)
  b_iso_max        = 55.30   (limit = 80.00)
  b_iso_mean       = 36.97               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.20    (limit = 1.80)
  dist_sol_mol_max = 4.39    (limit = 6.00)
Number of peaks found at 2mFobs-DFmodel map (map cutoff=1.00 sigma)= 714         
Filter by distance & map next to the model:
   mapped sites are within: 0.007 - 0.500
   number of sites selected in [dist_min= 0.01, dist_max= 0.50]: 544 from: 714
   mapped sites are within: 0.020 - 0.500
Before filtering:
  number           = 96     
  b_iso_min        = 20.48   (limit = 1.00)
  b_iso_max        = 55.30   (limit = 80.00)
  b_iso_mean       = 36.97               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.15    (limit = 1.80)
  dist_sol_mol_max = 4.39    (limit = 6.00)
Before RSCC filtering:  95
After RSCC filtering:  92
2mFo-DFmodel map selection:
  number           = 92     
  b_iso_min        = 20.48   (limit = 1.00)
  b_iso_max        = 55.30   (limit = 80.00)
  b_iso_mean       = 36.56               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.15    (limit = 1.80)
  dist_sol_mol_max = 4.39    (limit = 6.00)
Final:
  number           = 92     
  b_iso_min        = 20.48   (limit = 1.00)
  b_iso_max        = 55.30   (limit = 80.00)
  b_iso_mean       = 36.56               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.15    (limit = 1.80)
  dist_sol_mol_max = 4.39    (limit = 6.00)

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

|--(resolution: 1.60 - 28.77 A, n_refl.=11748 (all), 4.76  % free)------------|
|                                                                             |
| r_work= 0.2173 r_free= 0.2499 coordinate error (max.-lik. estimate): 0.15 A |
|                                                                             |
| normalized target function (ml) (work): 4.463325                            |
| target function (ml) not normalized (work): 49940.145505                    |
| target function (ml) not normalized (free): 2531.598230                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 28.7731 -  2.5413 0.99   2938  136 0.2042 0.2322      5.4243      5.4321|
|  2:  2.5413 -  2.0173 1.00   2785  149 0.2335 0.2470      4.7543      4.8106|
|  3:  2.0173 -  1.7623 1.00   2756  131 0.2306 0.2961      4.0681      4.2028|
|  4:  1.7623 -  1.6012 1.00   2710  143 0.2503 0.3165      3.5244      3.6747|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 28.7731 -  2.5413  2938   136  0.85  19.17   1.00     1.17       6339.35|
|  2:  2.5413 -  2.0173  2785   149  0.77  28.50   1.03     1.13       2709.41|
|  3:  2.0173 -  1.7623  2756   131  0.78  27.91   0.99     1.10        673.01|
|  4:  1.7623 -  1.6012  2710   143  0.77  29.17   1.01     1.06        230.13|
|alpha:            min =        1.06 max =            1.17 mean =         1.12|
|beta:             min =      230.13 max =         6339.35 mean =      2560.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.79|
|phase err.(work): min =        0.00 max =           89.99 mean =        26.07|
|phase err.(test): min =        0.00 max =           88.36 mean =        26.18|
|-----------------------------------------------------------------------------|

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


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

                   start: r(all,work,free)=0.2188 0.2173 0.2499 n_refl.: 11748
       re-set all scales: r(all,work,free)=0.2927 0.2937 0.2758 n_refl.: 11748
         remove outliers: r(all,work,free)=0.2927 0.2937 0.2758 n_refl.: 11748
overall B=-0.15 to atoms: r(all,work,free)=0.2912 0.2921 0.2753 n_refl.: 11748
bulk-solvent and scaling: r(all,work,free)=0.2187 0.2172 0.2508 n_refl.: 11748
         remove outliers: r(all,work,free)=0.2187 0.2172 0.2508 n_refl.: 11748

======================== 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
 28.768-8.096    81.97    96     4 0.2063   292.180   280.068 0.923 1.000 0.312
  8.025-6.498    99.01    97     3 0.2616   224.188   221.373 0.844 1.000 0.295
  6.467-5.218    98.92   177     6 0.2196   254.841   245.520 0.912 1.000 0.282
  5.202-4.200    99.41   323    16 0.1797   323.484   315.415 0.963 1.000 0.277
  4.197-3.385    99.84   606    16 0.1877   290.333   285.481 0.992 1.000 0.235
  3.383-2.727   100.00  1105    62 0.2167   183.580   178.002 0.988 1.000 0.000
  2.726-2.198   100.00  2070   114 0.2220   116.304   112.304 1.028 0.999 0.000
  2.197-1.771   100.00  3892   188 0.2368    59.667    58.362 1.096 0.998 0.000
  1.771-1.601    99.60  2823   150 0.2523    27.833    26.684 0.974 0.998 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=0.9964   b_overall=-0.4513 

================= 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_wat: ordered solvent update (add / remove)                            
1_occ: refinement of occupancies                                        
------------------------------------------------------------------------
 stage r-work r-free bonds angles b_min b_max b_ave n_water shift
      0    : 0.2749 0.3123 0.014  1.293  11.4  54.3  23.8  87      0.000
      1_bss: 0.2268 0.2789 0.014  1.293  12.6  55.4  24.9  87      0.000
1_settarget: 0.2268 0.2789 0.014  1.293  12.6  55.4  24.9  87      0.000
      1_nqh: 0.2269 0.2789 0.014  1.293  12.6  55.4  24.9  87      0.006
   1_weight: 0.2269 0.2789 0.014  1.293  12.6  55.4  24.9  87      0.006
   1_xyzrec: 0.2298 0.2798 0.003  0.616  12.6  55.4  24.9  87      0.065
      1_adp: 0.2219 0.2708 0.003  0.616  14.4  65.9  26.9  87      0.065
      1_occ: 0.2218 0.2705 0.003  0.616  14.4  65.9  26.9  87      0.065
      2_bss: 0.2217 0.2703 0.003  0.616  14.3  65.8  26.8  87      0.065
2_settarget: 0.2217 0.2703 0.003  0.616  14.3  65.8  26.8  87      0.065
2_updatecdl: 0.2217 0.2703 0.003  0.621  14.3  65.8  26.8  87      0.065
      2_nqh: 0.2217 0.2703 0.003  0.621  14.3  65.8  26.8  87      0.065
      2_sol: 0.2197 0.2658 0.003  0.621  14.3  65.8  27.2  92       n/a
  2_realsrl: 0.2253 0.2641 0.003  0.688  14.3  65.8  27.2  92       n/a
   2_weight: 0.2253 0.2641 0.003  0.688  14.3  65.8  27.2  92       n/a
   2_xyzrec: 0.2164 0.2559 0.007  0.858  14.3  65.8  27.2  92       n/a
 2_realsrl2: 0.2164 0.2559 0.007  0.858  14.3  65.8  27.2  92       n/a
      2_adp: 0.2119 0.2543 0.007  0.858  13.7  60.8  27.4  92       n/a
      2_occ: 0.2119 0.2542 0.007  0.858  13.7  60.8  27.4  92       n/a
      3_bss: 0.2116 0.2546 0.007  0.858  13.6  60.7  27.3  92       n/a
3_settarget: 0.2116 0.2546 0.007  0.858  13.6  60.7  27.3  92       n/a
3_updatecdl: 0.2116 0.2546 0.007  0.864  13.6  60.7  27.3  92       n/a
    3_setrh: 0.2116 0.2546 0.007  0.864  13.6  60.7  27.3  92       n/a
      3_nqh: 0.2116 0.2546 0.007  0.864  13.6  60.7  27.3  92       n/a
      3_sol: 0.2103 0.2527 0.007  0.864  13.6  60.7  27.6  97       n/a
  3_realsrl: 0.2136 0.2520 0.007  0.868  13.6  60.7  27.6  97       n/a
   3_weight: 0.2136 0.2520 0.007  0.868  13.6  60.7  27.6  97       n/a
   3_xyzrec: 0.2174 0.2529 0.003  0.542  13.6  60.7  27.6  97       n/a
 3_realsrl2: 0.2174 0.2529 0.003  0.542  13.6  60.7  27.6  97       n/a
      3_adp: 0.2168 0.2538 0.003  0.542  13.3  59.3  27.8  97       n/a
      3_occ: 0.2168 0.2540 0.003  0.542  13.3  59.3  27.8  97       n/a
        end: 0.2172 0.2508 0.003  0.542  13.2  59.1  27.6  92       n/a
------------------------------------------------------------------------

CPU time actual refinement: 63.43


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

Writing refined structure to PDB file:
  /Users/pafonine/Desktop/QR2019April/low_high_res_pair/3ds1_refine_001.pdb
n_use            =  815
n_use_u_iso      =  815
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
total number of scatterers =  815

Writing refined structure to CIF file:
  /Users/pafonine/Desktop/QR2019April/low_high_res_pair/3ds1_refine_001.cif
Writing default parameters for subsequent refinement:
  /Users/pafonine/Desktop/QR2019April/low_high_res_pair/3ds1_refine_002.def


=============================== Detailed timings ==============================

  Micro-tasks:
    mask                            = 0.00   
    f_calc                          = 0.00   
    alpha_beta                      = 0.09   
    target                          = 0.05   
    gradients_wrt_atomic_parameters = 0.00   
    fmodel                         = 0.00   
    r_factors                      = 0.00   
    phase_errors                   = 0.29   
    foms                           = 0.00   
    TOTAL for micro-tasks          = 0.43   
NUMBER OF MASK CALCS=  0
Total CPU time: 75.57 seconds
from_scatterers_fft:    311 calls, 6.53 s
gradients_fft:          219 calls, 4.68 s

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

# Date 2019-04-19 Time 09:19:38 CST +0800 (1555636778.43 s)
wall clock time: 109.80 s

Start R-work = 0.2268, R-free = 0.2789
Final R-work = 0.2172, R-free = 0.2508