# Date 2008-01-16 Time 01:03:59 PST -0800 (1200474239.11 s)
#phil __OFF__

Command line arguments: "../270.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28779
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 270

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.2261, 86.822, 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: 3.26, per 1000 atoms: 1.15


================================== 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: (69.1963, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8486 1.97033
Completeness in resolution range: 0.966881
Completeness with d_max=infinity: 0.963883

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8486
                             d_min =   1.9703

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: (69.1963, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8486 1.97033
Completeness in resolution range: 0.966881
Completeness with d_max=infinity: 0.963883

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8490 -  4.2156 [2138/2162]  1920   218  10.2%
  bin  2:  4.2156 -  3.3588 [2039/2059]  1841   198   9.7%
  bin  3:  3.3588 -  2.9380 [2018/2037]  1815   203  10.1%
  bin  4:  2.9380 -  2.6710 [1980/2010]  1776   204  10.3%
  bin  5:  2.6710 -  2.4805 [2004/2023]  1808   196   9.8%
  bin  6:  2.4805 -  2.3349 [1980/2005]  1781   199  10.1%
  bin  7:  2.3349 -  2.2183 [1959/1987]  1765   194   9.9%
  bin  8:  2.2183 -  2.1221 [1961/1997]  1763   198  10.1%
  bin  9:  2.1221 -  2.0406 [1951/1993]  1760   191   9.8%
  bin 10:  2.0406 -  1.9703 [1559/1987]  1401   158  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_270/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: 0.15 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:
        1.79 -     2.41: 39
        2.41 -     3.03: 2158
        3.03 -     3.66: 4762
        3.66 -     4.28: 9197
        4.28 -     4.90: 12529
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.788 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  70 " - " O   HOH Z 302 "  1.841 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.901 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.928 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28680 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_270/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_270/model_refine_001.geo

CPU time processing inputs: 9.23


============================ 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 = 69.19625 46.22605 86.82195 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4722   r_free= 0.4671   ksol= 0.00   Bsol= 0.00   scale= 0.806    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.272682                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7017 0.99   1389  152 0.3906 0.3838       6.574      6.5674|
|  2:  4.7017 -  3.7517 0.99   1320  154 0.3778 0.3739       6.742      6.7489|
|  3:  3.7517 -  3.2833 0.99   1299  140 0.4215 0.3932      6.6568      6.6496|
|  4:  3.2833 -  2.9857 0.99   1307  142 0.4564 0.4464      6.5233      6.4869|
|  5:  2.9857 -  2.7732 0.99   1279  145 0.4983 0.4846      6.3677      6.3821|
|  6:  2.7732 -  2.6106 0.99   1289  142 0.4981 0.5480      6.2813      6.2143|
|  7:  2.6106 -  2.4805 0.99   1277  144 0.5032 0.4935      6.2452       6.186|
|  8:  2.4805 -  2.3730 0.98   1270  138 0.5221 0.4947        6.19      6.2174|
|  9:  2.3730 -  2.2820 0.98   1267  143 0.5103 0.5611      6.1079      6.1735|
| 10:  2.2820 -  2.2035 1.00   1273  142 0.5362 0.5100      6.1314      6.0723|
| 11:  2.2035 -  2.1348 0.97   1257  135 0.5355 0.5033      6.0404      6.0778|
| 12:  2.1348 -  2.0740 0.98   1243  141 0.5273 0.5055      5.9873      6.0331|
| 13:  2.0740 -  2.0195 1.00   1263  135 0.5312 0.4984      5.9007      5.8397|
| 14:  2.0195 -  1.9703 0.70    897  106 0.5402 0.5455      5.8801      5.7675|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7017  1389   152  0.69  35.54   0.80     0.73      75436.15|
|  2:  4.7017 -  3.7517  1320   154  0.72  33.69   0.89     0.79      99311.53|
|  3:  3.7517 -  3.2833  1299   140  0.63  41.62   0.87     0.74     105241.10|
|  4:  3.2833 -  2.9857  1307   142  0.54  48.74   0.81     0.63      95117.52|
|  5:  2.9857 -  2.7732  1279   145  0.43  57.81   0.76     0.51      81333.58|
|  6:  2.7732 -  2.6106  1289   142  0.38  61.17   0.72     0.43      73281.89|
|  7:  2.6106 -  2.4805  1277   144  0.32  65.92   0.76     0.37      70414.44|
|  8:  2.4805 -  2.3730  1270   138  0.31  67.02   0.73     0.36      64159.83|
|  9:  2.3730 -  2.2820  1267   143  0.32  65.76   0.74     0.39      57682.48|
| 10:  2.2820 -  2.2035  1273   142  0.36  62.91   0.75     0.43      48669.76|
| 11:  2.2035 -  2.1348  1257   135  0.36  62.85   0.75     0.45      45700.01|
| 12:  2.1348 -  2.0740  1243   141  0.35  64.25   0.78     0.43      42032.37|
| 13:  2.0740 -  2.0195  1263   135  0.32  66.12   0.74     0.40      36996.76|
| 14:  2.0195 -  1.9703   897   106  0.32  65.83   0.73     0.35      29749.59|
|alpha:            min =        0.35 max =            0.79 mean =         0.51|
|beta:             min =    29749.59 max =       105241.10 mean =     67211.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.63|
|phase err.(test): min =        0.00 max =           89.95 mean =        56.84|
|-----------------------------------------------------------------------------|

============================== 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 = 13.018883             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.256   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.298476              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.455   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       33 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      178 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      706 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1542 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2662 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4015 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5141 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6637 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7794 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.171 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.196 |       2.204 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    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:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     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:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4796   r_free= 0.4680   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.274839                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4642   r_free= 0.4521   ksol= 0.39   Bsol= 20.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.41,9.73,8.18,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.265499                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.688385             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.837   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.167085              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.617   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4642      final r-factor (work) = 0.3795          |
| start r-factor (free) = 0.4521      final r-factor (free) = 0.3961          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.6977 = 10.69 * 0.50 * 6.2735 + 1.00 * 53.1710                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.1469 = 10.69 * 0.50 * 6.1773 + 1.00 * 0.1342                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3795      final r-factor (work) = 0.3326          |
| start r-factor (free) = 0.3961      final r-factor (free) = 0.3844          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2238 = 1.17 * 1.00 * 6.1773 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1083 = 1.17 * 1.00 * 6.0764 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    54.64   12.25    None  None   None       |
|    all(noH): 2823   0      0.00    54.64   12.25    None  None   None       |
|    Sol.    : 438    0      0.00    54.64   23.30    None  None   None       |
|    Mac.    : 2385   0      0.00    48.53   10.22    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 -   5.464:  790   |   5:    27.319 -  32.783:  121        |
|      1:     5.464 -  10.928:  724   |   6:    32.783 -  38.247:   78        |
|      2:    10.928 -  16.391:  521   |   7:    38.247 -  43.710:   33        |
|      3:    16.391 -  21.855:  336   |   8:    43.710 -  49.174:   12        |
|      4:    21.855 -  27.319:  200   |   9:    49.174 -  54.638:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3326 r_free = 0.3844             target_work(ml) = 6.058         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3321 r_free = 0.3842             target_work(ml) = 6.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3321   r_free= 0.3842   ksol= 0.39   Bsol= 20.00   scale= 1.113   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.41,9.73,8.18,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.057704                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3284   r_free= 0.3794   ksol= 0.33   Bsol= 20.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.01,5.35,4.89,0.00,0.00,0.00); trace/3= 4.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.057583                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.918094              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.637   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.527156              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.061  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3284      final r-factor (work) = 0.2418          |
| start r-factor (free) = 0.3794      final r-factor (free) = 0.2975          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1049 = 5.92 * 0.50 * 6.0731 + 1.00 * 0.1342                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6290 = 5.92 * 0.50 * 5.9298 + 1.00 * 0.0824                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2418      final r-factor (work) = 0.2151          |
| start r-factor (free) = 0.2975      final r-factor (free) = 0.2706          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1427 = 0.53 * 1.00 * 5.9298 + 1.00 * 0.0168                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0422 = 0.53 * 1.00 * 5.7489 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.61   12.48    None  None   None       |
|    all(noH): 2823   0      0.00    74.61   12.48    None  None   None       |
|    Sol.    : 438    0      0.00    74.61   31.18    None  None   None       |
|    Mac.    : 2385   0      0.00    61.98   9.05     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 -   7.461: 1285   |   5:    37.304 -  44.765:   94        |
|      1:     7.461 -  14.922:  792   |   6:    44.765 -  52.226:   61        |
|      2:    14.922 -  22.383:  270   |   7:    52.226 -  59.687:   19        |
|      3:    22.383 -  29.843:  165   |   8:    59.687 -  67.148:    5        |
|      4:    29.843 -  37.304:  131   |   9:    67.148 -  74.609:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2151 r_free = 0.2706             target_work(ml) = 5.706         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2148 r_free = 0.2704             target_work(ml) = 5.706         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2148   r_free= 0.2704   ksol= 0.33   Bsol= 20.00   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.01,5.35,4.89,0.00,0.00,0.00); trace/3= 4.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.705538                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2133   r_free= 0.2689   ksol= 0.34   Bsol= 40.48   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.35,3.27,3.83,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.702795                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.351247              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.134   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.321855              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.553  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2133      final r-factor (work) = 0.1559          |
| start r-factor (free) = 0.2689      final r-factor (free) = 0.2041          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7212 = 3.35 * 0.50 * 5.7526 + 1.00 * 0.0820                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4031 = 3.35 * 0.50 * 5.5725 + 1.00 * 0.0657                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1559      final r-factor (work) = 0.1422          |
| start r-factor (free) = 0.2041      final r-factor (free) = 0.1895          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8051 = 0.32 * 1.00 * 5.5725 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7395 = 0.32 * 1.00 * 5.3723 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.00   12.65    None  None   None       |
|    all(noH): 2823   0      0.00    76.00   12.65    None  None   None       |
|    Sol.    : 438    0      2.13    76.00   34.72    None  None   None       |
|    Mac.    : 2385   0      0.00    71.14   8.59     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 -   7.600: 1441   |   5:    37.999 -  45.599:  109        |
|      1:     7.600 -  15.200:  713   |   6:    45.599 -  53.198:   71        |
|      2:    15.200 -  22.799:  209   |   7:    53.198 -  60.798:   42        |
|      3:    22.799 -  30.399:  112   |   8:    60.798 -  68.398:   13        |
|      4:    30.399 -  37.999:  110   |   9:    68.398 -  75.998:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1422 r_free = 0.1895             target_work(ml) = 5.337         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1419 r_free = 0.1892             target_work(ml) = 5.336         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1892   ksol= 0.34   Bsol= 40.48   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.35,3.27,3.83,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.336238                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1416   r_free= 0.1887   ksol= 0.33   Bsol= 40.14   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,2.22,3.50,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.333478                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.655429              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.885  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.252509              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.036  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1416      final r-factor (work) = 0.1221          |
| start r-factor (free) = 0.1887      final r-factor (free) = 0.1670          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2018 = 2.66 * 0.50 * 5.3747 + 1.00 * 0.0657                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0605 = 2.66 * 0.50 * 5.2704 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1670      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3425 = 0.25 * 1.00 * 5.2704 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3413 = 0.25 * 1.00 * 5.1970 + 1.00 * 0.0291                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.35   12.53    None  None   None       |
|    all(noH): 2823   0      0.00    79.35   12.53    None  None   None       |
|    Sol.    : 438    0      2.28    74.53   34.78    None  None   None       |
|    Mac.    : 2385   0      0.00    79.35   8.45     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 -   7.936: 1534   |   5:    39.677 -  47.613:   92        |
|      1:     7.936 -  15.871:  669   |   6:    47.613 -  55.548:   72        |
|      2:    15.871 -  23.806:  180   |   7:    55.548 -  63.484:   30        |
|      3:    23.806 -  31.742:  113   |   8:    63.484 -  71.419:   10        |
|      4:    31.742 -  39.677:  119   |   9:    71.419 -  79.355:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1190 r_free = 0.1628             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1188 r_free = 0.1626             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1626   ksol= 0.33   Bsol= 40.14   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,2.22,3.50,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.181705                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1626   ksol= 0.32   Bsol= 40.14   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,2.04,3.53,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.181332                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.383473              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.037  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.457111              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.206   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1626      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6572 = 1.38 * 0.50 * 5.1960 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6326 = 1.38 * 0.50 * 5.1777 + 1.00 * 0.0509                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3789 = 0.46 * 1.00 * 5.1777 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3709 = 0.46 * 1.00 * 5.1628 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 36     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.07   12.58    None  None   None       |
|    all(noH): 2823   0      0.00    83.07   12.58    None  None   None       |
|    Sol.    : 438    0      2.26    75.61   35.35    None  None   None       |
|    Mac.    : 2385   0      0.00    83.07   8.40     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 -   8.307: 1598   |   5:    41.533 -  49.840:   92        |
|      1:     8.307 -  16.613:  635   |   6:    49.840 -  58.146:   66        |
|      2:    16.613 -  24.920:  162   |   7:    58.146 -  66.453:   26        |
|      3:    24.920 -  33.227:  123   |   8:    66.453 -  74.760:    6        |
|      4:    33.227 -  41.533:  111   |   9:    74.760 -  83.066:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1162 r_free = 0.1585             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1161 r_free = 0.1585             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1585   ksol= 0.32   Bsol= 40.14   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,2.04,3.53,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.163819                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7017 0.99   1389  152 0.1048 0.1218      5.4021      5.5023|
|  2:  4.7017 -  3.7517 0.99   1320  154 0.0894 0.1138      5.4632      5.6384|
|  3:  3.7517 -  3.2833 0.99   1299  140 0.1103 0.1460       5.505      5.8475|
|  4:  3.2833 -  2.9857 0.99   1307  142 0.1266 0.1678      5.4784      5.6174|
|  5:  2.9857 -  2.7732 0.99   1279  145 0.1359 0.1732      5.3507      5.5426|
|  6:  2.7732 -  2.6106 0.99   1289  142 0.1235 0.2040      5.2124      5.5191|
|  7:  2.6106 -  2.4805 0.99   1277  144 0.1301 0.1546      5.1845      5.3124|
|  8:  2.4805 -  2.3730 0.98   1270  138 0.1213 0.1640         5.1      5.3381|
|  9:  2.3730 -  2.2820 0.98   1267  143 0.1240 0.1895      5.0654      5.3339|
| 10:  2.2820 -  2.2035 1.00   1273  142 0.1162 0.1621      4.9863      5.1814|
| 11:  2.2035 -  2.1348 0.97   1257  135 0.1177 0.1771       4.965       5.285|
| 12:  2.1348 -  2.0740 0.98   1243  141 0.1185 0.1726      4.9074      5.2564|
| 13:  2.0740 -  2.0195 1.00   1263  135 0.1146 0.1756      4.8089      5.0629|
| 14:  2.0195 -  1.9703 0.70    897  106 0.1010 0.1660       4.651      4.8915|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7017  1389   152  0.94   8.92   0.98     0.96       6844.42|
|  2:  4.7017 -  3.7517  1320   154  0.95   7.74   1.02     1.01       8889.79|
|  3:  3.7517 -  3.2833  1299   140  0.93  11.32   1.04     1.03      10446.98|
|  4:  3.2833 -  2.9857  1307   142  0.92  13.53   1.01     1.01      10363.24|
|  5:  2.9857 -  2.7732  1279   145  0.90  15.64   1.00     0.97       8313.71|
|  6:  2.7732 -  2.6106  1289   142  0.90  15.87   0.98     0.96       6910.29|
|  7:  2.6106 -  2.4805  1277   144  0.90  15.65   0.99     0.96       6093.69|
|  8:  2.4805 -  2.3730  1270   138  0.91  15.22   1.00     0.98       5470.61|
|  9:  2.3730 -  2.2820  1267   143  0.91  15.61   1.01     0.98       5286.31|
| 10:  2.2820 -  2.2035  1273   142  0.90  15.99   1.00     0.96       4489.77|
| 11:  2.2035 -  2.1348  1257   135  0.90  16.49   1.01     0.98       4657.18|
| 12:  2.1348 -  2.0740  1243   141  0.90  16.18   1.02     1.01       4140.02|
| 13:  2.0740 -  2.0195  1263   135  0.91  15.82   1.01     1.00       3409.25|
| 14:  2.0195 -  1.9703   897   106  0.93  13.39   0.99     0.96       2408.97|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2408.97 max =        10446.98 mean =      6381.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.05|
|phase err.(test): min =        0.00 max =           88.12 mean =        13.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1590   ksol= 0.32   Bsol= 42.53   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,-0.40,1.17,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164176                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1590   ksol= 0.32   Bsol= 42.53   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,-0.40,1.17,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164176                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7017 0.99   1389  152 0.1035 0.1255       5.405      5.5174|
|  2:  4.7017 -  3.7517 0.99   1320  154 0.0904 0.1136      5.4708      5.6358|
|  3:  3.7517 -  3.2833 0.99   1299  140 0.1107 0.1462       5.506      5.8467|
|  4:  3.2833 -  2.9857 0.99   1307  142 0.1267 0.1694      5.4783      5.6245|
|  5:  2.9857 -  2.7732 0.99   1279  145 0.1356 0.1721      5.3509      5.5382|
|  6:  2.7732 -  2.6106 0.99   1289  142 0.1233 0.2026      5.2099      5.5178|
|  7:  2.6106 -  2.4805 0.99   1277  144 0.1300 0.1550      5.1832      5.3126|
|  8:  2.4805 -  2.3730 0.98   1270  138 0.1215 0.1637      5.0984      5.3377|
|  9:  2.3730 -  2.2820 0.98   1267  143 0.1236 0.1890       5.064      5.3324|
| 10:  2.2820 -  2.2035 1.00   1273  142 0.1160 0.1618      4.9861      5.1831|
| 11:  2.2035 -  2.1348 0.97   1257  135 0.1175 0.1769      4.9653      5.2859|
| 12:  2.1348 -  2.0740 0.98   1243  141 0.1183 0.1729      4.9072      5.2582|
| 13:  2.0740 -  2.0195 1.00   1263  135 0.1147 0.1755      4.8088      5.0621|
| 14:  2.0195 -  1.9703 0.70    897  106 0.1012 0.1657      4.6506      4.8917|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7017  1389   152  0.94   9.20   0.98     0.96       7122.16|
|  2:  4.7017 -  3.7517  1320   154  0.95   7.86   1.02     1.01       9041.17|
|  3:  3.7517 -  3.2833  1299   140  0.93  11.39   1.04     1.03      10473.88|
|  4:  3.2833 -  2.9857  1307   142  0.92  13.60   1.02     1.01      10380.44|
|  5:  2.9857 -  2.7732  1279   145  0.90  15.62   1.00     0.97       8306.42|
|  6:  2.7732 -  2.6106  1289   142  0.90  15.81   0.98     0.96       6869.11|
|  7:  2.6106 -  2.4805  1277   144  0.90  15.64   0.99     0.96       6085.85|
|  8:  2.4805 -  2.3730  1270   138  0.91  15.21   1.00     0.98       5451.31|
|  9:  2.3730 -  2.2820  1267   143  0.91  15.59   1.01     0.98       5282.33|
| 10:  2.2820 -  2.2035  1273   142  0.90  15.98   1.00     0.96       4480.86|
| 11:  2.2035 -  2.1348  1257   135  0.90  16.50   1.01     0.98       4666.92|
| 12:  2.1348 -  2.0740  1243   141  0.90  16.21   1.02     1.01       4150.00|
| 13:  2.0740 -  2.0195  1263   135  0.91  15.82   1.01     1.00       3411.77|
| 14:  2.0195 -  1.9703   897   106  0.93  13.38   0.99     0.96       2404.05|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2404.05 max =        10473.88 mean =      6412.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.09|
|phase err.(test): min =        0.00 max =           87.87 mean =        13.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.556)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.40    85.46   14.98    None  None   None       |
|    all(noH): 2823   0      2.40    85.46   14.98    None  None   None       |
|    Sol.    : 438    0      4.66    78.00   37.75    None  None   None       |
|    Mac.    : 2385   0      2.40    85.46   10.80    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:     2.398 -  10.705: 1598   |   5:    43.931 -  52.238:   92        |
|      1:    10.705 -  19.011:  635   |   6:    52.238 -  60.544:   66        |
|      2:    19.011 -  27.318:  162   |   7:    60.544 -  68.851:   26        |
|      3:    27.318 -  35.624:  123   |   8:    68.851 -  77.157:    6        |
|      4:    35.624 -  43.931:  111   |   9:    77.157 -  85.464:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 303         
Filter by distance & map next to the model:
   mapped sites are within: 0.352 - 3.997
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 300 from: 303
   mapped sites are within: 0.746 - 3.997

peak=   10.914 closest distance to " CB  VAL A 230 " =    1.429
peak=   10.608 closest distance to " CB  VAL A 296 " =    1.578
peak=    7.992 closest distance to " O   HOH Z 130 " =    1.517
peak=    6.348 closest distance to " CD2 LEU A   5 " =    1.234
peak=    5.914 closest distance to " NE2 GLN A  11 " =    1.188
peak=    5.731 closest distance to " CG  LEU A   5 " =    1.201
peak=    5.643 closest distance to " O   HOH Z 142 " =    1.958
peak=    5.627 closest distance to " CG  PRO A  54 " =    1.401
peak=    5.345 closest distance to " O   HOH Z   9 " =    1.728
peak=    5.292 closest distance to " CB  ARG A 275 " =    1.004
peak=    5.224 closest distance to " CB  PRO A  54 " =    1.048
peak=    5.181 closest distance to " NH2 ARG A  56 " =    2.032
peak=    5.130 closest distance to " O   HOH Z 232 " =    2.350
peak=    5.091 closest distance to " CG  LEU A 228 " =    1.200
peak=    5.068 closest distance to " O   HOH Z  65 " =    1.113
peak=    4.997 closest distance to " CD1AILE A 234 " =    0.971
peak=    4.979 closest distance to " O   HOH Z 423 " =    1.621
peak=    4.964 closest distance to " CB  VAL A 230 " =    1.172
peak=    4.908 closest distance to " O   HOH Z 124 " =    1.351
peak=    4.880 closest distance to " O   HOH Z 427 " =    2.605
peak=    4.757 closest distance to " O   HOH Z 209 " =    2.370
peak=    4.729 closest distance to " CB  SER A   3 " =    1.285
peak=    4.694 closest distance to " O   HOH Z  78 " =    1.647
peak=    4.629 closest distance to " O   HOH Z 380 " =    1.786
peak=    4.585 closest distance to " O   HOH Z 346 " =    1.591
peak=    4.577 closest distance to " CB  GLN A 223 " =    1.549
peak=    4.503 closest distance to " O   HOH Z 112 " =    1.203
peak=    4.471 closest distance to " CG  PRO A 243 " =    1.158
peak=    4.460 closest distance to " CG  PRO A 198 " =    1.303
peak=    4.459 closest distance to " O   HOH Z  85 " =    1.423
peak=    4.408 closest distance to " O   HOH Z 403 " =    1.746
peak=    4.382 closest distance to " O   HOH Z 193 " =    1.666
peak=    4.376 closest distance to " O   HOH Z 272 " =    1.836
peak=    4.361 closest distance to " CB  ASN A 148 " =    1.355
peak=    4.336 closest distance to " CG2 VAL A 257 " =    0.871
peak=    4.327 closest distance to " O   HOH Z 369 " =    2.287
peak=    4.313 closest distance to " O   HOH Z 236 " =    1.431
peak=    4.288 closest distance to " O   SER A  87 " =    2.282
peak=    4.254 closest distance to " CB  GLN A 183 " =    1.195
peak=    4.239 closest distance to " CB  SER A  63 " =    1.237
peak=    4.237 closest distance to " CG  PRO A 213 " =    1.254
peak=    4.231 closest distance to " O   HOH Z 419 " =    2.069
peak=    4.225 closest distance to " ND2 ASN A 187 " =    1.747
peak=    4.222 closest distance to " O   HOH Z  68 " =    2.116
peak=    4.218 closest distance to " O   HOH Z 126 " =    1.816
peak=    4.212 closest distance to " CB  VAL A 265 " =    1.318
peak=    4.209 closest distance to " NH2AARG A 190 " =    1.786
peak=    4.204 closest distance to " O   HOH Z 417 " =    1.319
peak=    4.134 closest distance to " O   HOH Z 123 " =    1.213
peak=    4.126 closest distance to " O   HOH Z 366 " =    2.739
peak=    4.092 closest distance to " O   HOH Z 203 " =    1.628
peak=    4.088 closest distance to " O   HOH Z 424 " =    1.278
peak=    4.087 closest distance to " O   HOH Z  39 " =    1.324
peak=    4.087 closest distance to " O   HOH Z 425 " =    1.488
peak=    4.076 closest distance to " CB  VAL A 202 " =    1.670
peak=    4.053 closest distance to " CB BVAL A  41 " =    1.213
peak=    4.051 closest distance to " CB  ASN A 142 " =    1.032
peak=    4.047 closest distance to " O   HOH Z 422 " =    2.468
peak=    4.044 closest distance to " OG ASER A 258 " =    2.963
peak=    4.044 closest distance to " O   HOH Z 234 " =    3.653
peak=    4.042 closest distance to " O   HOH Z 130 " =    2.096
peak=    4.029 closest distance to " N   PHE A 130 " =    1.306
peak=    4.007 closest distance to " O   HOH Z  30 " =    1.624
peak=    3.998 closest distance to " O   HOH Z  78 " =    1.935
peak=    3.988 closest distance to " CB  TRP A 266 " =    1.070
peak=    3.985 closest distance to " O   HOH Z 368 " =    2.056
peak=    3.960 closest distance to " CB  ARG A  79 " =    1.392
peak=    3.946 closest distance to " O   HOH Z 261 " =    2.014
peak=    3.933 closest distance to " O   HOH Z 298 " =    1.754
peak=    3.930 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.930 closest distance to " O   HOH Z 362 " =    2.444
peak=    3.913 closest distance to " O   HOH Z 193 " =    1.700
peak=    3.903 closest distance to " CB  ASN A 187 " =    1.104
peak=    3.897 closest distance to " O   HOH Z 359 " =    1.324
peak=    3.887 closest distance to " CD2 LEU A 228 " =    1.153
peak=    3.884 closest distance to " C   PRO A 198 " =    1.487
peak=    3.879 closest distance to " CB  GLU A 277 " =    3.469
peak=    3.875 closest distance to " O   HOH Z   3 " =    2.101
peak=    3.864 closest distance to " CA  ASN A 215 " =    0.984
peak=    3.863 closest distance to " O   HOH Z 143 " =    1.414
peak=    3.861 closest distance to " O   HOH Z 222 " =    2.347
peak=    3.856 closest distance to " O   HOH Z   2 " =    1.783
peak=    3.837 closest distance to " O   HOH Z  55 " =    2.090
peak=    3.820 closest distance to " CA  PHE A 283 " =    1.118
peak=    3.809 closest distance to " O   HOH Z 287 " =    1.777
peak=    3.798 closest distance to " O   HOH Z 411 " =    3.592
peak=    3.795 closest distance to " O   HOH Z 375 " =    2.578
peak=    3.794 closest distance to " CD  ARG A 269 " =    1.039
peak=    3.793 closest distance to " O   HOH Z 248 " =    1.634
peak=    3.778 closest distance to " O   HOH Z 425 " =    2.032
peak=    3.775 closest distance to " O   HOH Z 145 " =    2.097
peak=    3.757 closest distance to " CA  TYR A  30 " =    0.984
peak=    3.756 closest distance to " O   HOH Z 389 " =    1.278
peak=    3.753 closest distance to " O   HOH Z 402 " =    1.361
peak=    3.748 closest distance to " NE  ARG A  56 " =    3.427
peak=    3.746 closest distance to " CB  ASN A  39 " =    0.947
peak=    3.746 closest distance to " O   HOH Z 146 " =    1.568
peak=    3.746 closest distance to " O   HOH Z  44 " =    1.720
peak=    3.731 closest distance to " CG  LEU A 167 " =    1.256
peak=    3.730 closest distance to " CB  GLU A 152 " =    1.206
peak=    3.717 closest distance to " CE AMET A  47 " =    1.382
peak=    3.707 closest distance to " CB  TRP A 179 " =    1.293
peak=    3.704 closest distance to " O   HOH Z 117 " =    1.959
peak=    3.694 closest distance to " O   HOH Z 261 " =    1.670
peak=    3.692 closest distance to " O   HOH Z  88 " =    2.798
peak=    3.685 closest distance to " O   HOH Z 118 " =    1.472
peak=    3.679 closest distance to " O   HOH Z 371 " =    2.864
peak=    3.678 closest distance to " O   HOH Z 423 " =    1.752
peak=    3.676 closest distance to " O   HOH Z  59 " =    1.673
peak=    3.671 closest distance to " CG  ARG A 138 " =    1.195
peak=    3.635 closest distance to " NZ  LYS A  48 " =    1.146
peak=    3.633 closest distance to " OG  SER A  97 " =    2.911
peak=    3.629 closest distance to " CB  ALA A 114 " =    1.533
peak=    3.622 closest distance to " OG BSER A 164 " =    2.138
peak=    3.614 closest distance to " O   HOH Z  97 " =    2.405
peak=    3.613 closest distance to " CG  LYS A  76 " =    1.616
peak=    3.611 closest distance to " CB  SER A 216 " =    0.811
peak=    3.611 closest distance to " CB  SER A  26 " =    1.653
peak=    3.592 closest distance to " CB  ALA A 248 " =    1.380
peak=    3.589 closest distance to " CB  ASN A 110 " =    1.030
peak=    3.584 closest distance to " O   HOH Z 405 " =    1.359
peak=    3.583 closest distance to " OE1 GLU A   2 " =    2.086
peak=    3.583 closest distance to " CB  HIS A 108 " =    0.861
peak=    3.575 closest distance to " CB  THR A  31 " =    1.550
peak=    3.569 closest distance to " CB  GLU A 128 " =    1.024
peak=    3.565 closest distance to " CG  TRP A 179 " =    2.177
peak=    3.561 closest distance to " CB  SER A 273 " =    0.910
peak=    3.559 closest distance to " OG BSER A 210 " =    1.448
peak=    3.552 closest distance to " O   PRO A 198 " =    1.375
peak=    3.542 closest distance to " CZ  PHE A 218 " =    1.164
peak=    3.540 closest distance to " O   HOH Z  10 " =    1.722
peak=    3.539 closest distance to " O   HOH Z 128 " =    2.090
peak=    3.536 closest distance to " CB  GLN A  88 " =    1.274
peak=    3.534 closest distance to " O   HOH Z 128 " =    2.085
peak=    3.533 closest distance to " CB  ASN A 215 " =    1.089
peak=    3.529 closest distance to " CA  LYS A 117 " =    1.190
peak=    3.528 closest distance to " CG AARG A 275 " =    1.108
peak=    3.528 closest distance to " O   HOH Z 352 " =    1.316
peak=    3.524 closest distance to " O   HOH Z 345 " =    3.241
peak=    3.517 closest distance to " O  BHOH Z 338 " =    2.460
peak=    3.516 closest distance to " N   ASN A  39 " =    1.116
peak=    3.515 closest distance to " CB  ARG A 138 " =    0.880
peak=    3.510 closest distance to " O   HOH Z 250 " =    1.392
peak=    3.509 closest distance to " CB  GLN A 278 " =    0.891
peak=    3.508 closest distance to " N   ARG A 156 " =    1.296
peak=    3.507 closest distance to " CG2 ILE A  20 " =    1.661
peak=    3.507 closest distance to " O   HOH Z 272 " =    2.112
peak=    3.503 closest distance to " O   HOH Z 109 " =    2.447
peak=    3.503 closest distance to " CG1 VAL A 153 " =    0.889
peak=    3.499 closest distance to " O   HOH Z  43 " =    1.962
peak=    3.495 closest distance to " CB  ARG A  79 " =    0.870
peak=    3.494 closest distance to " CG1BVAL A  72 " =    1.371
peak=    3.486 closest distance to " O   HOH Z 368 " =    3.495
peak=    3.486 closest distance to " NZ  LYS A 117 " =    2.958
peak=    3.485 closest distance to " NH1 ARG A  14 " =    1.132
peak=    3.481 closest distance to " O   HOH Z 257 " =    2.221
peak=    3.480 closest distance to " O   HOH Z 263 " =    1.581
peak=    3.479 closest distance to " CD2 TRP A 179 " =    1.357
peak=    3.476 closest distance to " O   HOH Z 153 " =    3.762
peak=    3.474 closest distance to " O   HOH Z 435 " =    1.958
peak=    3.472 closest distance to " CA  ASN A 127 " =    1.031
peak=    3.468 closest distance to " CG  MET A 113 " =    0.918
peak=    3.458 closest distance to " CA  ALA A  51 " =    0.997
peak=    3.458 closest distance to " NE1 TRP A 274 " =    0.995
peak=    3.458 closest distance to " N   SER A 135 " =    1.357
peak=    3.456 closest distance to " O   HOH Z 273 " =    2.947
peak=    3.446 closest distance to " CB  SER A 276 " =    1.212
peak=    3.446 closest distance to " O   HOH Z  40 " =    1.729
peak=    3.441 closest distance to " O   HOH Z 181 " =    2.159
peak=    3.439 closest distance to " O   HOH Z 437 " =    2.041
peak=    3.432 closest distance to " O   HOH Z 305 " =    3.432
peak=    3.432 closest distance to " CG2 ILE A 120 " =    1.208
peak=    3.432 closest distance to " O   HOH Z 365 " =    1.812
peak=    3.429 closest distance to " O   HOH Z 158 " =    3.125
peak=    3.427 closest distance to " O   HOH Z  61 " =    1.528
peak=    3.416 closest distance to " O   HOH Z 375 " =    1.044
peak=    3.413 closest distance to " CG2 ILE A 234 " =    0.772
peak=    3.411 closest distance to " NH1BARG A 145 " =    1.370
peak=    3.406 closest distance to " CG  LEU A 281 " =    1.045
peak=    3.405 closest distance to " O  BHOH Z  74 " =    1.196
peak=    3.401 closest distance to " CB  ARG A 139 " =    0.971
peak=    3.399 closest distance to " O   HOH Z 196 " =    1.487
peak=    3.394 closest distance to " N   SER A 271 " =    1.001
peak=    3.394 closest distance to " CG BARG A 102 " =    1.855
peak=    3.392 closest distance to " O   HOH Z 357 " =    1.889
peak=    3.389 closest distance to " CG  GLN A  88 " =    1.108
peak=    3.384 closest distance to " CA  SER A  87 " =    0.987
peak=    3.378 closest distance to " O   ASP A 124 " =    1.111
peak=    3.376 closest distance to " CB  ALA A   9 " =    1.492
peak=    3.373 closest distance to " O   HOH Z   1 " =    1.613
peak=    3.371 closest distance to " CA  ARG A 195 " =    1.188
peak=    3.364 closest distance to " N   GLN A 278 " =    1.262
peak=    3.362 closest distance to " ND2 ASN A 249 " =    0.855
peak=    3.359 closest distance to " CD  GLN A 194 " =    1.357
peak=    3.354 closest distance to " CB  GLU A 175 " =    1.134
peak=    3.353 closest distance to " O   HOH Z  89 " =    2.146
peak=    3.347 closest distance to " CG  MET A 185 " =    1.287
peak=    3.344 closest distance to " OE2 GLU A   2 " =    1.848
peak=    3.339 closest distance to " CB  LYS A 117 " =    1.232
peak=    3.337 closest distance to " CB  ALA A 291 " =    1.221
peak=    3.333 closest distance to " O   HOH Z   9 " =    1.812
peak=    3.333 closest distance to " CB  ARG A 190 " =    1.685
peak=    3.332 closest distance to " O   HOH Z 234 " =    1.994
peak=    3.332 closest distance to " O   HOH Z 371 " =    1.654
peak=    3.331 closest distance to " CB  SER A 210 " =    0.760
peak=    3.330 closest distance to " O   HOH Z  58 " =    1.739
peak=    3.330 closest distance to " O   HOH Z  59 " =    2.028
peak=    3.324 closest distance to " CG1 ILE A  33 " =    1.373
peak=    3.321 closest distance to " CB  LEU A 300 " =    0.895
peak=    3.320 closest distance to " CA  ILE A 234 " =    0.992
peak=    3.318 closest distance to " NH2BARG A 190 " =    1.532
peak=    3.318 closest distance to " O   HOH Z 126 " =    1.480
peak=    3.315 closest distance to " CA  MET A 105 " =    0.958
peak=    3.314 closest distance to " CE3 TRP A 150 " =    0.988
peak=    3.309 closest distance to " OH  TYR A 116 " =    1.083
peak=    3.307 closest distance to " CB  ARG A 219 " =    0.939
peak=    3.304 closest distance to " OG  SER A  62 " =    2.586
peak=    3.304 closest distance to " CB  PRO A  90 " =    1.153
peak=    3.298 closest distance to " NH1AARG A 145 " =    1.101
peak=    3.298 closest distance to " CB  PHE A 204 " =    0.967
peak=    3.295 closest distance to " NZ  LYS A 119 " =    2.694
peak=    3.295 closest distance to " CG2 THR A 294 " =    1.741
peak=    3.295 closest distance to " CE  LYS A  76 " =    0.883
peak=    3.290 closest distance to " O   HOH Z 327 " =    1.885
peak=    3.288 closest distance to " O   HOH Z 116 " =    2.809
peak=    3.284 closest distance to " O   HOH Z 303 " =    1.683
peak=    3.281 closest distance to " CG  LYS A 119 " =    1.132
peak=    3.275 closest distance to " OG ASER A  99 " =    1.540
peak=    3.271 closest distance to " CE1 HIS A 108 " =    1.235
peak=    3.267 closest distance to " O   HOH Z 194 " =    2.084
peak=    3.265 closest distance to " CD1 LEU A   5 " =    1.673
peak=    3.263 closest distance to " O   HOH Z 435 " =    1.823
peak=    3.261 closest distance to " O   HOH Z 132 " =    2.402
peak=    3.260 closest distance to " CD1 ILE A  33 " =    1.793
peak=    3.258 closest distance to " OG  SER A  62 " =    2.890
peak=    3.257 closest distance to " O   ASN A  74 " =    1.547
peak=    3.257 closest distance to " O   HOH Z 284 " =    2.932
peak=    3.257 closest distance to " CE1 TYR A 186 " =    1.297
peak=    3.248 closest distance to " CB  ALA A  10 " =    0.746
peak=    3.247 closest distance to " CB  TYR A  30 " =    1.690
peak=    3.244 closest distance to " CE  MET A  40 " =    1.074
peak=    3.242 closest distance to " O   HOH Z 389 " =    1.601
peak=    3.241 closest distance to " O   HOH Z 392 " =    1.273
peak=    3.238 closest distance to " O   HOH Z 251 " =    1.712
peak=    3.236 closest distance to " O   HOH Z 197 " =    3.112
peak=    3.233 closest distance to " OD1 ASN A  69 " =    2.397
peak=    3.232 closest distance to " N   ASP A 162 " =    1.127
peak=    3.232 closest distance to " CB  SER A  62 " =    1.288
peak=    3.229 closest distance to " CB  THR A 157 " =    1.156
peak=    3.227 closest distance to " O   HOH Z 344 " =    2.882
peak=    3.225 closest distance to " O   HOH Z 329 " =    3.989
peak=    3.224 closest distance to " O   THR A 182 " =    1.460
peak=    3.221 closest distance to " CA  ALA A  84 " =    1.283
peak=    3.220 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.215 closest distance to " C   ALA A 299 " =    0.982
peak=    3.209 closest distance to " O   HOH Z 334 " =    1.376
peak=    3.205 closest distance to " CA  ALA A 129 " =    1.395
peak=    3.205 closest distance to " CH2 TRP A 266 " =    1.134
peak=    3.205 closest distance to " ND1 HIS A  86 " =    1.801
peak=    3.204 closest distance to " O   HOH Z 148 " =    2.304
peak=    3.201 closest distance to " O   HOH Z 291 " =    1.689
peak=    3.197 closest distance to " O   HOH Z  47 " =    1.534
peak=    3.194 closest distance to " CB  ASP A 124 " =    0.773
peak=    3.194 closest distance to " O   ARG A 145 " =    1.794
peak=    3.189 closest distance to " CA  LYS A 290 " =    1.257
peak=    3.189 closest distance to " CB  PRO A 198 " =    0.884
peak=    3.187 closest distance to " CB  ALA A 114 " =    1.189
peak=    3.185 closest distance to " O   HOH Z   6 " =    1.512
peak=    3.185 closest distance to " O   HOH Z 396 " =    1.485
peak=    3.184 closest distance to " CG  GLN A  89 " =    1.436
peak=    3.175 closest distance to " NH2BARG A 145 " =    2.068
peak=    3.168 closest distance to " CA  ASN A 217 " =    1.178
peak=    3.165 closest distance to " CA  ARG A  36 " =    0.964
peak=    3.158 closest distance to " CB  VAL A 268 " =    0.842
peak=    3.156 closest distance to " CG1 ILE A 151 " =    1.031
peak=    3.154 closest distance to " CE  LYS A  48 " =    1.128
peak=    3.152 closest distance to " OE2 GLU A  53 " =    1.957
peak=    3.146 closest distance to " CG1 ILE A 120 " =    1.322
peak=    3.144 closest distance to " CG1 ILE A 263 " =    1.241
peak=    3.144 closest distance to " O   HOH Z 323 " =    1.474
peak=    3.139 closest distance to " O   HOH Z 180 " =    2.082
peak=    3.135 closest distance to " O   HOH Z 193 " =    1.784
peak=    3.130 closest distance to " CB  SER A  99 " =    0.983
peak=    3.126 closest distance to " O   HOH Z 302 " =    1.672
peak=    3.122 closest distance to " O   HOH Z 234 " =    2.236
peak=    3.118 closest distance to " O   HOH Z 156 " =    3.137
peak=    3.115 closest distance to " O   HOH Z 366 " =    2.217
peak=    3.112 closest distance to " CB  ASP A 140 " =    0.880
peak=    3.105 closest distance to " N   GLU A   2 " =    1.479
peak=    3.086 closest distance to " O   HOH Z   7 " =    1.395
peak=    3.086 closest distance to " O   HOH Z  51 " =    1.192
peak=    3.084 closest distance to " O   HOH Z 189 " =    3.923
peak=    3.083 closest distance to " NE2 GLN A  58 " =    3.997
peak=    3.077 closest distance to " ND2 ASN A 110 " =    1.624
peak=    3.062 closest distance to " CD1 LEU A 261 " =    1.188
peak=    3.057 closest distance to " O   HOH Z  59 " =    2.082
peak=    3.052 closest distance to " N   ALA A 256 " =    1.066
peak=    3.049 closest distance to " O   HOH Z 105 " =    1.622
peak=    3.034 closest distance to " N   VAL A 257 " =    1.550
peak=    3.026 closest distance to " O   HOH Z  88 " =    2.912

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.711 - 5.425
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 184 from: 185
   mapped sites are within: 0.711 - 5.425

peak=   -4.832 closest distance to " CG2 VAL A 230 " =    0.711
peak=   -4.578 closest distance to " CD  ARG A 156 " =    2.014
peak=   -4.432 closest distance to " CG  GLN A  58 " =    0.938
peak=   -4.221 closest distance to " O   VAL A  67 " =    2.456
peak=   -4.216 closest distance to " CD1 LEU A 255 " =    2.795
peak=   -4.213 closest distance to " O   HOH Z 290 " =    0.985
peak=   -4.176 closest distance to " CB  PRO A 243 " =    2.646
peak=   -4.157 closest distance to " CB  ALA A  43 " =    2.411
peak=   -4.141 closest distance to " O   HOH Z 429 " =    2.012
peak=   -4.093 closest distance to " SG  CYS A 254 " =    3.313
peak=   -4.068 closest distance to " C   HIS A 108 " =    1.217
peak=   -4.067 closest distance to " O   PRO A 198 " =    1.165
peak=   -4.022 closest distance to " OG BSER A 134 " =    1.287
peak=   -4.008 closest distance to " O   HOH Z 351 " =    1.499
peak=   -3.982 closest distance to " CG  GLN A 223 " =    1.858
peak=   -3.947 closest distance to " O   HOH Z  11 " =    1.808
peak=   -3.936 closest distance to " O   HOH Z 211 " =    1.471
peak=   -3.917 closest distance to " OD2 ASP A 191 " =    1.305
peak=   -3.904 closest distance to " CG2 ILE A  20 " =    2.892
peak=   -3.890 closest distance to " O   HOH Z 266 " =    5.081
peak=   -3.885 closest distance to " O   ALA A 292 " =    2.173
peak=   -3.853 closest distance to " OG  SER A   3 " =    1.430
peak=   -3.797 closest distance to " O   HOH Z 185 " =    2.125
peak=   -3.783 closest distance to " O   HOH Z 131 " =    4.091
peak=   -3.773 closest distance to " CB  PHE A 192 " =    1.891
peak=   -3.751 closest distance to " O   HOH Z 377 " =    0.992
peak=   -3.747 closest distance to " N   THR A 157 " =    1.421
peak=   -3.728 closest distance to " O   SER A 135 " =    1.438
peak=   -3.708 closest distance to " CB  VAL A 230 " =    1.106
peak=   -3.686 closest distance to " NH2 ARG A  79 " =    2.029
peak=   -3.686 closest distance to " O   PRO A 163 " =    1.982
peak=   -3.683 closest distance to " N   GLN A  58 " =    1.967
peak=   -3.678 closest distance to " O   HOH Z 231 " =    1.891
peak=   -3.674 closest distance to " O   HOH Z 313 " =    1.601
peak=   -3.673 closest distance to " CZ2 TRP A 274 " =    0.894
peak=   -3.669 closest distance to " N   THR A  52 " =    1.744
peak=   -3.669 closest distance to " CE2 TYR A  30 " =    2.824
peak=   -3.668 closest distance to " ND2 ASN A 187 " =    1.510
peak=   -3.647 closest distance to " O   SER A  22 " =    2.274
peak=   -3.647 closest distance to " CA  GLY A 133 " =    1.963
peak=   -3.617 closest distance to " CD  LYS A 289 " =    2.418
peak=   -3.605 closest distance to " ND2 ASN A 249 " =    2.416
peak=   -3.604 closest distance to " CG  PHE A 283 " =    2.604
peak=   -3.599 closest distance to " O   ALA A 161 " =    1.653
peak=   -3.590 closest distance to " CA  GLY A 203 " =    2.326
peak=   -3.590 closest distance to " CB  SER A 210 " =    1.135
peak=   -3.577 closest distance to " OE1 GLN A  88 " =    1.183
peak=   -3.576 closest distance to " CE2 PHE A 218 " =    2.447
peak=   -3.570 closest distance to " CB  ALA A 244 " =    2.119
peak=   -3.569 closest distance to " CA  GLY A 241 " =    2.233
peak=   -3.568 closest distance to " O   HOH Z 231 " =    1.272
peak=   -3.568 closest distance to " CE1 PHE A  59 " =    2.057
peak=   -3.565 closest distance to " O   HOH Z 359 " =    3.361
peak=   -3.563 closest distance to " O   HOH Z 359 " =    1.670
peak=   -3.562 closest distance to " C   MET A 188 " =    1.473
peak=   -3.560 closest distance to " CE  LYS A  76 " =    2.804
peak=   -3.534 closest distance to " O   HOH Z 423 " =    2.443
peak=   -3.532 closest distance to " N   ALA A 226 " =    1.937
peak=   -3.529 closest distance to " OG  SER A  97 " =    2.141
peak=   -3.519 closest distance to " CD  GLN A 278 " =    1.963
peak=   -3.516 closest distance to " CG  TRP A 266 " =    1.972
peak=   -3.514 closest distance to " O   HOH Z 130 " =    1.965
peak=   -3.509 closest distance to " O   HOH Z 102 " =    1.627
peak=   -3.503 closest distance to " OD1 ASN A  39 " =    2.092
peak=   -3.501 closest distance to " O   TRP A 179 " =    1.499
peak=   -3.486 closest distance to " C   ASN A 285 " =    2.225
peak=   -3.484 closest distance to " O   HOH Z 191 " =    5.425
peak=   -3.481 closest distance to " CZ3 TRP A 179 " =    1.293
peak=   -3.480 closest distance to " O   HOH Z 114 " =    3.029
peak=   -3.475 closest distance to " CB  ASP A 132 " =    2.348
peak=   -3.474 closest distance to " CD2 LEU A   5 " =    1.068
peak=   -3.468 closest distance to " CG2 VAL A 202 " =    2.722
peak=   -3.467 closest distance to " O   HOH Z 165 " =    2.124
peak=   -3.462 closest distance to " N   ALA A  43 " =    2.579
peak=   -3.459 closest distance to " O   GLN A 240 " =    1.973
peak=   -3.457 closest distance to " CA  GLY A  23 " =    1.951
peak=   -3.456 closest distance to " C   ASP A 231 " =    2.586
peak=   -3.455 closest distance to " CB  ALA A 114 " =    2.409
peak=   -3.454 closest distance to " O   HOH Z 427 " =    1.651
peak=   -3.449 closest distance to " O   HOH Z 140 " =    1.357
peak=   -3.447 closest distance to " CB  ALA A 161 " =    2.476
peak=   -3.446 closest distance to " O   HOH Z 394 " =    1.466
peak=   -3.445 closest distance to " O   ALA A   1 " =    1.582
peak=   -3.430 closest distance to " CD  GLN A  88 " =    1.205
peak=   -3.424 closest distance to " O   HOH Z  51 " =    0.955
peak=   -3.421 closest distance to " O   HOH Z 166 " =    1.876
peak=   -3.417 closest distance to " O   HOH Z 235 " =    1.156
peak=   -3.406 closest distance to " O   PRO A 198 " =    1.228
peak=   -3.403 closest distance to " CD2 TYR A 293 " =    1.951
peak=   -3.401 closest distance to " OXT GLY A 302 " =    2.944
peak=   -3.400 closest distance to " CB  ALA A 291 " =    2.178
peak=   -3.397 closest distance to " CB  PRO A 163 " =    2.370
peak=   -3.390 closest distance to " O   PRO A 243 " =    2.572
peak=   -3.387 closest distance to " C   ALA A 114 " =    2.186
peak=   -3.386 closest distance to " CG1 VAL A 112 " =    2.854
peak=   -3.379 closest distance to " OE2 GLU A 152 " =    1.200
peak=   -3.375 closest distance to " CG  ASP A 231 " =    0.767
peak=   -3.375 closest distance to " O   HOH Z 406 " =    1.079
peak=   -3.364 closest distance to " NE2 GLN A 278 " =    1.781
peak=   -3.362 closest distance to " CB  GLN A  55 " =    1.160
peak=   -3.362 closest distance to " O   SER A 271 " =    2.143
peak=   -3.360 closest distance to " O   HOH Z 372 " =    2.233
peak=   -3.360 closest distance to " CA  ASN A 127 " =    1.339
peak=   -3.358 closest distance to " O   HOH Z 389 " =    2.143
peak=   -3.353 closest distance to " O   HOH Z 407 " =    2.758
peak=   -3.348 closest distance to " O   HOH Z 364 " =    1.428
peak=   -3.343 closest distance to " CZ  TYR A 169 " =    1.742
peak=   -3.342 closest distance to " OD1 ASN A 301 " =    1.959
peak=   -3.339 closest distance to " N   ALA A 248 " =    1.620
peak=   -3.337 closest distance to " O   HOH Z 134 " =    3.873
peak=   -3.337 closest distance to " CB  ASN A  39 " =    2.238
peak=   -3.336 closest distance to " O   GLU A 152 " =    1.425
peak=   -3.335 closest distance to " OD2 ASP A 171 " =    2.129
peak=   -3.324 closest distance to " N   VAL A  72 " =    1.644
peak=   -3.321 closest distance to " CE  MET A 105 " =    2.438
peak=   -3.317 closest distance to " O   HOH Z  15 " =    1.324
peak=   -3.313 closest distance to " OG  SER A  63 " =    1.195
peak=   -3.312 closest distance to " O   HOH Z 377 " =    2.130
peak=   -3.309 closest distance to " O   ARG A 145 " =    1.515
peak=   -3.308 closest distance to " O   HOH Z 339 " =    1.769
peak=   -3.306 closest distance to " CD1 LEU A 101 " =    2.214
peak=   -3.303 closest distance to " CD2 LEU A 237 " =    2.712
peak=   -3.298 closest distance to " OG  SER A  87 " =    1.322
peak=   -3.292 closest distance to " O   ARG A  24 " =    1.932
peak=   -3.291 closest distance to " O   HOH Z 134 " =    3.241
peak=   -3.285 closest distance to " O   HOH Z 385 " =    1.988
peak=   -3.280 closest distance to " CG1 VAL A 230 " =    1.951
peak=   -3.278 closest distance to " CD2 HIS A 207 " =    2.310
peak=   -3.274 closest distance to " ND2 ASN A 252 " =    1.855
peak=   -3.274 closest distance to " O   HOH Z 103 " =    1.681
peak=   -3.265 closest distance to " N   PRO A 163 " =    1.619
peak=   -3.264 closest distance to " O   HOH Z  65 " =    1.117
peak=   -3.262 closest distance to " O   HOH Z 111 " =    4.481
peak=   -3.259 closest distance to " O   HOH Z 256 " =    1.321
peak=   -3.255 closest distance to " C   LYS A  76 " =    1.657
peak=   -3.251 closest distance to " CZ  PHE A  59 " =    1.338
peak=   -3.250 closest distance to " O   HOH Z 100 " =    1.083
peak=   -3.247 closest distance to " CE2 TRP A  70 " =    2.184
peak=   -3.242 closest distance to " O   ALA A 180 " =    1.168
peak=   -3.242 closest distance to " ND2BASN A 224 " =    1.687
peak=   -3.242 closest distance to " CB  GLN A  11 " =    1.935
peak=   -3.239 closest distance to " CA  ASP A 298 " =    1.087
peak=   -3.238 closest distance to " ND2 ASN A  39 " =    1.338
peak=   -3.237 closest distance to " O   HOH Z 149 " =    2.130
peak=   -3.234 closest distance to " CA  GLY A  35 " =    2.012
peak=   -3.232 closest distance to " O   HOH Z 201 " =    2.229
peak=   -3.231 closest distance to " C   LEU A 222 " =    0.915
peak=   -3.228 closest distance to " C   ALA A  84 " =    2.523
peak=   -3.227 closest distance to " O   SER A 210 " =    1.933
peak=   -3.225 closest distance to " O   HOH Z 158 " =    1.975
peak=   -3.223 closest distance to " CZ  ARG A 259 " =    0.995
peak=   -3.219 closest distance to " O   HOH Z 298 " =    1.176
peak=   -3.217 closest distance to " ND2 ASN A  45 " =    2.000
peak=   -3.214 closest distance to " O   HOH Z 384 " =    1.835
peak=   -3.213 closest distance to " O   HOH Z  63 " =    1.827
peak=   -3.213 closest distance to " CE BMET A  47 " =    1.099
peak=   -3.211 closest distance to " CB  ALA A 291 " =    2.343
peak=   -3.192 closest distance to " O   VAL A 189 " =    2.530
peak=   -3.192 closest distance to " O   HOH Z 350 " =    2.021
peak=   -3.188 closest distance to " CG  MET A 105 " =    0.894
peak=   -3.187 closest distance to " O   VAL A 125 " =    2.389
peak=   -3.183 closest distance to " O   LEU A 101 " =    2.717
peak=   -3.174 closest distance to " O   SER A  95 " =    1.500
peak=   -3.172 closest distance to " CG2 THR A 178 " =    2.228
peak=   -3.167 closest distance to " CB  ALA A  64 " =    2.693
peak=   -3.167 closest distance to " OE1 GLN A 183 " =    1.486
peak=   -3.164 closest distance to " CG2 THR A  42 " =    1.759
peak=   -3.158 closest distance to " CA  GLY A  57 " =    2.127
peak=   -3.154 closest distance to " CD  GLU A 277 " =    1.102
peak=   -3.154 closest distance to " O   HOH Z 175 " =    4.102
peak=   -3.151 closest distance to " CG1 VAL A 197 " =    2.249
peak=   -3.142 closest distance to " O   ASN A 187 " =    1.536
peak=   -3.139 closest distance to " CA  GLY A  98 " =    1.763
peak=   -3.138 closest distance to " O   ALA A  51 " =    1.234
peak=   -3.125 closest distance to " O   HOH Z 288 " =    1.294
peak=   -3.107 closest distance to " CG  ARG A 219 " =    2.849
peak=   -3.093 closest distance to " O   HOH Z 389 " =    1.481
peak=   -3.081 closest distance to " CH2 TRP A 179 " =    2.035
peak=   -3.069 closest distance to " C   ARG A 269 " =    1.406
peak=   -3.050 closest distance to " CE1 PHE A  59 " =    2.077
peak=   -3.043 closest distance to " O   HOH Z 393 " =    3.446
peak=   -3.040 closest distance to " CG  GLU A 152 " =    1.317
peak=   -3.037 closest distance to " O   LEU A 101 " =    2.274
peak=   -3.021 closest distance to " O   HOH Z  89 " =    2.742

================= 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    :  0.4722 0.4671   6.272682e+00   6.259431e+00
   1_bss:  0.4642 0.4521   6.265499e+00   6.246026e+00
   1_xyz:  0.3795 0.3961   6.144610e+00   6.170063e+00
   1_adp:  0.3326 0.3844   6.058381e+00   6.145673e+00
   1_occ:  0.3321 0.3842   6.057704e+00   6.146415e+00
   2_bss:  0.3284 0.3794   6.057583e+00   6.144127e+00
   2_xyz:  0.2418 0.2975   5.802036e+00   5.955648e+00
   2_adp:  0.2151 0.2706   5.706138e+00   5.878463e+00
   2_occ:  0.2148 0.2704   5.705538e+00   5.878061e+00
   3_bss:  0.2133 0.2689   5.702795e+00   5.873059e+00
   3_xyz:  0.1559 0.2041   5.416539e+00   5.623276e+00
   3_adp:  0.1422 0.1895   5.337097e+00   5.554078e+00
   3_occ:  0.1419 0.1892   5.336238e+00   5.553082e+00
   4_bss:  0.1416 0.1887   5.333478e+00   5.549865e+00
   4_xyz:  0.1221 0.1670   5.206628e+00   5.437958e+00
   4_adp:  0.1190 0.1628   5.182945e+00   5.412767e+00
   4_occ:  0.1188 0.1626   5.181705e+00   5.411284e+00
   5_bss:  0.1188 0.1626   5.181332e+00   5.410926e+00
   5_xyz:  0.1174 0.1585   5.168304e+00   5.392515e+00
   5_adp:  0.1162 0.1585   5.163958e+00   5.393240e+00
   5_occ:  0.1161 0.1585   5.163819e+00   5.393129e+00
   5_bss:  0.1161 0.1590   5.164176e+00   5.394273e+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:  0.388  20.000   7.405   9.734   8.183   0.000   0.000   0.000
   1_xyz:  0.388  20.000   7.405   9.734   8.183   0.000   0.000   0.000
   1_adp:  0.388  20.000   7.405   9.734   8.183   0.000   0.000   0.000
   1_occ:  0.388  20.000   7.405   9.734   8.183   0.000   0.000   0.000
   2_bss:  0.334  20.000   4.006   5.350   4.891   0.000   0.000   0.000
   2_xyz:  0.334  20.000   4.006   5.350   4.891   0.000   0.000   0.000
   2_adp:  0.334  20.000   4.006   5.350   4.891   0.000   0.000   0.000
   2_occ:  0.334  20.000   4.006   5.350   4.891   0.000   0.000   0.000
   3_bss:  0.335  40.479   2.346   3.265   3.828   0.000   0.000   0.000
   3_xyz:  0.335  40.479   2.346   3.265   3.828   0.000   0.000   0.000
   3_adp:  0.335  40.479   2.346   3.265   3.828   0.000   0.000   0.000
   3_occ:  0.335  40.479   2.346   3.265   3.828   0.000   0.000   0.000
   4_bss:  0.326  40.136   1.672   2.216   3.504   0.000   0.000   0.000
   4_xyz:  0.326  40.136   1.672   2.216   3.504   0.000   0.000   0.000
   4_adp:  0.326  40.136   1.672   2.216   3.504   0.000   0.000   0.000
   4_occ:  0.326  40.136   1.672   2.216   3.504   0.000   0.000   0.000
   5_bss:  0.323  40.136   1.615   2.043   3.529   0.000   0.000   0.000
   5_xyz:  0.323  40.136   1.615   2.043   3.529   0.000   0.000   0.000
   5_adp:  0.323  40.136   1.615   2.043   3.529   0.000   0.000   0.000
   5_occ:  0.323  40.136   1.615   2.043   3.529   0.000   0.000   0.000
   5_bss:  0.323  42.534  -0.771  -0.398   1.169  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.655 0.4368  0.5080    67207.537
   1_bss:  55.931 0.4442  0.6622    63617.380
   1_xyz:  45.227 0.5783  0.8440    45695.265
   1_adp:  42.226 0.6156  0.9356    42044.801
   1_occ:  42.309 0.6145  0.9327    42070.949
   2_bss:  41.964 0.6185  0.8214    41517.723
   2_xyz:  30.837 0.7478  0.9699    23523.979
   2_adp:  27.027 0.7903  1.0009    19080.109
   2_occ:  27.008 0.7905  1.0007    19051.820
   3_bss:  26.746 0.7932  0.9474    18757.420
   3_xyz:  19.365 0.8675  0.9994    10476.980
   3_adp:  17.590 0.8844  1.0042     9089.834
   3_occ:  17.566 0.8846  1.0042     9064.749
   4_bss:  17.485 0.8852  0.9794     8968.579
   4_xyz:  15.058 0.9060  0.9891     7022.695
   4_adp:  14.458 0.9112  0.9885     6695.700
   4_occ:  14.434 0.9114  0.9884     6670.886
   5_bss:  14.426 0.9114  0.9859     6663.600
   5_xyz:  14.011 0.9150  0.9872     6382.395
   5_adp:  14.005 0.9152  0.9842     6384.168
   5_occ:  14.003 0.9152  0.9842     6380.677
   5_bss:  14.041 0.9149  0.9840     6412.065
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3171e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3171e+01
   1_xyz:   1.654  0.013  0.104 18.056  0.006  4.105   1.3420e-01
   1_adp:   1.654  0.013  0.104 18.056  0.006  4.105   1.3420e-01
   1_occ:   1.654  0.013  0.104 18.056  0.006  4.105   1.3420e-01
   2_bss:   1.654  0.013  0.104 18.056  0.006  4.105   1.3420e-01
   2_xyz:   1.143  0.008  0.080 15.820  0.005  4.119   8.2414e-02
   2_adp:   1.143  0.008  0.080 15.820  0.005  4.119   8.2414e-02
   2_occ:   1.143  0.008  0.080 15.820  0.005  4.119   8.2414e-02
   3_bss:   1.143  0.008  0.080 15.820  0.005  4.119   8.2414e-02
   3_xyz:   1.035  0.007  0.074 15.702  0.004  4.117   6.5659e-02
   3_adp:   1.035  0.007  0.074 15.702  0.004  4.117   6.5659e-02
   3_occ:   1.035  0.007  0.074 15.702  0.004  4.117   6.5659e-02
   4_bss:   1.035  0.007  0.074 15.702  0.004  4.117   6.5659e-02
   4_xyz:   1.017  0.006  0.075 15.785  0.004  4.109   6.2918e-02
   4_adp:   1.017  0.006  0.075 15.785  0.004  4.109   6.2918e-02
   4_occ:   1.017  0.006  0.075 15.785  0.004  4.109   6.2918e-02
   5_bss:   1.017  0.006  0.075 15.785  0.004  4.109   6.2918e-02
   5_xyz:   0.882  0.005  0.068 15.337  0.003  4.109   5.0930e-02
   5_adp:   0.882  0.005  0.068 15.337  0.003  4.109   5.0930e-02
   5_occ:   0.882  0.005  0.068 15.337  0.003  4.109   5.0930e-02
   5_bss:   0.882  0.005  0.068 15.337  0.003  4.109   5.0930e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8902e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8902e+00
   1_xyz:  13.384  0.164  0.410 87.290  0.029  2.212   9.4250e-02
   1_adp:  13.384  0.164  0.410 87.290  0.029  2.212   9.4250e-02
   1_occ:  13.384  0.164  0.410 87.290  0.029  2.212   9.4250e-02
   2_bss:  13.384  0.164  0.410 87.290  0.029  2.212   9.4250e-02
   2_xyz:   7.086  0.088  0.274 84.320  0.033  2.236   1.2975e-01
   2_adp:   7.086  0.088  0.274 84.320  0.033  2.236   1.2975e-01
   2_occ:   7.086  0.088  0.274 84.320  0.033  2.236   1.2975e-01
   3_bss:   7.086  0.088  0.274 84.320  0.033  2.236   1.2975e-01
   3_xyz:   7.592  0.052  0.269 82.604  0.030  2.317   7.4014e-02
   3_adp:   7.592  0.052  0.269 82.604  0.030  2.317   7.4014e-02
   3_occ:   7.592  0.052  0.269 82.604  0.030  2.317   7.4014e-02
   4_bss:   7.592  0.052  0.269 82.604  0.030  2.317   7.4014e-02
   4_xyz:   8.551  0.052  0.264 84.731  0.033  2.323   6.0674e-02
   4_adp:   8.551  0.052  0.264 84.731  0.033  2.323   6.0674e-02
   4_occ:   8.551  0.052  0.264 84.731  0.033  2.323   6.0674e-02
   5_bss:   8.551  0.052  0.264 84.731  0.033  2.323   6.0674e-02
   5_xyz:   6.333  0.043  0.213 84.613  0.033  2.365   2.9079e-02
   5_adp:   6.333  0.043  0.213 84.613  0.033  2.365   2.9079e-02
   5_occ:   6.333  0.043  0.213 84.613  0.033  2.365   2.9079e-02
   5_bss:   6.333  0.043  0.213 84.613  0.033  2.365   2.9079e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  54.64   0.00  12.25  48.53   0.00  10.22  54.64   0.00  23.30
   1_occ:  54.64   0.00  12.25  48.53   0.00  10.22  54.64   0.00  23.30
   2_bss:  54.64   0.00  12.25  48.53   0.00  10.22  54.64   0.00  23.30
   2_xyz:  54.64   0.00  12.25  48.53   0.00  10.22  54.64   0.00  23.30
   2_adp:  74.61   0.00  12.48  61.98   0.00   9.05  74.61   0.00  31.18
   2_occ:  74.61   0.00  12.48  61.98   0.00   9.05  74.61   0.00  31.18
   3_bss:  74.61   0.00  12.48  61.98   0.00   9.05  74.61   0.00  31.18
   3_xyz:  74.61   0.00  12.48  61.98   0.00   9.05  74.61   0.00  31.18
   3_adp:  76.00   0.00  12.65  71.14   0.00   8.59  76.00   2.13  34.72
   3_occ:  76.00   0.00  12.65  71.14   0.00   8.59  76.00   2.13  34.72
   4_bss:  76.00   0.00  12.65  71.14   0.00   8.59  76.00   2.13  34.72
   4_xyz:  76.00   0.00  12.65  71.14   0.00   8.59  76.00   2.13  34.72
   4_adp:  79.35   0.00  12.53  79.35   0.00   8.45  74.53   2.28  34.78
   4_occ:  79.35   0.00  12.53  79.35   0.00   8.45  74.53   2.28  34.78
   5_bss:  79.35   0.00  12.53  79.35   0.00   8.45  74.53   2.28  34.78
   5_xyz:  79.35   0.00  12.53  79.35   0.00   8.45  74.53   2.28  34.78
   5_adp:  83.07   0.00  12.58  83.07   0.00   8.40  75.61   2.26  35.35
   5_occ:  83.07   0.00  12.58  83.07   0.00   8.40  75.61   2.26  35.35
   5_bss:  85.46   2.40  14.98  85.46   2.40  10.80  78.00   4.66  37.75
------------------------------------------------------------------------
 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:    1.258    0.026    0.407
   1_adp:    1.258    0.026    0.407
   1_occ:    1.258    0.026    0.407
   2_bss:    1.258    0.026    0.407
   2_xyz:    1.516    0.031    0.573
   2_adp:    1.516    0.031    0.573
   2_occ:    1.516    0.031    0.573
   3_bss:    1.516    0.031    0.573
   3_xyz:    1.487    0.048    0.650
   3_adp:    1.487    0.048    0.650
   3_occ:    1.487    0.048    0.650
   4_bss:    1.487    0.048    0.650
   4_xyz:    1.611    0.017    0.686
   4_adp:    1.611    0.017    0.686
   4_occ:    1.611    0.017    0.686
   5_bss:    1.611    0.017    0.686
   5_xyz:    1.624    0.029    0.694
   5_adp:    1.624    0.029    0.694
   5_occ:    1.624    0.029    0.694
   5_bss:    1.624    0.029    0.694
------------------------------------------------------------------------

CPU time actual refinement: 345.85


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_270/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/trial/run_270/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_270/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_270/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_270/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.70 
  Macro-tasks:
    bulk solvent and scale       = 47.47  
    individual site refinement   = 143.50 
    weights calculation          = 31.71  
    collect and process          = 6.43   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 229.23 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 104.67 
    alpha_beta                      = 8.16   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 116.48 
    fmodel                         = 8.06   
    r_factors                      = 0.29   
    phase_errors                   = 10.41  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 251.79 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.762 micro seconds
Total CPU time: 5.99 minutes
from_scatterers_fft:    674 calls, 104.29 s
gradients_fft:          619 calls, 102.54 s

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

# Date 2008-01-16 Time 01:09:57 PST -0800 (1200474597.25 s)
Start R-work = 0.4722, R-free = 0.4671 (no bulk solvent and anisotropic scale)
Final R-work = 0.1334, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.4642, R-free = 0.4521
Final R-work = 0.1161, R-free = 0.1590