# Date 2008-01-16 Time 04:57:42 PST -0800 (1200488262.07 s)
#phil __OFF__

Command line arguments: "../536.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2576
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 536

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  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
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.6953, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.99033
Completeness in resolution range: 0.967071
Completeness with d_max=infinity: 0.964073

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9985
                             d_min =   1.9903

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.99033
Completeness in resolution range: 0.967071
Completeness with d_max=infinity: 0.964073

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9990 -  4.2584 [2138/2162]  1920   218  10.2%
  bin  2:  4.2584 -  3.3929 [2038/2058]  1840   198   9.7%
  bin  3:  3.3929 -  2.9678 [2018/2037]  1815   203  10.1%
  bin  4:  2.9678 -  2.6981 [1981/2011]  1777   204  10.3%
  bin  5:  2.6981 -  2.5057 [2002/2021]  1806   196   9.8%
  bin  6:  2.5057 -  2.3586 [1978/2003]  1779   199  10.1%
  bin  7:  2.3586 -  2.2409 [1959/1987]  1765   194   9.9%
  bin  8:  2.2409 -  2.1436 [1962/1998]  1766   196  10.0%
  bin  9:  2.1436 -  2.0613 [1949/1991]  1757   192   9.9%
  bin 10:  2.0613 -  1.9903 [1564/1988]  1405   159  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_536/model_refine_data.mtz


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

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

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 14
        2.35 -     2.98: 1820
        2.98 -     3.62: 4579
        3.62 -     4.26: 9109
        4.26 -     4.90: 12701
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.708 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.830 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.953 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.137 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28218 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

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


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


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

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


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


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


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

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
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
n_anisotropic_flag =  0
total number of scatterers =  2823

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

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

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

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_536/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_536/model_refine_001.geo

CPU time processing inputs: 9.70


============================ 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 = 69.89875 46.69535 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


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


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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3104   r_free= 0.3065   ksol= 0.00   Bsol= 0.00   scale= 0.974    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.009519                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7494 0.99   1389  152 0.2722 0.2658      6.3292      6.2322|
|  2:  4.7494 -  3.7897 0.99   1318  153 0.2322 0.2484      6.3545      6.3994|
|  3:  3.7897 -  3.3166 0.99   1300  141 0.2655 0.2482      6.3091      6.3155|
|  4:  3.3166 -  3.0160 0.99   1308  142 0.2879 0.3168      6.2072      6.2656|
|  5:  3.0160 -  2.8014 0.99   1278  144 0.3201 0.2624      6.0686      5.9425|
|  6:  2.8014 -  2.6371 0.99   1287  143 0.3129 0.3586      5.9668      5.9585|
|  7:  2.6371 -  2.5057 0.99   1278  144 0.3144 0.3029      5.9386      5.9037|
|  8:  2.5057 -  2.3971 0.98   1269  138 0.3554 0.3124       5.973      5.9296|
|  9:  2.3971 -  2.3052 0.98   1267  143 0.3415 0.3363       5.895      5.8554|
| 10:  2.3052 -  2.2259 1.00   1275  142 0.3679 0.3425      5.9265      5.8363|
| 11:  2.2259 -  2.1565 0.97   1251  134 0.3672 0.3809      5.8426      5.9108|
| 12:  2.1565 -  2.0950 0.98   1244  142 0.3673 0.3391      5.7954      5.8277|
| 13:  2.0950 -  2.0400 1.00   1267  135 0.3706 0.3523      5.7026      5.6636|
| 14:  2.0400 -  1.9903 0.70    899  106 0.3514 0.3826      5.6589      5.6013|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7494  1389   152  0.82  23.57   0.86     0.83      35897.26|
|  2:  4.7494 -  3.7897  1318   153  0.86  20.44   0.98     0.93      41198.28|
|  3:  3.7897 -  3.3166  1300   141  0.83  23.68   0.99     0.96      39725.52|
|  4:  3.3166 -  3.0160  1308   142  0.81  26.03   0.99     0.94      34136.31|
|  5:  3.0160 -  2.8014  1278   144  0.76  30.52   1.01     0.91      26824.99|
|  6:  2.8014 -  2.6371  1287   143  0.75  31.15   0.99     0.89      24045.22|
|  7:  2.6371 -  2.5057  1278   144  0.74  32.22   1.02     0.90      22611.97|
|  8:  2.5057 -  2.3971  1269   138  0.73  32.68   0.99     0.91      21615.02|
|  9:  2.3971 -  2.3052  1267   143  0.74  32.37   1.03     0.93      20282.38|
| 10:  2.3052 -  2.2259  1275   142  0.71  34.56   1.05     0.93      19540.73|
| 11:  2.2259 -  2.1565  1251   134  0.70  35.66   1.02     0.96      19881.26|
| 12:  2.1565 -  2.0950  1244   142  0.69  36.92   1.05     0.96      19229.39|
| 13:  2.0950 -  2.0400  1267   135  0.67  38.49   1.03     0.92      17068.92|
| 14:  2.0400 -  1.9903   899   106  0.68  37.50   1.07     0.84      13749.32|
|alpha:            min =        0.83 max =            0.96 mean =         0.92|
|beta:             min =    13749.32 max =        41198.28 mean =     25831.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.75|
|phase err.(work): min =        0.00 max =           89.97 mean =        30.88|
|phase err.(test): min =        0.00 max =           89.79 mean =        30.75|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.062818              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.353   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.527379              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.218   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.708 -  2.027:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.027 -  2.346:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.346 -  2.665:       78 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.665 -  2.985:     1742 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.985 -  3.304:     1875 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.304 -  3.623:     2704 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.623 -  3.942:     4696 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.942 -  4.261:     4413 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.261 -  4.581:     5810 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.581 -  4.900:     6891 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.708 |       0.204 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3104   r_free= 0.3065   ksol= 0.00   Bsol= 0.00   scale= 0.974    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.009519                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2942   r_free= 0.2909   ksol= 0.33   Bsol= 50.00   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-2.18,2.52,-0.00,0.00,0.00); trace/3= -0.87                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.980605                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.336309              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.169   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.300848              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.030   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2942      final r-factor (work) = 0.1594          |
| start r-factor (free) = 0.2909      final r-factor (free) = 0.1831          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1413 = 4.34 * 0.50 * 5.9851 + 1.00 * 0.1646                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3256 = 4.34 * 0.50 * 5.6528 + 1.00 * 0.0694                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1594      final r-factor (work) = 0.1473          |
| start r-factor (free) = 0.1831      final r-factor (free) = 0.1862          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7071 = 0.30 * 1.00 * 5.6528 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6695 = 0.30 * 1.00 * 5.3396 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.64   16.44    None  None   None       |
|    all(noH): 2823   0      0.00    79.64   16.44    None  None   None       |
|    Sol.    : 438    0      5.93    62.98   37.44    None  None   None       |
|    Mac.    : 2385   0      0.00    79.64   12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.964:  490   |   5:    39.819 -  47.783:  110        |
|      1:     7.964 -  15.928: 1442   |   6:    47.783 -  55.747:   77        |
|      2:    15.928 -  23.891:  397   |   7:    55.747 -  63.710:   35        |
|      3:    23.891 -  31.855:  151   |   8:    63.710 -  71.674:    0        |
|      4:    31.855 -  39.819:  120   |   9:    71.674 -  79.638:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1473 r_free = 0.1862             target_work(ml) = 5.350         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1469 r_free = 0.1858             target_work(ml) = 5.348         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1469   r_free= 0.1858   ksol= 0.33   Bsol= 50.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-2.18,2.52,-0.00,0.00,0.00); trace/3= -0.87                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.348221                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1448   r_free= 0.1831   ksol= 0.33   Bsol= 57.73   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.17,-2.64,-0.14,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.338973                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.370091              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.239  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.348303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.946   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1448      final r-factor (work) = 0.1272          |
| start r-factor (free) = 0.1831      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7356 = 1.37 * 0.50 * 5.3517 + 1.00 * 0.0694                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6660 = 1.37 * 0.50 * 5.2790 + 1.00 * 0.0497                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1272      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0315 = 0.35 * 1.00 * 5.2790 + 1.00 * 0.1928                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8195 = 0.35 * 1.00 * 5.1994 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.73    69.84   16.95    None  None   None       |
|    all(noH): 2823   0      0.73    69.84   16.95    None  None   None       |
|    Sol.    : 438    0      6.51    69.84   39.30    None  None   None       |
|    Mac.    : 2385   0      0.73    68.59   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.726 -   7.637:  470   |   5:    35.282 -  42.193:  102        |
|      1:     7.637 -  14.548: 1339   |   6:    42.193 -  49.104:   87        |
|      2:    14.548 -  21.459:  426   |   7:    49.104 -  56.015:   85        |
|      3:    21.459 -  28.371:  145   |   8:    56.015 -  62.927:   50        |
|      4:    28.371 -  35.282:  100   |   9:    62.927 -  69.838:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1218 r_free = 0.1619             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1618             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1618   ksol= 0.33   Bsol= 57.73   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.17,-2.64,-0.14,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.197167                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1616   ksol= 0.33   Bsol= 57.73   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.40,-0.42,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.196174                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.629424              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.167  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.148266              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.946  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1558          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2855 = 1.63 * 0.50 * 5.1992 + 1.00 * 0.0497                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2646 = 1.63 * 0.50 * 5.1678 + 1.00 * 0.0544                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1145      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1558      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9425 = 1.15 * 1.00 * 5.1678 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9164 = 1.15 * 1.00 * 5.1438 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.45    86.08   17.13    None  None   None       |
|    all(noH): 2823   0      0.45    86.08   17.13    None  None   None       |
|    Sol.    : 438    0      5.95    79.46   40.56    None  None   None       |
|    Mac.    : 2385   0      0.45    86.08   12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.454 -   9.016:  846   |   5:    43.265 -  51.827:   96        |
|      1:     9.016 -  17.578: 1220   |   6:    51.827 -  60.390:   80        |
|      2:    17.578 -  26.141:  277   |   7:    60.390 -  68.952:   38        |
|      3:    26.141 -  34.703:  122   |   8:    68.952 -  77.514:   21        |
|      4:    34.703 -  43.265:  117   |   9:    77.514 -  86.076:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1556             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1131 r_free = 0.1557             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1557   ksol= 0.33   Bsol= 57.73   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.40,-0.42,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.144160                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1553   ksol= 0.33   Bsol= 57.73   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.16,-0.40,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.143027                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.172190              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.691  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.092560              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.604  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6414 = 2.17 * 0.50 * 5.1442 + 1.00 * 0.0544                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6299 = 2.17 * 0.50 * 5.1269 + 1.00 * 0.0616                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1090      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4843 = 0.09 * 1.00 * 5.1269 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4823 = 0.09 * 1.00 * 5.1440 + 1.00 * 0.0062                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.09    73.53   15.95    None  None   None       |
|    all(noH): 2823   0      2.09    73.53   15.95    None  None   None       |
|    Sol.    : 438    0      6.19    72.90   35.43    None  None   None       |
|    Mac.    : 2385   0      2.09    73.53   12.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.092 -   9.236:  871   |   5:    37.813 -  44.958:  109        |
|      1:     9.236 -  16.380: 1163   |   6:    44.958 -  52.102:   78        |
|      2:    16.380 -  23.525:  298   |   7:    52.102 -  59.246:   28        |
|      3:    23.525 -  30.669:  123   |   8:    59.246 -  66.391:   10        |
|      4:    30.669 -  37.813:  136   |   9:    66.391 -  73.535:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1541             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1540             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1540   ksol= 0.33   Bsol= 57.73   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.16,-0.40,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136399                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1540   ksol= 0.33   Bsol= 57.73   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.16,-0.40,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136501                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.067089              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.600  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.159764              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 166.931  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9497 = 3.07 * 0.50 * 5.1437 + 1.00 * 0.0616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9280 = 3.07 * 0.50 * 5.1224 + 1.00 * 0.0726                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8245 = 0.16 * 1.00 * 5.1224 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8242 = 0.16 * 1.00 * 5.1178 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.72    73.05   15.89    None  None   None       |
|    all(noH): 2823   0      1.72    73.05   15.89    None  None   None       |
|    Sol.    : 438    0      6.19    72.06   35.81    None  None   None       |
|    Mac.    : 2385   0      1.72    73.05   12.24    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.723 -   8.856:  817   |   5:    37.388 -  44.521:  107        |
|      1:     8.856 -  15.989: 1182   |   6:    44.521 -  51.653:   89        |
|      2:    15.989 -  23.122:  320   |   7:    51.653 -  58.786:   37        |
|      3:    23.122 -  30.255:  125   |   8:    58.786 -  65.919:   12        |
|      4:    30.255 -  37.388:  128   |   9:    65.919 -  73.052:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1080 r_free = 0.1543             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1080 r_free = 0.1543             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1543   ksol= 0.33   Bsol= 57.73   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.16,-0.40,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.118088                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7494 0.99   1389  152 0.1013 0.1282      5.4015      5.5288|
|  2:  4.7494 -  3.7897 0.99   1318  153 0.0870 0.1161      5.4576      5.6679|
|  3:  3.7897 -  3.3166 0.99   1300  141 0.1040 0.1489      5.4684      5.8388|
|  4:  3.3166 -  3.0160 0.99   1308  142 0.1169 0.1545      5.4168      5.5567|
|  5:  3.0160 -  2.8014 0.99   1278  144 0.1268 0.1620      5.2936      5.5357|
|  6:  2.8014 -  2.6371 0.99   1287  143 0.1151 0.2009       5.185      5.4869|
|  7:  2.6371 -  2.5057 0.99   1278  144 0.1223 0.1577      5.1485      5.3213|
|  8:  2.5057 -  2.3971 0.98   1269  138 0.1103 0.1608      5.0444      5.2969|
|  9:  2.3971 -  2.3052 0.98   1267  143 0.1118 0.1804       5.005      5.2787|
| 10:  2.3052 -  2.2259 1.00   1275  142 0.1086 0.1706      4.9306       5.184|
| 11:  2.2259 -  2.1565 0.97   1251  134 0.1078 0.1607      4.9029      5.1885|
| 12:  2.1565 -  2.0950 0.98   1244  142 0.1068 0.1685      4.8366      5.2362|
| 13:  2.0950 -  2.0400 1.00   1267  135 0.1020 0.1632      4.7391      4.9954|
| 14:  2.0400 -  1.9903 0.70    899  106 0.0925 0.1604      4.6052      4.8761|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7494  1389   152  0.94   9.29   0.98     0.95       7323.76|
|  2:  4.7494 -  3.7897  1318   153  0.95   7.96   1.01     1.00       9422.39|
|  3:  3.7897 -  3.3166  1300   141  0.94  10.97   1.01     1.01      10173.67|
|  4:  3.3166 -  3.0160  1308   142  0.92  12.96   1.00     0.98       9592.43|
|  5:  3.0160 -  2.8014  1278   144  0.91  14.98   0.99     0.95       7689.92|
|  6:  2.8014 -  2.6371  1287   143  0.90  15.68   0.98     0.95       6766.68|
|  7:  2.6371 -  2.5057  1278   144  0.91  15.34   0.98     0.95       6066.56|
|  8:  2.5057 -  2.3971  1269   138  0.91  14.57   0.99     0.97       5104.58|
|  9:  2.3971 -  2.3052  1267   143  0.91  14.79   1.00     0.96       4821.45|
| 10:  2.3052 -  2.2259  1275   142  0.90  15.35   0.99     0.96       4136.12|
| 11:  2.2259 -  2.1565  1251   134  0.91  15.36   0.99     0.96       4145.11|
| 12:  2.1565 -  2.0950  1244   142  0.91  15.01   1.00     0.99       3681.14|
| 13:  2.0950 -  2.0400  1267   135  0.91  14.90   0.99     0.98       3084.35|
| 14:  2.0400 -  1.9903   899   106  0.93  13.07   0.97     0.93       2275.01|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2275.01 max =        10173.67 mean =      6139.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.55|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.08|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1542   ksol= 0.33   Bsol= 57.67   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.98,-0.26,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1542   ksol= 0.33   Bsol= 57.67   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.98,-0.26,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118122                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7494 0.99   1389  152 0.1013 0.1283      5.4019      5.5296|
|  2:  4.7494 -  3.7897 0.99   1318  153 0.0871 0.1161      5.4579      5.6679|
|  3:  3.7897 -  3.3166 0.99   1300  141 0.1040 0.1490      5.4685      5.8393|
|  4:  3.3166 -  3.0160 0.99   1308  142 0.1169 0.1545      5.4169      5.5568|
|  5:  3.0160 -  2.8014 0.99   1278  144 0.1268 0.1619      5.2935      5.5353|
|  6:  2.8014 -  2.6371 0.99   1287  143 0.1151 0.2010       5.185      5.4872|
|  7:  2.6371 -  2.5057 0.99   1278  144 0.1222 0.1577      5.1486      5.3213|
|  8:  2.5057 -  2.3971 0.98   1269  138 0.1103 0.1607      5.0446      5.2969|
|  9:  2.3971 -  2.3052 0.98   1267  143 0.1117 0.1803      5.0048      5.2786|
| 10:  2.3052 -  2.2259 1.00   1275  142 0.1086 0.1706      4.9305       5.184|
| 11:  2.2259 -  2.1565 0.97   1251  134 0.1078 0.1606      4.9027      5.1879|
| 12:  2.1565 -  2.0950 0.98   1244  142 0.1068 0.1683      4.8363      5.2354|
| 13:  2.0950 -  2.0400 1.00   1267  135 0.1019 0.1635       4.739      4.9964|
| 14:  2.0400 -  1.9903 0.70    899  106 0.0925 0.1602      4.6056      4.8757|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7494  1389   152  0.94   9.30   0.98     0.95       7334.85|
|  2:  4.7494 -  3.7897  1318   153  0.95   7.97   1.01     1.00       9431.46|
|  3:  3.7897 -  3.3166  1300   141  0.94  10.97   1.02     1.01      10178.92|
|  4:  3.3166 -  3.0160  1308   142  0.92  12.97   1.00     0.98       9593.89|
|  5:  3.0160 -  2.8014  1278   144  0.91  14.98   0.99     0.96       7690.22|
|  6:  2.8014 -  2.6371  1287   143  0.90  15.67   0.98     0.95       6764.34|
|  7:  2.6371 -  2.5057  1278   144  0.91  15.34   0.98     0.96       6067.60|
|  8:  2.5057 -  2.3971  1269   138  0.91  14.57   0.99     0.97       5104.62|
|  9:  2.3971 -  2.3052  1267   143  0.91  14.79   1.00     0.97       4822.16|
| 10:  2.3052 -  2.2259  1275   142  0.90  15.34   1.00     0.96       4133.04|
| 11:  2.2259 -  2.1565  1251   134  0.91  15.35   1.00     0.96       4141.96|
| 12:  2.1565 -  2.0950  1244   142  0.91  15.00   1.01     0.99       3678.75|
| 13:  2.0950 -  2.0400  1267   135  0.91  14.90   1.00     0.99       3084.29|
| 14:  2.0400 -  1.9903   899   106  0.93  13.08   0.97     0.94       2276.36|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2276.36 max =        10178.92 mean =      6140.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.55|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.08|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.66    72.99   15.83    None  None   None       |
|    all(noH): 2823   0      1.66    72.99   15.83    None  None   None       |
|    Sol.    : 438    0      6.13    72.00   35.75    None  None   None       |
|    Mac.    : 2385   0      1.66    72.99   12.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.662 -   8.795:  817   |   5:    37.326 -  44.459:  107        |
|      1:     8.795 -  15.927: 1182   |   6:    44.459 -  51.592:   89        |
|      2:    15.927 -  23.060:  320   |   7:    51.592 -  58.725:   37        |
|      3:    23.060 -  30.193:  125   |   8:    58.725 -  65.857:   12        |
|      4:    30.193 -  37.326:  128   |   9:    65.857 -  72.990:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 276         
Filter by distance & map next to the model:
   mapped sites are within: 0.523 - 4.830
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 276
   mapped sites are within: 0.719 - 4.830

peak=    5.871 closest distance to " NH2 ARG A  56 " =    2.172
peak=    5.277 closest distance to " CB  ARG A 275 " =    0.925
peak=    5.131 closest distance to " O   HOH Z 142 " =    1.797
peak=    5.078 closest distance to " O   HOH Z 126 " =    1.842
peak=    5.067 closest distance to " CG  PRO A  54 " =    1.320
peak=    4.899 closest distance to " CB  GLN A 223 " =    1.433
peak=    4.899 closest distance to " O   HOH Z 232 " =    2.420
peak=    4.857 closest distance to " NE2 GLN A  11 " =    1.166
peak=    4.851 closest distance to " CB  ARG A  79 " =    1.368
peak=    4.726 closest distance to " CB  GLU A 152 " =    1.204
peak=    4.725 closest distance to " CB  GLN A 183 " =    1.151
peak=    4.697 closest distance to " O   HOH Z 303 " =    2.095
peak=    4.589 closest distance to " O   HOH Z  78 " =    1.844
peak=    4.462 closest distance to " O   HOH Z  15 " =    2.172
peak=    4.445 closest distance to " O   HOH Z 369 " =    2.131
peak=    4.430 closest distance to " O   HOH Z 158 " =    3.190
peak=    4.418 closest distance to " O   HOH Z 236 " =    2.099
peak=    4.398 closest distance to " O   HOH Z 298 " =    1.893
peak=    4.394 closest distance to " O   HOH Z  61 " =    1.678
peak=    4.390 closest distance to " ND2 ASN A 187 " =    1.546
peak=    4.381 closest distance to " CB  SER A  63 " =    1.157
peak=    4.372 closest distance to " CB  ARG A 190 " =    1.598
peak=    4.370 closest distance to " CB  ASN A 148 " =    1.552
peak=    4.308 closest distance to " O   HOH Z 189 " =    2.602
peak=    4.298 closest distance to " CG2 VAL A 257 " =    0.906
peak=    4.296 closest distance to " CB  VAL A 265 " =    1.286
peak=    4.250 closest distance to " CZ  PHE A 218 " =    1.100
peak=    4.223 closest distance to " O   SER A  87 " =    2.176
peak=    4.213 closest distance to " C   PRO A 198 " =    1.437
peak=    4.157 closest distance to " O   HOH Z 250 " =    1.484
peak=    4.132 closest distance to " CG  PRO A 213 " =    1.199
peak=    4.120 closest distance to " CB  PRO A  54 " =    0.923
peak=    4.103 closest distance to " CD2 TRP A 179 " =    1.292
peak=    4.094 closest distance to " O   HOH Z 248 " =    1.609
peak=    4.089 closest distance to " O   HOH Z 346 " =    1.650
peak=    4.087 closest distance to " CA  ASN A 215 " =    1.042
peak=    4.083 closest distance to " O   HOH Z 209 " =    2.298
peak=    4.079 closest distance to " O   HOH Z 392 " =    3.140
peak=    4.070 closest distance to " O   HOH Z 272 " =    1.842
peak=    4.063 closest distance to " CA  TYR A  30 " =    0.936
peak=    4.062 closest distance to " O   HOH Z 423 " =    1.954
peak=    4.059 closest distance to " O   HOH Z  40 " =    1.677
peak=    4.030 closest distance to " O   HOH Z 193 " =    1.921
peak=    4.025 closest distance to " O   HOH Z 427 " =    2.919
peak=    3.981 closest distance to " CB  GLU A  46 " =    0.939
peak=    3.970 closest distance to " CB  ASN A 187 " =    1.049
peak=    3.966 closest distance to " O   HOH Z 234 " =    3.713
peak=    3.951 closest distance to " CB  ASP A 140 " =    1.005
peak=    3.941 closest distance to " O   HOH Z 419 " =    2.085
peak=    3.941 closest distance to " O   HOH Z 406 " =    1.655
peak=    3.939 closest distance to " O   HOH Z 313 " =    2.016
peak=    3.907 closest distance to " O   HOH Z 368 " =    2.083
peak=    3.904 closest distance to " O   HOH Z  10 " =    1.825
peak=    3.872 closest distance to " OD1 ASN A  69 " =    2.627
peak=    3.862 closest distance to " CB  LEU A 228 " =    1.053
peak=    3.862 closest distance to " CE  LYS A  76 " =    0.892
peak=    3.862 closest distance to " O   HOH Z   1 " =    1.981
peak=    3.852 closest distance to " O   HOH Z  92 " =    2.559
peak=    3.847 closest distance to " CB  TRP A 266 " =    0.979
peak=    3.828 closest distance to " CB  ASN A  39 " =    0.843
peak=    3.824 closest distance to " CB  ASN A 142 " =    1.046
peak=    3.819 closest distance to " CB  VAL A 202 " =    1.546
peak=    3.802 closest distance to " O   HOH Z 265 " =    2.362
peak=    3.790 closest distance to " O   HOH Z 291 " =    1.561
peak=    3.787 closest distance to " O   HOH Z 128 " =    2.110
peak=    3.764 closest distance to " NH1AARG A 145 " =    1.244
peak=    3.763 closest distance to " O   HOH Z 389 " =    1.845
peak=    3.760 closest distance to " O   HOH Z  21 " =    1.785
peak=    3.746 closest distance to " NZ  LYS A 117 " =    3.266
peak=    3.733 closest distance to " CA  SER A  87 " =    0.975
peak=    3.731 closest distance to " CB  GLU A 277 " =    3.566
peak=    3.728 closest distance to " CB  ASN A 110 " =    1.048
peak=    3.723 closest distance to " CG2AVAL A  72 " =    1.608
peak=    3.721 closest distance to " CG  PRO A 198 " =    1.390
peak=    3.721 closest distance to " CB  SER A   3 " =    1.368
peak=    3.713 closest distance to " CG2 ILE A 120 " =    1.133
peak=    3.711 closest distance to " O   HOH Z 214 " =    2.084
peak=    3.708 closest distance to " O   HOH Z  97 " =    2.532
peak=    3.659 closest distance to " O   HOH Z 147 " =    1.826
peak=    3.659 closest distance to " CG  PRO A 243 " =    1.081
peak=    3.641 closest distance to " O   HOH Z   9 " =    2.031
peak=    3.634 closest distance to " O   HOH Z 213 " =    1.983
peak=    3.626 closest distance to " CA  THR A 264 " =    0.910
peak=    3.625 closest distance to " O   HOH Z 133 " =    2.605
peak=    3.623 closest distance to " CA  ASP A 162 " =    1.025
peak=    3.615 closest distance to " O   HOH Z 402 " =    1.447
peak=    3.607 closest distance to " O   HOH Z 203 " =    1.657
peak=    3.600 closest distance to " O   HOH Z 261 " =    2.036
peak=    3.591 closest distance to " CB  PRO A  90 " =    1.135
peak=    3.591 closest distance to " O   HOH Z 294 " =    1.455
peak=    3.585 closest distance to " O   HOH Z 353 " =    2.634
peak=    3.585 closest distance to " CB  TYR A 169 " =    0.726
peak=    3.584 closest distance to " N   PHE A 130 " =    1.267
peak=    3.584 closest distance to " CB  GLU A 128 " =    0.887
peak=    3.573 closest distance to " O   HOH Z 368 " =    3.500
peak=    3.571 closest distance to " CB  ARG A 139 " =    1.047
peak=    3.570 closest distance to " O   HOH Z 245 " =    1.357
peak=    3.558 closest distance to " O   HOH Z 148 " =    3.393
peak=    3.556 closest distance to " CZ2 TRP A 179 " =    1.804
peak=    3.553 closest distance to " CG1 VAL A 153 " =    0.969
peak=    3.552 closest distance to " OG ASER A 258 " =    3.089
peak=    3.546 closest distance to " O   HOH Z 188 " =    2.036
peak=    3.539 closest distance to " CB  SER A 212 " =    1.143
peak=    3.532 closest distance to " O  BHOH Z 338 " =    2.347
peak=    3.532 closest distance to " O   HOH Z 403 " =    1.438
peak=    3.531 closest distance to " CG  LEU A 167 " =    1.288
peak=    3.530 closest distance to " N   ASN A  39 " =    1.219
peak=    3.528 closest distance to " O   HOH Z 172 " =    3.138
peak=    3.517 closest distance to " CA  ALA A 233 " =    1.200
peak=    3.507 closest distance to " O   HOH Z 273 " =    2.801
peak=    3.507 closest distance to " CB  GLN A  88 " =    1.181
peak=    3.498 closest distance to " O   HOH Z 180 " =    2.118
peak=    3.498 closest distance to " O   HOH Z  66 " =    2.276
peak=    3.496 closest distance to " CD  LYS A 166 " =    1.231
peak=    3.494 closest distance to " O   HOH Z 325 " =    3.979
peak=    3.492 closest distance to " CA  ALA A  51 " =    0.897
peak=    3.488 closest distance to " O   HOH Z 433 " =    1.800
peak=    3.487 closest distance to " CD  ARG A  66 " =    2.342
peak=    3.478 closest distance to " CA  TYR A 116 " =    1.352
peak=    3.477 closest distance to " O   HOH Z 234 " =    1.895
peak=    3.475 closest distance to " O   HOH Z 337 " =    3.609
peak=    3.474 closest distance to " CD1 ILE A 106 " =    0.847
peak=    3.470 closest distance to " NE2 HIS A 207 " =    1.277
peak=    3.469 closest distance to " CA  ARG A  36 " =    0.978
peak=    3.469 closest distance to " O   HOH Z 417 " =    3.367
peak=    3.467 closest distance to " O   HOH Z 261 " =    1.671
peak=    3.465 closest distance to " O   HOH Z 380 " =    1.766
peak=    3.465 closest distance to " CB  TRP A 179 " =    1.412
peak=    3.461 closest distance to " O   HOH Z 359 " =    1.592
peak=    3.454 closest distance to " O   HOH Z 371 " =    2.863
peak=    3.453 closest distance to " ND2 ASN A 249 " =    0.883
peak=    3.452 closest distance to " O   HOH Z 305 " =    3.588
peak=    3.450 closest distance to " O   HOH Z  43 " =    1.854
peak=    3.448 closest distance to " O   HOH Z 132 " =    2.558
peak=    3.446 closest distance to " CG  GLN A  11 " =    1.715
peak=    3.445 closest distance to " O   HOH Z 287 " =    2.369
peak=    3.444 closest distance to " O   HOH Z   1 " =    1.676
peak=    3.444 closest distance to " CD  ARG A 269 " =    0.882
peak=    3.438 closest distance to " O   HOH Z 371 " =    1.768
peak=    3.438 closest distance to " O   HOH Z 403 " =    1.553
peak=    3.437 closest distance to " CB  SER A  26 " =    1.676
peak=    3.437 closest distance to " O   ASN A  74 " =    1.472
peak=    3.435 closest distance to " O   HOH Z 285 " =    2.460
peak=    3.432 closest distance to " CB  ILE A 120 " =    1.227
peak=    3.424 closest distance to " CB  ALA A 114 " =    1.167
peak=    3.420 closest distance to " O   HOH Z 425 " =    2.022
peak=    3.415 closest distance to " CA  ALA A 291 " =    0.843
peak=    3.413 closest distance to " CE1 TYR A 186 " =    1.410
peak=    3.407 closest distance to " CB  LEU A  83 " =    0.753
peak=    3.407 closest distance to " ND1 HIS A  86 " =    1.630
peak=    3.402 closest distance to " N   TYR A 116 " =    1.542
peak=    3.396 closest distance to " NZ  LYS A  48 " =    1.180
peak=    3.395 closest distance to " O   HOH Z 128 " =    2.140
peak=    3.389 closest distance to " CD  ARG A  66 " =    2.443
peak=    3.388 closest distance to " CG  LYS A 119 " =    1.151
peak=    3.388 closest distance to " CG  MET A 185 " =    1.146
peak=    3.385 closest distance to " CG2 ILE A  20 " =    1.425
peak=    3.382 closest distance to " CD1 LEU A 300 " =    1.226
peak=    3.382 closest distance to " O   HOH Z 175 " =    2.143
peak=    3.381 closest distance to " CB  PHE A 204 " =    0.719
peak=    3.379 closest distance to " OG BSER A 164 " =    2.388
peak=    3.379 closest distance to " CB  TYR A 116 " =    0.764
peak=    3.374 closest distance to " N   ARG A 156 " =    1.363
peak=    3.371 closest distance to " O   HOH Z 261 " =    2.425
peak=    3.368 closest distance to " CG1 ILE A  49 " =    1.458
peak=    3.367 closest distance to " O   HOH Z 280 " =    3.015
peak=    3.366 closest distance to " O   PHE A 192 " =    1.406
peak=    3.362 closest distance to " O   HOH Z 299 " =    4.355
peak=    3.362 closest distance to " O   HOH Z 185 " =    1.818
peak=    3.361 closest distance to " CB  MET A  47 " =    1.211
peak=    3.349 closest distance to " O   HOH Z 365 " =    2.806
peak=    3.345 closest distance to " O   HOH Z 187 " =    2.235
peak=    3.345 closest distance to " O   HOH Z 329 " =    4.022
peak=    3.341 closest distance to " O   HOH Z  88 " =    2.641
peak=    3.341 closest distance to " O   HOH Z 248 " =    1.744
peak=    3.333 closest distance to " CB  ASP A 298 " =    1.146
peak=    3.332 closest distance to " O   HOH Z  54 " =    1.582
peak=    3.329 closest distance to " O   HOH Z 325 " =    2.484
peak=    3.327 closest distance to " O   HOH Z 302 " =    1.993
peak=    3.323 closest distance to " CD1 LEU A  96 " =    0.732
peak=    3.314 closest distance to " CB  ALA A 291 " =    1.273
peak=    3.314 closest distance to " CB  ALA A  34 " =    1.011
peak=    3.305 closest distance to " O   HOH Z 193 " =    1.966
peak=    3.298 closest distance to " CG  GLN A  77 " =    1.839
peak=    3.295 closest distance to " CG AARG A 275 " =    1.125
peak=    3.295 closest distance to " CB  GLN A 103 " =    0.820
peak=    3.292 closest distance to " O   HOH Z 407 " =    2.453
peak=    3.289 closest distance to " NH2 ARG A 156 " =    1.156
peak=    3.288 closest distance to " O   HOH Z  44 " =    2.933
peak=    3.285 closest distance to " OG BSER A  99 " =    2.289
peak=    3.284 closest distance to " CG2 THR A 221 " =    1.049
peak=    3.284 closest distance to " O   HOH Z 336 " =    1.792
peak=    3.283 closest distance to " CA  ASN A 217 " =    1.230
peak=    3.280 closest distance to " CE1 PHE A  38 " =    1.249
peak=    3.280 closest distance to " CA  ARG A 159 " =    1.226
peak=    3.277 closest distance to " O   HOH Z  40 " =    1.811
peak=    3.274 closest distance to " O   HOH Z  97 " =    1.921
peak=    3.272 closest distance to " OG  SER A  22 " =    2.637
peak=    3.270 closest distance to " O   HOH Z  88 " =    1.883
peak=    3.268 closest distance to " O   HOH Z 344 " =    3.235
peak=    3.265 closest distance to " O   HOH Z 388 " =    2.114
peak=    3.263 closest distance to " CB  THR A  31 " =    1.560
peak=    3.260 closest distance to " O   HOH Z  88 " =    2.554
peak=    3.259 closest distance to " NH2BARG A 145 " =    2.114
peak=    3.259 closest distance to " CB  ALA A   9 " =    1.568
peak=    3.257 closest distance to " N   ASP A 162 " =    1.210
peak=    3.255 closest distance to " O   HOH Z 152 " =    1.728
peak=    3.250 closest distance to " O   HOH Z 421 " =    1.880
peak=    3.249 closest distance to " O   SER A 164 " =    1.177
peak=    3.244 closest distance to " CB  MET A  40 " =    0.795
peak=    3.243 closest distance to " CA  ALA A  84 " =    1.257
peak=    3.238 closest distance to " O   GLY A  75 " =    1.460
peak=    3.236 closest distance to " OG1 THR A 294 " =    2.455
peak=    3.236 closest distance to " N   ASN A 127 " =    1.281
peak=    3.235 closest distance to " CD1 ILE A 263 " =    1.293
peak=    3.235 closest distance to " CB  SER A 141 " =    0.927
peak=    3.233 closest distance to " CA  ILE A 234 " =    0.892
peak=    3.231 closest distance to " CG  LYS A  76 " =    0.917
peak=    3.231 closest distance to " CB  GLN A 278 " =    0.829
peak=    3.225 closest distance to " CG  MET A 113 " =    1.091
peak=    3.225 closest distance to " O   HOH Z 258 " =    1.658
peak=    3.222 closest distance to " O   HOH Z 234 " =    2.299
peak=    3.221 closest distance to " CB  LYS A 117 " =    1.242
peak=    3.221 closest distance to " CA  THR A 221 " =    1.032
peak=    3.219 closest distance to " CD2 TYR A 186 " =    1.015
peak=    3.214 closest distance to " O   HOH Z 327 " =    1.634
peak=    3.213 closest distance to " CB  PRO A 243 " =    1.485
peak=    3.211 closest distance to " O   HOH Z 116 " =    3.034
peak=    3.211 closest distance to " O   HOH Z 411 " =    3.870
peak=    3.207 closest distance to " O   HOH Z 173 " =    1.872
peak=    3.202 closest distance to " CB  ASN A 224 " =    0.973
peak=    3.201 closest distance to " O   ALA A 165 " =    1.554
peak=    3.201 closest distance to " CB  ASN A 215 " =    1.129
peak=    3.195 closest distance to " O   HOH Z  66 " =    2.191
peak=    3.195 closest distance to " CB  LEU A 300 " =    0.920
peak=    3.195 closest distance to " O   HOH Z 141 " =    1.645
peak=    3.194 closest distance to " O   HOH Z  44 " =    1.713
peak=    3.190 closest distance to " O   TRP A 274 " =    1.835
peak=    3.183 closest distance to " O   HOH Z 193 " =    1.713
peak=    3.178 closest distance to " O   HOH Z 257 " =    2.192
peak=    3.174 closest distance to " CA  ARG A 195 " =    1.162
peak=    3.173 closest distance to " O   ALA A   1 " =    1.700
peak=    3.164 closest distance to " O   HOH Z   6 " =    2.105
peak=    3.159 closest distance to " O   HOH Z 171 " =    4.054
peak=    3.159 closest distance to " O   HOH Z 250 " =    2.128
peak=    3.149 closest distance to " ND2 ASN A 110 " =    1.690
peak=    3.149 closest distance to " CB  ALA A 248 " =    0.915
peak=    3.148 closest distance to " O   HOH Z  61 " =    1.463
peak=    3.145 closest distance to " OG1 THR A 294 " =    1.661
peak=    3.140 closest distance to " CA  VAL A 125 " =    1.069
peak=    3.140 closest distance to " O   HOH Z 188 " =    2.483
peak=    3.136 closest distance to " CE1 TYR A 116 " =    1.295
peak=    3.131 closest distance to " CA  ALA A 248 " =    1.103
peak=    3.128 closest distance to " CG  GLN A 278 " =    1.312
peak=    3.119 closest distance to " O   HOH Z 390 " =    2.516
peak=    3.109 closest distance to " N   SER A 135 " =    1.254
peak=    3.102 closest distance to " O   HOH Z 152 " =    2.519
peak=    3.092 closest distance to " O   HOH Z 358 " =    3.626
peak=    3.092 closest distance to " CG1 VAL A 189 " =    1.855
peak=    3.090 closest distance to " CB  ALA A   1 " =    4.830
peak=    3.090 closest distance to " CG BARG A 102 " =    1.721
peak=    3.083 closest distance to " N   GLY A  98 " =    1.054
peak=    3.073 closest distance to " O   HOH Z 371 " =    3.208
peak=    3.061 closest distance to " CB  ALA A 291 " =    0.762
peak=    3.045 closest distance to " O   HOH Z  85 " =    2.001
peak=    3.035 closest distance to " NE AARG A 190 " =    2.032
peak=    3.032 closest distance to " CB  ALA A 114 " =    1.030
peak=    3.023 closest distance to " CB  SER A  62 " =    1.163
peak=    3.019 closest distance to " CG1 ILE A  33 " =    1.254

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.466 - 5.604
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 195
   mapped sites are within: 0.741 - 5.604

peak=   -4.622 closest distance to " CD  GLN A  58 " =    0.921
peak=   -4.516 closest distance to " CB  PRO A 243 " =    2.659
peak=   -4.469 closest distance to " CD  ARG A 156 " =    2.062
peak=   -4.449 closest distance to " CD  ARG A  14 " =    3.541
peak=   -4.400 closest distance to " O   HOH Z 266 " =    5.299
peak=   -4.352 closest distance to " O   VAL A  67 " =    2.642
peak=   -4.264 closest distance to " CZ3 TRP A 179 " =    1.136
peak=   -4.261 closest distance to " OG BSER A 134 " =    1.308
peak=   -4.248 closest distance to " CD2 PHE A 192 " =    1.985
peak=   -4.169 closest distance to " C   HIS A 108 " =    1.166
peak=   -4.143 closest distance to " CG1 VAL A 112 " =    2.797
peak=   -4.136 closest distance to " CB  PRO A 280 " =    2.180
peak=   -4.049 closest distance to " CG1 VAL A 112 " =    2.614
peak=   -4.029 closest distance to " CG  GLN A 223 " =    1.928
peak=   -4.026 closest distance to " O   HOH Z 290 " =    1.117
peak=   -4.005 closest distance to " O   HOH Z 231 " =    2.249
peak=   -3.973 closest distance to " O   PRO A 198 " =    1.242
peak=   -3.965 closest distance to " O   HOH Z 389 " =    1.969
peak=   -3.963 closest distance to " CG1 VAL A  67 " =    2.888
peak=   -3.958 closest distance to " OG  SER A  97 " =    2.254
peak=   -3.913 closest distance to " O   HOH Z 185 " =    2.319
peak=   -3.900 closest distance to " O   HOH Z 211 " =    1.578
peak=   -3.888 closest distance to " O   HOH Z 372 " =    2.369
peak=   -3.885 closest distance to " CB  ALA A 291 " =    2.135
peak=   -3.857 closest distance to " OD1 ASP A 171 " =    1.710
peak=   -3.848 closest distance to " N   ALA A  43 " =    2.550
peak=   -3.807 closest distance to " O   HOH Z 351 " =    1.462
peak=   -3.804 closest distance to " O   HOH Z 407 " =    3.098
peak=   -3.795 closest distance to " ND2 ASN A  45 " =    1.909
peak=   -3.790 closest distance to " CG2 ILE A 263 " =    2.254
peak=   -3.770 closest distance to " CB  ALA A  43 " =    2.517
peak=   -3.756 closest distance to " CD1 LEU A 255 " =    2.876
peak=   -3.740 closest distance to " O   HOH Z 313 " =    1.883
peak=   -3.683 closest distance to " CA  ASP A 298 " =    1.126
peak=   -3.672 closest distance to " CE  MET A 105 " =    2.482
peak=   -3.669 closest distance to " CD  ARG A 139 " =    1.624
peak=   -3.661 closest distance to " CE BMET A  47 " =    1.371
peak=   -3.659 closest distance to " O   HOH Z  73 " =    2.294
peak=   -3.658 closest distance to " CE3 TRP A 274 " =    1.075
peak=   -3.654 closest distance to " CB  ASN A  39 " =    2.307
peak=   -3.644 closest distance to " OXT GLY A 302 " =    2.784
peak=   -3.613 closest distance to " O   HOH Z 114 " =    3.082
peak=   -3.606 closest distance to " O   HOH Z 429 " =    2.203
peak=   -3.604 closest distance to " O   SER A 210 " =    2.028
peak=   -3.593 closest distance to " N   ALA A 248 " =    1.668
peak=   -3.591 closest distance to " OD1 ASN A 148 " =    1.514
peak=   -3.584 closest distance to " CZ  TYR A 169 " =    1.764
peak=   -3.572 closest distance to " CB  ALA A 161 " =    2.577
peak=   -3.566 closest distance to " ND2 ASN A 249 " =    2.320
peak=   -3.560 closest distance to " CB  PRO A 163 " =    2.466
peak=   -3.555 closest distance to " O   VAL A 189 " =    2.603
peak=   -3.536 closest distance to " OG BSER A 134 " =    1.729
peak=   -3.533 closest distance to " CD2 LEU A 237 " =    2.846
peak=   -3.531 closest distance to " CB  ALA A 248 " =    2.383
peak=   -3.524 closest distance to " CG  ARG A 269 " =    2.321
peak=   -3.523 closest distance to " CG  ASP A 231 " =    0.741
peak=   -3.523 closest distance to " NE2 GLN A 278 " =    1.679
peak=   -3.522 closest distance to " NH2AARG A 275 " =    5.290
peak=   -3.516 closest distance to " CD2 TYR A 293 " =    1.979
peak=   -3.512 closest distance to " CB  ASP A 132 " =    2.263
peak=   -3.506 closest distance to " NE2 GLN A 194 " =    1.826
peak=   -3.499 closest distance to " CE2 TYR A  30 " =    2.715
peak=   -3.495 closest distance to " CD1 PHE A  59 " =    1.997
peak=   -3.490 closest distance to " OD2 ASP A 171 " =    2.426
peak=   -3.484 closest distance to " O   HOH Z 394 " =    1.390
peak=   -3.482 closest distance to " O   HOH Z 196 " =    1.994
peak=   -3.479 closest distance to " O   HOH Z  10 " =    1.442
peak=   -3.475 closest distance to " O   HOH Z  38 " =    1.531
peak=   -3.465 closest distance to " ND2 ASN A 187 " =    1.426
peak=   -3.463 closest distance to " CG2 THR A 178 " =    2.305
peak=   -3.462 closest distance to " O   HOH Z 174 " =    2.621
peak=   -3.457 closest distance to " N   GLN A  58 " =    1.753
peak=   -3.453 closest distance to " N   THR A 157 " =    1.546
peak=   -3.451 closest distance to " NH2 ARG A  79 " =    1.632
peak=   -3.451 closest distance to " CG  GLU A 277 " =    1.244
peak=   -3.444 closest distance to " CD1 ILE A 239 " =    2.354
peak=   -3.441 closest distance to " CD1 LEU A 101 " =    2.332
peak=   -3.435 closest distance to " O   PRO A 163 " =    2.026
peak=   -3.435 closest distance to " O   HOH Z 198 " =    1.883
peak=   -3.429 closest distance to " CD2 PHE A  61 " =    2.572
peak=   -3.429 closest distance to " O   HOH Z  15 " =    1.491
peak=   -3.429 closest distance to " CA  GLY A 241 " =    3.251
peak=   -3.421 closest distance to " O   HOH Z 134 " =    3.171
peak=   -3.420 closest distance to " O   HOH Z  11 " =    1.713
peak=   -3.401 closest distance to " C   GLY A 262 " =    1.894
peak=   -3.400 closest distance to " O   ARG A 145 " =    1.596
peak=   -3.392 closest distance to " C   MET A 188 " =    1.319
peak=   -3.386 closest distance to " CD  GLN A  88 " =    0.782
peak=   -3.374 closest distance to " CB  PHE A 208 " =    2.288
peak=   -3.371 closest distance to " O   HOH Z 174 " =    4.243
peak=   -3.369 closest distance to " ND2 ASN A  60 " =    4.152
peak=   -3.366 closest distance to " CB  ASP A 286 " =    1.973
peak=   -3.359 closest distance to " O   SER A 276 " =    1.695
peak=   -3.359 closest distance to " N   GLY A  23 " =    2.447
peak=   -3.353 closest distance to " CG1 VAL A 197 " =    2.224
peak=   -3.351 closest distance to " CB  ALA A 291 " =    2.212
peak=   -3.351 closest distance to " O   HOH Z 353 " =    2.205
peak=   -3.349 closest distance to " CD  ARG A 195 " =    5.218
peak=   -3.344 closest distance to " O   HOH Z 359 " =    3.179
peak=   -3.334 closest distance to " O   HOH Z  60 " =    2.016
peak=   -3.334 closest distance to " O   VAL A 189 " =    1.617
peak=   -3.333 closest distance to " CA  GLY A 241 " =    2.324
peak=   -3.326 closest distance to " O   GLN A 240 " =    2.096
peak=   -3.325 closest distance to " CE2 PHE A 218 " =    2.432
peak=   -3.320 closest distance to " O   HOH Z  91 " =    1.580
peak=   -3.316 closest distance to " OD2 ASP A 191 " =    1.390
peak=   -3.315 closest distance to " O   HOH Z 298 " =    1.259
peak=   -3.314 closest distance to " O   SER A  95 " =    1.567
peak=   -3.301 closest distance to " NH2BARG A 275 " =    1.872
peak=   -3.299 closest distance to " CZ  PHE A 155 " =    1.163
peak=   -3.298 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.292 closest distance to " O   HOH Z 421 " =    3.119
peak=   -3.289 closest distance to " O   HOH Z 126 " =    1.888
peak=   -3.286 closest distance to " O   HOH Z 253 " =    3.851
peak=   -3.286 closest distance to " O   PHE A 218 " =    1.620
peak=   -3.278 closest distance to " O   ALA A 292 " =    2.140
peak=   -3.277 closest distance to " CD1 ILE A 199 " =    2.481
peak=   -3.276 closest distance to " CG  ARG A  66 " =    2.319
peak=   -3.276 closest distance to " O   HOH Z 385 " =    2.087
peak=   -3.273 closest distance to " OH  TYR A 247 " =    2.060
peak=   -3.273 closest distance to " CG  GLU A 152 " =    0.773
peak=   -3.266 closest distance to " O   HOH Z  51 " =    1.568
peak=   -3.264 closest distance to " O   LEU A 101 " =    2.599
peak=   -3.261 closest distance to " O   HOH Z 131 " =    4.124
peak=   -3.261 closest distance to " CA  GLY A 203 " =    2.328
peak=   -3.260 closest distance to " CG1 VAL A 230 " =    2.037
peak=   -3.258 closest distance to " O   HOH Z 311 " =    3.698
peak=   -3.258 closest distance to " O   HOH Z 317 " =    1.453
peak=   -3.243 closest distance to " C   LEU A 143 " =    1.013
peak=   -3.242 closest distance to " C   PRO A  90 " =    1.465
peak=   -3.242 closest distance to " O   HOH Z 266 " =    5.074
peak=   -3.238 closest distance to " CG1 VAL A 250 " =    2.696
peak=   -3.237 closest distance to " CA  GLY A 133 " =    2.038
peak=   -3.234 closest distance to " O   ALA A  10 " =    1.638
peak=   -3.234 closest distance to " O   HOH Z 166 " =    1.910
peak=   -3.228 closest distance to " O   HOH Z  71 " =    2.178
peak=   -3.222 closest distance to " CG  LEU A  83 " =    1.875
peak=   -3.219 closest distance to " O   HOH Z 357 " =    2.032
peak=   -3.219 closest distance to " O   HOH Z 243 " =    1.888
peak=   -3.207 closest distance to " CE3 TRP A 274 " =    2.511
peak=   -3.188 closest distance to " CA  GLY A 241 " =    2.857
peak=   -3.188 closest distance to " O   LEU A 167 " =    1.519
peak=   -3.183 closest distance to " O   PRO A 198 " =    1.619
peak=   -3.182 closest distance to " CD1 LEU A 297 " =    2.336
peak=   -3.182 closest distance to " CD2 PHE A 225 " =    1.150
peak=   -3.181 closest distance to " CB  ALA A 114 " =    2.554
peak=   -3.178 closest distance to " O   HOH Z  13 " =    1.651
peak=   -3.170 closest distance to " CB  ASN A  69 " =    1.204
peak=   -3.170 closest distance to " CG  PHE A 283 " =    2.637
peak=   -3.170 closest distance to " CB  TRP A  85 " =    2.595
peak=   -3.168 closest distance to " C   ALA A 158 " =    1.463
peak=   -3.168 closest distance to " O   SER A 135 " =    1.437
peak=   -3.166 closest distance to " O   HOH Z  43 " =    1.698
peak=   -3.165 closest distance to " C   ALA A 114 " =    2.195
peak=   -3.164 closest distance to " O   HOH Z  37 " =    1.740
peak=   -3.163 closest distance to " CB  TYR A  15 " =    2.221
peak=   -3.161 closest distance to " O   ALA A  34 " =    2.025
peak=   -3.159 closest distance to " O   HOH Z 200 " =    4.576
peak=   -3.156 closest distance to " O   HOH Z 191 " =    5.604
peak=   -3.154 closest distance to " SG ACYS A 201 " =    1.878
peak=   -3.153 closest distance to " CG  GLU A 152 " =    0.980
peak=   -3.152 closest distance to " O   HOH Z 371 " =    1.531
peak=   -3.151 closest distance to " CB  ASP A 132 " =    2.421
peak=   -3.149 closest distance to " O   ALA A 161 " =    1.735
peak=   -3.145 closest distance to " CG2 VAL A 189 " =    2.007
peak=   -3.144 closest distance to " CG  TRP A 266 " =    1.940
peak=   -3.142 closest distance to " CE3 TRP A 150 " =    2.268
peak=   -3.138 closest distance to " O   TRP A  70 " =    1.476
peak=   -3.137 closest distance to " O   HOH Z 426 " =    1.557
peak=   -3.133 closest distance to " O   HOH Z 339 " =    1.828
peak=   -3.129 closest distance to " O   VAL A 174 " =    2.112
peak=   -3.128 closest distance to " O   HOH Z 281 " =    2.788
peak=   -3.120 closest distance to " NH2 ARG A  79 " =    2.032
peak=   -3.117 closest distance to " O   HOH Z  51 " =    1.240
peak=   -3.116 closest distance to " O   HOH Z 111 " =    1.927
peak=   -3.114 closest distance to " CE1 TYR A 172 " =    1.945
peak=   -3.111 closest distance to " CG  PRO A 163 " =    2.695
peak=   -3.108 closest distance to " O   HOH Z 407 " =    3.208
peak=   -3.103 closest distance to " CG1 VAL A 125 " =    1.883
peak=   -3.097 closest distance to " O   HOH Z  55 " =    0.831
peak=   -3.091 closest distance to " CA  SER A 135 " =    1.333
peak=   -3.076 closest distance to " CG1 VAL A  67 " =    3.135
peak=   -3.075 closest distance to " ND2 ASN A  60 " =    1.274
peak=   -3.073 closest distance to " CG2 THR A 221 " =    2.242
peak=   -3.070 closest distance to " CB  ALA A 100 " =    2.216
peak=   -3.069 closest distance to " CB  GLN A  11 " =    1.826
peak=   -3.064 closest distance to " NH2 ARG A  24 " =    1.816
peak=   -3.064 closest distance to " O   HOH Z 244 " =    1.927
peak=   -3.058 closest distance to " O   HOH Z 323 " =    1.403
peak=   -3.033 closest distance to " O   LYS A 289 " =    2.895
peak=   -3.033 closest distance to " CG  ARG A 269 " =    2.033
peak=   -3.030 closest distance to " NE2 GLN A  88 " =    0.973

================= 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 individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.3104 0.3065   6.009519e+00   5.986092e+00
   1_bss:  0.2942 0.2909   5.980605e+00   5.951462e+00
   1_xyz:  0.1594 0.1831   5.396742e+00   5.503609e+00
   1_adp:  0.1473 0.1862   5.350056e+00   5.532348e+00
   1_occ:  0.1469 0.1858   5.348221e+00   5.531439e+00
   2_bss:  0.1448 0.1831   5.338973e+00   5.521450e+00
   2_xyz:  0.1272 0.1620   5.224569e+00   5.414423e+00
   2_adp:  0.1218 0.1619   5.197481e+00   5.407551e+00
   2_occ:  0.1217 0.1618   5.197167e+00   5.407428e+00
   3_bss:  0.1215 0.1616   5.196174e+00   5.406746e+00
   3_xyz:  0.1145 0.1558   5.151145e+00   5.379767e+00
   3_adp:  0.1132 0.1556   5.144055e+00   5.378615e+00
   3_occ:  0.1131 0.1557   5.144160e+00   5.379040e+00
   4_bss:  0.1131 0.1553   5.143027e+00   5.376296e+00
   4_xyz:  0.1090 0.1560   5.128259e+00   5.379889e+00
   4_adp:  0.1122 0.1541   5.136585e+00   5.370199e+00
   4_occ:  0.1121 0.1540   5.136399e+00   5.370367e+00
   5_bss:  0.1121 0.1540   5.136501e+00   5.370504e+00
   5_xyz:  0.1088 0.1544   5.122124e+00   5.370959e+00
   5_adp:  0.1080 0.1543   5.118011e+00   5.369842e+00
   5_occ:  0.1080 0.1543   5.118088e+00   5.370053e+00
   5_bss:  0.1079 0.1542   5.118122e+00   5.370092e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.328  50.001  -2.954  -2.179   2.520  -0.000   0.000   0.000
   1_xyz:  0.328  50.001  -2.954  -2.179   2.520  -0.000   0.000   0.000
   1_adp:  0.328  50.001  -2.954  -2.179   2.520  -0.000   0.000   0.000
   1_occ:  0.328  50.001  -2.954  -2.179   2.520  -0.000   0.000   0.000
   2_bss:  0.330  57.734  -3.173  -2.641  -0.144  -0.000  -0.000  -0.000
   2_xyz:  0.330  57.734  -3.173  -2.641  -0.144  -0.000  -0.000  -0.000
   2_adp:  0.330  57.734  -3.173  -2.641  -0.144  -0.000  -0.000  -0.000
   2_occ:  0.330  57.734  -3.173  -2.641  -0.144  -0.000  -0.000  -0.000
   3_bss:  0.330  57.734  -2.828  -2.397  -0.419  -0.000  -0.000  -0.000
   3_xyz:  0.330  57.734  -2.828  -2.397  -0.419  -0.000  -0.000  -0.000
   3_adp:  0.330  57.734  -2.828  -2.397  -0.419  -0.000  -0.000  -0.000
   3_occ:  0.330  57.734  -2.828  -2.397  -0.419  -0.000  -0.000  -0.000
   4_bss:  0.327  57.734  -2.545  -2.163  -0.398  -0.000  -0.000  -0.000
   4_xyz:  0.327  57.734  -2.545  -2.163  -0.398  -0.000  -0.000  -0.000
   4_adp:  0.327  57.734  -2.545  -2.163  -0.398  -0.000  -0.000  -0.000
   4_occ:  0.327  57.734  -2.545  -2.163  -0.398  -0.000  -0.000  -0.000
   5_bss:  0.332  57.734  -2.545  -2.163  -0.398  -0.000  -0.000  -0.000
   5_xyz:  0.332  57.734  -2.545  -2.163  -0.398  -0.000  -0.000  -0.000
   5_adp:  0.332  57.734  -2.545  -2.163  -0.398  -0.000  -0.000  -0.000
   5_occ:  0.332  57.734  -2.545  -2.163  -0.398  -0.000  -0.000  -0.000
   5_bss:  0.332  57.672  -2.326  -1.981  -0.255  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  30.864 0.7519  0.9160    25829.925
   1_bss:  29.360 0.7665  0.9074    22581.574
   1_xyz:  16.606 0.8935  1.0088     8228.563
   1_adp:  17.244 0.8874  1.0032     8635.395
   1_occ:  17.216 0.8876  1.0030     8601.964
   2_bss:  16.908 0.8906  0.9676     8469.673
   2_xyz:  14.578 0.9103  0.9734     6700.204
   2_adp:  14.428 0.9116  0.9683     6603.783
   2_occ:  14.423 0.9116  0.9682     6602.181
   3_bss:  14.399 0.9118  0.9723     6598.228
   3_xyz:  13.789 0.9168  0.9753     6219.477
   3_adp:  13.742 0.9172  0.9683     6189.081
   3_occ:  13.747 0.9172  0.9682     6194.263
   4_bss:  13.705 0.9175  0.9745     6145.802
   4_xyz:  13.749 0.9172  0.9751     6204.703
   4_adp:  13.501 0.9193  0.9724     6123.363
   4_occ:  13.506 0.9192  0.9723     6122.186
   5_bss:  13.510 0.9192  0.9723     6125.624
   5_xyz:  13.516 0.9191  0.9726     6156.718
   5_adp:  13.498 0.9193  0.9675     6137.006
   5_occ:  13.502 0.9193  0.9674     6138.575
   5_bss:  13.502 0.9192  0.9717     6140.054
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6459e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6459e-01
   1_xyz:   1.070  0.009  0.075 15.455  0.005  4.116   6.9387e-02
   1_adp:   1.070  0.009  0.075 15.455  0.005  4.116   6.9387e-02
   1_occ:   1.070  0.009  0.075 15.455  0.005  4.116   6.9387e-02
   2_bss:   1.070  0.009  0.075 15.455  0.005  4.116   6.9387e-02
   2_xyz:   0.888  0.005  0.069 14.950  0.003  4.118   4.9665e-02
   2_adp:   0.888  0.005  0.069 14.950  0.003  4.118   4.9665e-02
   2_occ:   0.888  0.005  0.069 14.950  0.003  4.118   4.9665e-02
   3_bss:   0.888  0.005  0.069 14.950  0.003  4.118   4.9665e-02
   3_xyz:   0.934  0.006  0.073 14.889  0.003  4.112   5.4360e-02
   3_adp:   0.934  0.006  0.073 14.889  0.003  4.112   5.4360e-02
   3_occ:   0.934  0.006  0.073 14.889  0.003  4.112   5.4360e-02
   4_bss:   0.934  0.006  0.073 14.889  0.003  4.112   5.4360e-02
   4_xyz:   1.004  0.008  0.078 14.927  0.004  4.114   6.1580e-02
   4_adp:   1.004  0.008  0.078 14.927  0.004  4.114   6.1580e-02
   4_occ:   1.004  0.008  0.078 14.927  0.004  4.114   6.1580e-02
   5_bss:   1.004  0.008  0.078 14.927  0.004  4.114   6.1580e-02
   5_xyz:   1.082  0.010  0.085 15.015  0.004  4.115   7.2589e-02
   5_adp:   1.082  0.010  0.085 15.015  0.004  4.115   7.2589e-02
   5_occ:   1.082  0.010  0.085 15.015  0.004  4.115   7.2589e-02
   5_bss:   1.082  0.010  0.085 15.015  0.004  4.115   7.2589e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.708   2.4149e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.708   2.4149e-01
   1_xyz:   6.757  0.059  0.242 83.493  0.038  2.252   9.8357e-02
   1_adp:   6.757  0.059  0.242 83.493  0.038  2.252   9.8357e-02
   1_occ:   6.757  0.059  0.242 83.493  0.038  2.252   9.8357e-02
   2_bss:   6.757  0.059  0.242 83.493  0.038  2.252   9.8357e-02
   2_xyz:   6.142  0.036  0.209 81.379  0.031  2.396   3.0389e-02
   2_adp:   6.142  0.036  0.209 81.379  0.031  2.396   3.0389e-02
   2_occ:   6.142  0.036  0.209 81.379  0.031  2.396   3.0389e-02
   3_bss:   6.142  0.036  0.209 81.379  0.031  2.396   3.0389e-02
   3_xyz:   6.338  0.039  0.237 83.412  0.036  2.384   3.3898e-02
   3_adp:   6.338  0.039  0.237 83.412  0.036  2.384   3.3898e-02
   3_occ:   6.338  0.039  0.237 83.412  0.036  2.384   3.3898e-02
   4_bss:   6.338  0.039  0.237 83.412  0.036  2.384   3.3898e-02
   4_xyz:   6.718  0.049  0.253 83.034  0.034  2.332   4.3488e-02
   4_adp:   6.718  0.049  0.253 83.034  0.034  2.332   4.3488e-02
   4_occ:   6.718  0.049  0.253 83.034  0.034  2.332   4.3488e-02
   5_bss:   6.718  0.049  0.253 83.034  0.034  2.332   4.3488e-02
   5_xyz:   7.064  0.054  0.291 84.036  0.035  2.235   5.7891e-02
   5_adp:   7.064  0.054  0.291 84.036  0.035  2.235   5.7891e-02
   5_occ:   7.064  0.054  0.291 84.036  0.035  2.235   5.7891e-02
   5_bss:   7.064  0.054  0.291 84.036  0.035  2.235   5.7891e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  79.64   0.00  16.44  79.64   0.00  12.59  62.98   5.93  37.44
   1_occ:  79.64   0.00  16.44  79.64   0.00  12.59  62.98   5.93  37.44
   2_bss:  79.64   0.00  16.44  79.64   0.00  12.59  62.98   5.93  37.44
   2_xyz:  79.64   0.00  16.44  79.64   0.00  12.59  62.98   5.93  37.44
   2_adp:  69.84   0.73  16.95  68.59   0.73  12.85  69.84   6.51  39.30
   2_occ:  69.84   0.73  16.95  68.59   0.73  12.85  69.84   6.51  39.30
   3_bss:  69.84   0.73  16.95  68.59   0.73  12.85  69.84   6.51  39.30
   3_xyz:  69.84   0.73  16.95  68.59   0.73  12.85  69.84   6.51  39.30
   3_adp:  86.08   0.45  17.13  86.08   0.45  12.82  79.46   5.95  40.56
   3_occ:  86.08   0.45  17.13  86.08   0.45  12.82  79.46   5.95  40.56
   4_bss:  86.08   0.45  17.13  86.08   0.45  12.82  79.46   5.95  40.56
   4_xyz:  86.08   0.45  17.13  86.08   0.45  12.82  79.46   5.95  40.56
   4_adp:  73.53   2.09  15.95  73.53   2.09  12.37  72.90   6.19  35.43
   4_occ:  73.53   2.09  15.95  73.53   2.09  12.37  72.90   6.19  35.43
   5_bss:  73.53   2.09  15.95  73.53   2.09  12.37  72.90   6.19  35.43
   5_xyz:  73.53   2.09  15.95  73.53   2.09  12.37  72.90   6.19  35.43
   5_adp:  73.05   1.72  15.89  73.05   1.72  12.24  72.06   6.19  35.81
   5_occ:  73.05   1.72  15.89  73.05   1.72  12.24  72.06   6.19  35.81
   5_bss:  72.99   1.66  15.83  72.99   1.66  12.18  72.00   6.13  35.75
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.942    0.016    0.309
   1_adp:    0.942    0.016    0.309
   1_occ:    0.942    0.016    0.309
   2_bss:    0.942    0.016    0.309
   2_xyz:    0.782    0.029    0.321
   2_adp:    0.782    0.029    0.321
   2_occ:    0.782    0.029    0.321
   3_bss:    0.782    0.029    0.321
   3_xyz:    1.067    0.027    0.348
   3_adp:    1.067    0.027    0.348
   3_occ:    1.067    0.027    0.348
   4_bss:    1.067    0.027    0.348
   4_xyz:    1.355    0.021    0.363
   4_adp:    1.355    0.021    0.363
   4_occ:    1.355    0.021    0.363
   5_bss:    1.355    0.021    0.363
   5_xyz:    1.405    0.039    0.369
   5_adp:    1.405    0.039    0.369
   5_occ:    1.405    0.039    0.369
   5_bss:    1.405    0.039    0.369
------------------------------------------------------------------------

CPU time actual refinement: 325.67


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_536/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_536/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_536/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_536/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_536/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.51 
  Macro-tasks:
    bulk solvent and scale       = 36.83  
    individual site refinement   = 135.92 
    weights calculation          = 29.29  
    collect and process          = 6.65   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 208.83 
  Micro-tasks:
    mask                            = 1.20   
    f_calc                          = 103.55 
    alpha_beta                      = 8.00   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.34 
    fmodel                         = 6.77   
    r_factors                      = 0.21   
    phase_errors                   = 10.92  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 245.49 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.588 micro seconds
Total CPU time: 5.66 minutes
from_scatterers_fft:    656 calls, 103.19 s
gradients_fft:          601 calls,  99.23 s

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

# Date 2008-01-16 Time 05:03:20 PST -0800 (1200488600.54 s)
Start R-work = 0.3104, R-free = 0.3065 (no bulk solvent and anisotropic scale)
Final R-work = 0.1318, R-free = 0.1738 (no bulk solvent and anisotropic scale)

Start R-work = 0.2942, R-free = 0.2909
Final R-work = 0.1079, R-free = 0.1542