# Date 2008-01-16 Time 00:33:46 PST -0800 (1200472426.45 s)
#phil __OFF__

Command line arguments: "../77.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1495
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 77

-------------------------------------------------------------------------------
  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: (68.4938, 47.3993, 84.2302, 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: (68.4938, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.793 1.95053
Completeness in resolution range: 0.953607
Completeness with d_max=infinity: 0.950692

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7930
                             d_min =   1.9505

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: (68.4938, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.793 1.95053
Completeness in resolution range: 0.953607
Completeness with d_max=infinity: 0.950692

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7934 -  4.1738 [2162/2191]  1945   217  10.0%
  bin  2:  4.1738 -  3.3252 [2066/2089]  1860   206  10.0%
  bin  3:  3.3252 -  2.9085 [2052/2077]  1843   209  10.2%
  bin  4:  2.9085 -  2.6443 [2012/2028]  1816   196   9.7%
  bin  5:  2.6443 -  2.4556 [2004/2048]  1799   205  10.2%
  bin  6:  2.4556 -  2.3114 [2011/2039]  1819   192   9.5%
  bin  7:  2.3114 -  2.1961 [1981/2017]  1780   201  10.1%
  bin  8:  2.1961 -  2.1007 [1989/2031]  1792   197   9.9%
  bin  9:  2.1007 -  2.0201 [1971/2017]  1772   199  10.1%
  bin 10:  2.0201 -  1.9505 [1341/2005]  1204   137  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_77/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.14 -     1.89: 23
        1.89 -     2.64: 141
        2.64 -     3.39: 4429
        3.39 -     4.15: 9579
        4.15 -     4.90: 14824
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.136 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.234 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.315 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.338 3.040 -x+1,y-1/2,-z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.341 3.440 -x+1,y-1/2,-z+1/2
  ... (remaining 28991 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_77/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_77/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 = 68.49375 47.3993 84.23025 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: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5092   r_free= 0.5038   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.304969                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6553 0.99   1400  158 0.4249 0.4145       6.643      6.6777|
|  2:  4.6553 -  3.7143 0.99   1345  148 0.4457 0.4277      6.8439      6.8497|
|  3:  3.7143 -  3.2504 0.99   1324  148 0.4760 0.4700      6.7255      6.7891|
|  4:  3.2504 -  2.9558 0.99   1315  137 0.4916 0.5101      6.5442      6.5417|
|  5:  2.9558 -  2.7454 0.98   1301  149 0.5379 0.5406      6.4064      6.4076|
|  6:  2.7454 -  2.5845 0.99   1299  146 0.5264 0.5457      6.2887      6.2099|
|  7:  2.5845 -  2.4556 0.98   1279  147 0.5565 0.4932      6.2814      6.1868|
|  8:  2.4556 -  2.3492 0.99   1299  137 0.5464 0.5294      6.1925      6.1776|
|  9:  2.3492 -  2.2591 0.99   1289  147 0.5551 0.5603      6.1266      6.1858|
| 10:  2.2591 -  2.1814 0.98   1275  141 0.5540 0.5590      6.1265      6.1357|
| 11:  2.1814 -  2.1134 0.97   1259  143 0.5477 0.5965      6.0443      6.0586|
| 12:  2.1134 -  2.0531 0.99   1283  142 0.5387 0.5608      5.9805      5.9922|
| 13:  2.0531 -  1.9992 0.94   1243  129 0.5645 0.5441       5.887       5.908|
| 14:  1.9992 -  1.9505 0.57    719   87 0.5527 0.4745      5.9118      5.6953|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7934 -  4.6553  1400   158  0.63  40.15   0.79     0.66      90470.35|
|  2:  4.6553 -  3.7143  1345   148  0.62  42.24   0.86     0.69     138949.50|
|  3:  3.7143 -  3.2504  1324   148  0.50  51.60   0.83     0.63     149284.84|
|  4:  3.2504 -  2.9558  1315   137  0.40  59.48   0.79     0.52     127408.50|
|  5:  2.9558 -  2.7454  1301   149  0.33  65.44   0.72     0.42      99706.92|
|  6:  2.7454 -  2.5845  1299   146  0.32  66.22   0.72     0.38      78560.96|
|  7:  2.5845 -  2.4556  1279   147  0.32  66.28   0.72     0.37      70179.08|
|  8:  2.4556 -  2.3492  1299   137  0.32  66.14   0.72     0.38      61737.47|
|  9:  2.3492 -  2.2591  1289   147  0.25  71.49   0.71     0.32      61403.55|
| 10:  2.2591 -  2.1814  1275   141  0.19  75.85   0.77     0.23      57662.16|
| 11:  2.1814 -  2.1134  1259   143  0.10  82.92   0.74     0.12      57007.86|
| 12:  2.1134 -  2.0531  1283   142  0.12  81.06   0.76     0.16      51867.43|
| 13:  2.0531 -  1.9992  1243   129  0.22  73.96   0.72     0.28      39950.97|
| 14:  1.9992 -  1.9505   719    87  0.46  55.21   0.73     0.51      24180.17|
|alpha:            min =        0.12 max =            0.69 mean =         0.40|
|beta:             min =    24180.17 max =       149284.84 mean =     81593.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           89.99 mean =        64.11|
|phase err.(test): min =        0.00 max =           90.00 mean =        64.46|
|-----------------------------------------------------------------------------|

============================== 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 = 26.774850             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.342   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.769546              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 86.158   (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 |  0.822 -  1.230:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.230 -  1.638:        9 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.638 -  2.045:       75 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.045 -  2.453:      377 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.453 -  2.861:     1151 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.861 -  3.269:     2404 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.269 -  3.677:     3924 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.677 -  4.084:     5347 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.084 -  4.492:     7136 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.492 -  4.900:     8599 |
|-----------------------------------------------------------------------------|
|-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 |       52.806 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.085    4.900  0.822 |       3.600 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.333)------------------------------------------|
|    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 = 11.333)------------------------------------------|
|    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: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5127   r_free= 0.5093   ksol= 0.00   Bsol= 0.00   scale= 0.755    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.305375                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5007   r_free= 0.4959   ksol= 0.36   Bsol= 2.66   scale= 0.976    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.47,8.44,8.71,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.302718                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.965444             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.640   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.725269              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.574   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5007      final r-factor (work) = 0.4297          |
| start r-factor (free) = 0.4959      final r-factor (free) = 0.4571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 122.0347 = 21.97 * 0.50 * 6.3034 + 1.00 * 52.8061                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 68.6917 = 21.97 * 0.50 * 6.2357 + 1.00 * 0.2069                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4297      final r-factor (work) = 0.3917          |
| start r-factor (free) = 0.4571      final r-factor (free) = 0.4507          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7725 = 1.73 * 1.00 * 6.2357 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6958 = 1.73 * 1.00 * 6.1880 + 1.00 * 0.0198                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.99   14.86    None  None   None       |
|    all(noH): 2823   0      0.00    83.99   14.86    None  None   None       |
|    Sol.    : 438    0      0.00    83.99   24.67    None  None   None       |
|    Mac.    : 2385   0      0.00    73.00   13.06    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 -   8.399: 1089   |   5:    41.995 -  50.394:   65        |
|      1:     8.399 -  16.798:  755   |   6:    50.394 -  58.793:   38        |
|      2:    16.798 -  25.197:  472   |   7:    58.793 -  67.192:   10        |
|      3:    25.197 -  33.596:  252   |   8:    67.192 -  75.591:   10        |
|      4:    33.596 -  41.995:  127   |   9:    75.591 -  83.990:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3917 r_free = 0.4507             target_work(ml) = 6.176         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3910 r_free = 0.4512             target_work(ml) = 6.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3910   r_free= 0.4512   ksol= 0.36   Bsol= 2.66   scale= 1.103    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.47,8.44,8.71,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.174473                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3897   r_free= 0.4469   ksol= 0.33   Bsol= 32.77   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.04,5.00,5.87,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.174474                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.702379             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.754  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.816718              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.162  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3897      final r-factor (work) = 0.3166          |
| start r-factor (free) = 0.4469      final r-factor (free) = 0.3787          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.4861 = 12.70 * 0.50 * 6.1846 + 1.00 * 0.2069                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.8711 = 12.70 * 0.50 * 6.1030 + 1.00 * 0.1095                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3166      final r-factor (work) = 0.2916          |
| start r-factor (free) = 0.3787      final r-factor (free) = 0.3584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0051 = 0.82 * 1.00 * 6.1030 + 1.00 * 0.0207                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8979 = 0.82 * 1.00 * 5.9791 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.49   15.20    None  None   None       |
|    all(noH): 2823   0      0.00    93.49   15.20    None  None   None       |
|    Sol.    : 438    0      0.00    93.49   31.79    None  None   None       |
|    Mac.    : 2385   0      0.00    73.68   12.15    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 -   9.349: 1255   |   5:    46.745 -  56.094:   56        |
|      1:     9.349 -  18.698:  746   |   6:    56.094 -  65.443:   30        |
|      2:    18.698 -  28.047:  375   |   7:    65.443 -  74.792:   19        |
|      3:    28.047 -  37.396:  210   |   8:    74.792 -  84.141:    3        |
|      4:    37.396 -  46.745:  127   |   9:    84.141 -  93.489:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2916 r_free = 0.3584             target_work(ml) = 5.955         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2915 r_free = 0.3584             target_work(ml) = 5.955         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2915   r_free= 0.3584   ksol= 0.33   Bsol= 32.77   scale= 1.081   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.04,5.00,5.87,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.954974                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2893   r_free= 0.3552   ksol= 0.32   Bsol= 32.77   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,3.19,3.71,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.951857                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.528955              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.673  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.273671              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.950  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2893      final r-factor (work) = 0.2289          |
| start r-factor (free) = 0.3552      final r-factor (free) = 0.2908          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6461 = 4.53 * 0.50 * 5.9778 + 1.00 * 0.1095                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3572 = 4.53 * 0.50 * 5.8660 + 1.00 * 0.0737                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2289      final r-factor (work) = 0.2163          |
| start r-factor (free) = 0.2908      final r-factor (free) = 0.2730          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6203 = 0.27 * 1.00 * 5.8660 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5855 = 0.27 * 1.00 * 5.7352 + 1.00 * 0.0160                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.17  14.98    None  None   None       |
|    all(noH): 2823   0      0.00    126.17  14.98    None  None   None       |
|    Sol.    : 438    0      1.68    91.54   33.12    None  None   None       |
|    Mac.    : 2385   0      0.00    126.17  11.65    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 -  12.617: 1695   |   5:    63.086 -  75.703:   21        |
|      1:    12.617 -  25.234:  607   |   6:    75.703 -  88.320:    2        |
|      2:    25.234 -  37.852:  306   |   7:    88.320 - 100.938:    2        |
|      3:    37.852 -  50.469:  132   |   8:   100.938 - 113.555:    0        |
|      4:    50.469 -  63.086:   57   |   9:   113.555 - 126.172:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2163 r_free = 0.2730             target_work(ml) = 5.706         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2159 r_free = 0.2733             target_work(ml) = 5.706         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2159   r_free= 0.2733   ksol= 0.32   Bsol= 32.77   scale= 1.058   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,3.19,3.71,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.705886                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2148   r_free= 0.2713   ksol= 0.32   Bsol= 30.98   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.68,2.19,2.23,0.00,0.00,0.00); trace/3= 1.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.702896                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.487348              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.083   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.648054              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.235   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2148      final r-factor (work) = 0.1760          |
| start r-factor (free) = 0.2713      final r-factor (free) = 0.2323          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2087 = 2.49 * 0.50 * 5.7372 + 1.00 * 0.0735                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0438 = 2.49 * 0.50 * 5.6154 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1760      final r-factor (work) = 0.1590          |
| start r-factor (free) = 0.2323      final r-factor (free) = 0.2133          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6566 = 0.65 * 1.00 * 5.6154 + 1.00 * 0.0175                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5736 = 0.65 * 1.00 * 5.4962 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.38   15.12    None  None   None       |
|    all(noH): 2823   0      0.00    95.38   15.12    None  None   None       |
|    Sol.    : 438    0      2.92    95.38   39.36    None  None   None       |
|    Mac.    : 2385   0      0.00    85.95   10.67    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 -   9.538: 1467   |   5:    47.689 -  57.227:  100        |
|      1:     9.538 -  19.076:  707   |   6:    57.227 -  66.765:   57        |
|      2:    19.076 -  28.614:  223   |   7:    66.765 -  76.303:   17        |
|      3:    28.614 -  38.151:  113   |   8:    76.303 -  85.841:    8        |
|      4:    38.151 -  47.689:  129   |   9:    85.841 -  95.379:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1590 r_free = 0.2133             target_work(ml) = 5.450         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1589 r_free = 0.2133             target_work(ml) = 5.450         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1589   r_free= 0.2133   ksol= 0.32   Bsol= 30.98   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.68,2.19,2.23,0.00,0.00,0.00); trace/3= 1.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.449685                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1589   r_free= 0.2124   ksol= 0.31   Bsol= 30.93   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.00,1.48,1.43,0.00,0.00,0.00); trace/3= 0.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.448099                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.262495              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.361  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.743123              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.008  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1589      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.2124      final r-factor (free) = 0.1825          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0314 = 3.26 * 0.50 * 5.4997 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8372 = 3.26 * 0.50 * 5.3752 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1825      final r-factor (free) = 0.1757          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0062 = 0.74 * 1.00 * 5.3752 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9274 = 0.74 * 1.00 * 5.2694 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.61   14.88    None  None   None       |
|    all(noH): 2823   0      0.00    96.61   14.88    None  None   None       |
|    Sol.    : 438    0      3.69    96.61   40.38    None  None   None       |
|    Mac.    : 2385   0      0.00    91.27   10.20    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 -   9.661: 1563   |   5:    48.303 -  57.964:   84        |
|      1:     9.661 -  19.321:  685   |   6:    57.964 -  67.624:   68        |
|      2:    19.321 -  28.982:  168   |   7:    67.624 -  77.285:   25        |
|      3:    28.982 -  38.642:  110   |   8:    77.285 -  86.945:    5        |
|      4:    38.642 -  48.303:  110   |   9:    86.945 -  96.606:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1264 r_free = 0.1757             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1263 r_free = 0.1755             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1263   r_free= 0.1755   ksol= 0.31   Bsol= 30.93   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.00,1.48,1.43,0.00,0.00,0.00); trace/3= 0.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.247249                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6553 0.99   1400  158 0.1038 0.1379      5.4515      5.6267|
|  2:  4.6553 -  3.7143 0.99   1345  148 0.0936 0.1231      5.5248      5.7726|
|  3:  3.7143 -  3.2504 0.99   1324  148 0.1177 0.1677      5.5761       5.891|
|  4:  3.2504 -  2.9558 0.99   1315  137 0.1439 0.1750      5.5556      5.7343|
|  5:  2.9558 -  2.7454 0.98   1301  149 0.1492 0.1729      5.4244      5.5625|
|  6:  2.7454 -  2.5845 0.99   1299  146 0.1408 0.2280      5.3241      5.5908|
|  7:  2.5845 -  2.4556 0.98   1279  147 0.1312 0.1796      5.2196       5.427|
|  8:  2.4556 -  2.3492 0.99   1299  137 0.1310 0.1822      5.1742      5.4027|
|  9:  2.3492 -  2.2591 0.99   1289  147 0.1351 0.2026      5.1253       5.419|
| 10:  2.2591 -  2.1814 0.98   1275  141 0.1313 0.1961       5.118        5.35|
| 11:  2.1814 -  2.1134 0.97   1259  143 0.1318 0.1972      5.0348      5.3351|
| 12:  2.1134 -  2.0531 0.99   1283  142 0.1289 0.1977      4.9792       5.243|
| 13:  2.0531 -  1.9992 0.94   1243  129 0.1343 0.1958      4.8902      5.1321|
| 14:  1.9992 -  1.9505 0.57    719   87 0.1238 0.1916      4.7981      5.0307|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7934 -  4.6553  1400   158  0.93  10.28   0.98     0.96       8860.80|
|  2:  4.6553 -  3.7143  1345   148  0.94   9.38   1.03     1.01      10957.53|
|  3:  3.7143 -  3.2504  1324   148  0.92  13.05   1.05     1.04      12811.60|
|  4:  3.2504 -  2.9558  1315   137  0.90  15.74   1.03     1.02      12300.51|
|  5:  2.9558 -  2.7454  1301   149  0.88  17.82   1.01     0.97       9927.55|
|  6:  2.7454 -  2.5845  1299   146  0.88  18.26   0.99     0.95       8908.60|
|  7:  2.5845 -  2.4556  1279   147  0.89  16.97   0.99     0.95       6948.20|
|  8:  2.4556 -  2.3492  1299   137  0.89  17.73   1.02     1.00       6841.30|
|  9:  2.3492 -  2.2591  1289   147  0.88  18.03   1.02     1.00       6131.91|
| 10:  2.2591 -  2.1814  1275   141  0.88  18.32   1.01     0.97       6187.32|
| 11:  2.1814 -  2.1134  1259   143  0.88  18.69   1.02     0.98       5352.44|
| 12:  2.1134 -  2.0531  1283   142  0.89  17.48   1.02     0.99       4828.59|
| 13:  2.0531 -  1.9992  1243   129  0.88  18.51   1.02     1.01       4080.81|
| 14:  1.9992 -  1.9505   719    87  0.89  17.31   1.00     0.97       3298.11|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     3298.11 max =        12811.60 mean =      7868.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        16.14|
|phase err.(test): min =        0.00 max =           87.78 mean =        15.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1760   ksol= 0.31   Bsol= 33.69   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,0.51,0.46,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.248122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1760   ksol= 0.31   Bsol= 33.69   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,0.51,0.46,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.248122                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6553 0.99   1400  158 0.1026 0.1422      5.4525      5.6402|
|  2:  4.6553 -  3.7143 0.99   1345  148 0.0953 0.1266      5.5427      5.7914|
|  3:  3.7143 -  3.2504 0.99   1324  148 0.1176 0.1666       5.583      5.8856|
|  4:  3.2504 -  2.9558 0.99   1315  137 0.1438 0.1749      5.5565      5.7357|
|  5:  2.9558 -  2.7454 0.98   1301  149 0.1490 0.1726      5.4228      5.5552|
|  6:  2.7454 -  2.5845 0.99   1299  146 0.1407 0.2289       5.322      5.5931|
|  7:  2.5845 -  2.4556 0.98   1279  147 0.1304 0.1798       5.218      5.4266|
|  8:  2.4556 -  2.3492 0.99   1299  137 0.1305 0.1822      5.1715      5.4026|
|  9:  2.3492 -  2.2591 0.99   1289  147 0.1346 0.2012      5.1223      5.4137|
| 10:  2.2591 -  2.1814 0.98   1275  141 0.1312 0.1954      5.1155      5.3477|
| 11:  2.1814 -  2.1134 0.97   1259  143 0.1313 0.1967      5.0323       5.333|
| 12:  2.1134 -  2.0531 0.99   1283  142 0.1286 0.1976      4.9794      5.2443|
| 13:  2.0531 -  1.9992 0.94   1243  129 0.1343 0.1962      4.8903      5.1342|
| 14:  1.9992 -  1.9505 0.57    719   87 0.1238 0.1909      4.7979      5.0293|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7934 -  4.6553  1400   158  0.93  10.38   0.98     0.96       9124.63|
|  2:  4.6553 -  3.7143  1345   148  0.94   9.57   1.03     1.01      11268.64|
|  3:  3.7143 -  3.2504  1324   148  0.92  13.22   1.05     1.04      13061.19|
|  4:  3.2504 -  2.9558  1315   137  0.90  15.70   1.03     1.03      12252.13|
|  5:  2.9558 -  2.7454  1301   149  0.88  17.76   1.01     0.97       9869.94|
|  6:  2.7454 -  2.5845  1299   146  0.88  18.22   0.99     0.95       8867.03|
|  7:  2.5845 -  2.4556  1279   147  0.89  16.93   0.99     0.95       6942.31|
|  8:  2.4556 -  2.3492  1299   137  0.89  17.71   1.02     1.00       6811.52|
|  9:  2.3492 -  2.2591  1289   147  0.88  17.98   1.02     1.00       6087.19|
| 10:  2.2591 -  2.1814  1275   141  0.88  18.27   1.01     0.98       6144.44|
| 11:  2.1814 -  2.1134  1259   143  0.88  18.66   1.02     0.98       5328.83|
| 12:  2.1134 -  2.0531  1283   142  0.89  17.49   1.02     0.99       4841.18|
| 13:  2.0531 -  1.9992  1243   129  0.88  18.53   1.02     1.01       4086.03|
| 14:  1.9992 -  1.9505   719    87  0.89  17.28   1.00     0.97       3292.76|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     3292.76 max =        13061.19 mean =      7910.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.16|
|phase err.(test): min =        0.00 max =           88.63 mean =        15.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.97    97.58   15.85    None  None   None       |
|    all(noH): 2823   0      0.97    97.58   15.85    None  None   None       |
|    Sol.    : 438    0      4.66    97.58   41.35    None  None   None       |
|    Mac.    : 2385   0      0.97    92.24   11.17    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:     0.970 -  10.631: 1563   |   5:    49.273 -  58.934:   84        |
|      1:    10.631 -  20.292:  685   |   6:    58.934 -  68.595:   68        |
|      2:    20.292 -  29.952:  168   |   7:    68.595 -  78.255:   25        |
|      3:    29.952 -  39.613:  110   |   8:    78.255 -  87.916:    5        |
|      4:    39.613 -  49.273:  110   |   9:    87.916 -  97.576:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.712 - 5.865
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 327
   mapped sites are within: 0.712 - 5.865

peak=   10.595 closest distance to " CB  VAL A 230 " =    1.368
peak=    9.566 closest distance to " O   HOH Z 138 " =    1.474
peak=    8.319 closest distance to " O   HOH Z 403 " =    1.260
peak=    8.017 closest distance to " O   HOH Z 120 " =    1.786
peak=    6.864 closest distance to " CG  ARG A 138 " =    1.154
peak=    6.812 closest distance to " O   HOH Z 199 " =    1.864
peak=    6.557 closest distance to " O   HOH Z 279 " =    1.493
peak=    6.486 closest distance to " O   HOH Z 403 " =    2.040
peak=    6.264 closest distance to " O   HOH Z 137 " =    1.218
peak=    6.164 closest distance to " CG1 VAL A 296 " =    1.164
peak=    5.962 closest distance to " O   HOH Z  92 " =    1.475
peak=    5.743 closest distance to " O   HOH Z 124 " =    1.778
peak=    5.730 closest distance to " O   HOH Z 278 " =    1.935
peak=    5.646 closest distance to " O   HOH Z 316 " =    1.162
peak=    5.513 closest distance to " O   HOH Z 249 " =    1.454
peak=    5.487 closest distance to " CD1AILE A 234 " =    1.105
peak=    5.363 closest distance to " O   HOH Z  37 " =    1.240
peak=    5.275 closest distance to " CB  VAL A 296 " =    1.210
peak=    5.241 closest distance to " O   HOH Z 247 " =    1.389
peak=    5.228 closest distance to " O   HOH Z 236 " =    1.771
peak=    5.164 closest distance to " O   HOH Z 193 " =    1.872
peak=    5.110 closest distance to " CD2 LEU A   5 " =    1.362
peak=    5.006 closest distance to " O   SER A  87 " =    2.304
peak=    4.998 closest distance to " O   HOH Z 406 " =    1.450
peak=    4.980 closest distance to " CG  LEU A   5 " =    1.361
peak=    4.940 closest distance to " O   HOH Z 411 " =    3.710
peak=    4.882 closest distance to " O   HOH Z 272 " =    1.961
peak=    4.850 closest distance to " O   HOH Z 191 " =    1.616
peak=    4.842 closest distance to " CB  ARG A 275 " =    1.011
peak=    4.834 closest distance to " O   HOH Z  92 " =    1.417
peak=    4.826 closest distance to " O   HOH Z  80 " =    2.109
peak=    4.780 closest distance to " O   HOH Z  97 " =    1.786
peak=    4.777 closest distance to " O   HOH Z  85 " =    1.848
peak=    4.762 closest distance to " O   HOH Z 255 " =    1.334
peak=    4.754 closest distance to " O   HOH Z  43 " =    1.450
peak=    4.726 closest distance to " O   HOH Z  78 " =    1.534
peak=    4.641 closest distance to " O   HOH Z 155 " =    2.094
peak=    4.630 closest distance to " NH2 ARG A  56 " =    2.100
peak=    4.581 closest distance to " O   HOH Z 394 " =    1.579
peak=    4.543 closest distance to " O   HOH Z 402 " =    1.562
peak=    4.542 closest distance to " CD2 LEU A 228 " =    1.185
peak=    4.541 closest distance to " CG AARG A 275 " =    1.190
peak=    4.484 closest distance to " O   HOH Z 117 " =    1.214
peak=    4.479 closest distance to " C   PRO A 198 " =    1.538
peak=    4.467 closest distance to " O   HOH Z 126 " =    2.133
peak=    4.465 closest distance to " O   HOH Z 232 " =    1.401
peak=    4.463 closest distance to " O   HOH Z  47 " =    1.778
peak=    4.460 closest distance to " CG  PRO A 198 " =    1.160
peak=    4.457 closest distance to " O   HOH Z 192 " =    1.543
peak=    4.417 closest distance to " O   HOH Z 327 " =    1.739
peak=    4.383 closest distance to " CB  GLN A 223 " =    1.552
peak=    4.383 closest distance to " O   HOH Z 108 " =    1.359
peak=    4.376 closest distance to " O   HOH Z 316 " =    2.109
peak=    4.372 closest distance to " CA  TYR A  30 " =    1.015
peak=    4.341 closest distance to " O   HOH Z 116 " =    1.071
peak=    4.303 closest distance to " CG  ARG A  66 " =    1.199
peak=    4.273 closest distance to " O   HOH Z 134 " =    1.977
peak=    4.265 closest distance to " O   HOH Z 425 " =    1.404
peak=    4.242 closest distance to " O   HOH Z 408 " =    1.929
peak=    4.232 closest distance to " O   HOH Z 214 " =    2.423
peak=    4.222 closest distance to " O   HOH Z 326 " =    1.544
peak=    4.213 closest distance to " O   HOH Z 214 " =    1.412
peak=    4.200 closest distance to " O   HOH Z 248 " =    1.185
peak=    4.193 closest distance to " O   HOH Z 169 " =    1.021
peak=    4.165 closest distance to " CD  ARG A 269 " =    1.111
peak=    4.157 closest distance to " CA  VAL A  41 " =    0.828
peak=    4.155 closest distance to " CB  VAL A 265 " =    1.253
peak=    4.141 closest distance to " CG  PRO A  54 " =    1.139
peak=    4.137 closest distance to " O   HOH Z   4 " =    1.365
peak=    4.137 closest distance to " O   HOH Z 156 " =    3.160
peak=    4.130 closest distance to " OE1 GLU A   2 " =    2.067
peak=    4.115 closest distance to " O   HOH Z 128 " =    1.752
peak=    4.110 closest distance to " O   HOH Z 303 " =    2.132
peak=    4.106 closest distance to " CB  SER A   3 " =    1.318
peak=    4.077 closest distance to " CA  ALA A  21 " =    1.168
peak=    4.075 closest distance to " CE  MET A  40 " =    1.172
peak=    4.066 closest distance to " NE2 GLN A  11 " =    0.979
peak=    4.063 closest distance to " NZ  LYS A 117 " =    3.269
peak=    4.061 closest distance to " O   HOH Z 132 " =    1.502
peak=    4.052 closest distance to " O   HOH Z 346 " =    1.434
peak=    4.047 closest distance to " O   HOH Z  40 " =    1.500
peak=    4.031 closest distance to " O   HOH Z 188 " =    1.219
peak=    4.029 closest distance to " O   HOH Z 138 " =    1.400
peak=    4.026 closest distance to " O   HOH Z 154 " =    1.634
peak=    4.022 closest distance to " O   HOH Z 389 " =    1.603
peak=    4.013 closest distance to " O   HOH Z 263 " =    1.404
peak=    4.004 closest distance to " CG  GLN A  77 " =    1.026
peak=    3.997 closest distance to " CD1BILE A 234 " =    0.920
peak=    3.971 closest distance to " NE BARG A 275 " =    1.345
peak=    3.962 closest distance to " O   HOH Z 276 " =    1.491
peak=    3.959 closest distance to " O   HOH Z 423 " =    1.844
peak=    3.955 closest distance to " O   HOH Z 291 " =    1.609
peak=    3.944 closest distance to " O   HOH Z 423 " =    2.123
peak=    3.943 closest distance to " CG1 ILE A  33 " =    1.266
peak=    3.931 closest distance to " O   HOH Z 322 " =    1.588
peak=    3.927 closest distance to " O   HOH Z 414 " =    1.605
peak=    3.920 closest distance to " O   HOH Z 357 " =    2.044
peak=    3.915 closest distance to " O   HOH Z  48 " =    1.690
peak=    3.906 closest distance to " CD  GLN A  58 " =    5.865
peak=    3.905 closest distance to " O   HOH Z 126 " =    2.864
peak=    3.902 closest distance to " CE BMET A  47 " =    1.147
peak=    3.890 closest distance to " CB  SER A  26 " =    1.654
peak=    3.888 closest distance to " O   HOH Z 426 " =    1.525
peak=    3.888 closest distance to " O   HOH Z 365 " =    1.653
peak=    3.888 closest distance to " CD2 TRP A 179 " =    1.426
peak=    3.875 closest distance to " O   HOH Z 189 " =    2.287
peak=    3.872 closest distance to " O   HOH Z 361 " =    2.936
peak=    3.861 closest distance to " CG  PRO A 213 " =    1.279
peak=    3.850 closest distance to " O   HOH Z  54 " =    1.493
peak=    3.829 closest distance to " O   HOH Z 234 " =    3.762
peak=    3.826 closest distance to " N   TYR A  15 " =    0.975
peak=    3.818 closest distance to " O   HOH Z  69 " =    1.033
peak=    3.814 closest distance to " CB  ASN A 148 " =    1.198
peak=    3.812 closest distance to " CG  LEU A 228 " =    1.228
peak=    3.811 closest distance to " O   HOH Z  50 " =    1.658
peak=    3.797 closest distance to " O   HOH Z 313 " =    1.519
peak=    3.795 closest distance to " O   HOH Z 344 " =    1.297
peak=    3.781 closest distance to " O   HOH Z 203 " =    1.529
peak=    3.775 closest distance to " NH1AARG A 275 " =    1.214
peak=    3.773 closest distance to " O   HOH Z  59 " =    2.081
peak=    3.758 closest distance to " CG2 VAL A 296 " =    1.039
peak=    3.758 closest distance to " OD1 ASN A  60 " =    1.070
peak=    3.757 closest distance to " O   HOH Z  44 " =    2.067
peak=    3.757 closest distance to " O   HOH Z  45 " =    0.983
peak=    3.755 closest distance to " O   GLY A  91 " =    1.345
peak=    3.754 closest distance to " O   HOH Z 209 " =    2.247
peak=    3.751 closest distance to " CB  VAL A 230 " =    1.152
peak=    3.749 closest distance to " O   HOH Z 136 " =    1.326
peak=    3.747 closest distance to " O   HOH Z 345 " =    2.019
peak=    3.738 closest distance to " CD  LYS A  76 " =    1.881
peak=    3.729 closest distance to " O   HOH Z 163 " =    1.511
peak=    3.726 closest distance to " O   HOH Z 112 " =    1.639
peak=    3.724 closest distance to " NH2 ARG A 156 " =    0.968
peak=    3.722 closest distance to " O   HOH Z 303 " =    2.125
peak=    3.721 closest distance to " CB  TRP A 179 " =    1.091
peak=    3.716 closest distance to " NH2AARG A 145 " =    2.083
peak=    3.702 closest distance to " CD1 PHE A  61 " =    1.124
peak=    3.702 closest distance to " O   HOH Z  68 " =    1.737
peak=    3.700 closest distance to " CB BVAL A  41 " =    1.197
peak=    3.692 closest distance to " OG  SER A  26 " =    1.273
peak=    3.690 closest distance to " O   HOH Z 367 " =    3.362
peak=    3.690 closest distance to " CG1BVAL A  72 " =    1.645
peak=    3.688 closest distance to " O   HOH Z 126 " =    2.407
peak=    3.681 closest distance to " CB  ALA A 100 " =    1.239
peak=    3.676 closest distance to " O   HOH Z 132 " =    2.835
peak=    3.664 closest distance to " O   HOH Z 118 " =    1.828
peak=    3.660 closest distance to " O   HOH Z 427 " =    2.875
peak=    3.657 closest distance to " O   HOH Z 392 " =    1.454
peak=    3.654 closest distance to " O   HOH Z 344 " =    2.433
peak=    3.653 closest distance to " O   HOH Z 260 " =    1.559
peak=    3.633 closest distance to " O   HOH Z 279 " =    2.083
peak=    3.628 closest distance to " O   HOH Z 245 " =    1.448
peak=    3.628 closest distance to " CB  GLU A 152 " =    0.978
peak=    3.625 closest distance to " CG2 ILE A 120 " =    1.418
peak=    3.622 closest distance to " O   HOH Z 379 " =    1.645
peak=    3.615 closest distance to " O   HOH Z  85 " =    1.797
peak=    3.611 closest distance to " O   HOH Z 250 " =    1.390
peak=    3.604 closest distance to " O   HOH Z 359 " =    1.427
peak=    3.604 closest distance to " O   HOH Z 208 " =    1.287
peak=    3.603 closest distance to " O   HOH Z  97 " =    2.220
peak=    3.596 closest distance to " O   HOH Z 284 " =    1.721
peak=    3.590 closest distance to " O   HOH Z 265 " =    2.427
peak=    3.587 closest distance to " NH2BARG A 145 " =    1.987
peak=    3.586 closest distance to " CD1 LEU A  96 " =    0.712
peak=    3.585 closest distance to " CD2 HIS A  81 " =    1.557
peak=    3.583 closest distance to " O   HOH Z 362 " =    3.575
peak=    3.582 closest distance to " O   HOH Z  66 " =    2.189
peak=    3.570 closest distance to " O   HOH Z 366 " =    2.751
peak=    3.569 closest distance to " CB  GLN A 183 " =    1.349
peak=    3.559 closest distance to " O   HOH Z 108 " =    1.971
peak=    3.556 closest distance to " CE  MET A  93 " =    1.256
peak=    3.555 closest distance to " CE  LYS A 119 " =    1.177
peak=    3.550 closest distance to " NE1 TRP A 274 " =    0.950
peak=    3.550 closest distance to " O   HOH Z 423 " =    1.237
peak=    3.548 closest distance to " CA  ALA A 295 " =    0.965
peak=    3.545 closest distance to " O   HOH Z 374 " =    2.508
peak=    3.543 closest distance to " O   HOH Z 416 " =    1.185
peak=    3.543 closest distance to " CB  ARG A 102 " =    0.827
peak=    3.543 closest distance to " CB  ALA A   9 " =    1.542
peak=    3.536 closest distance to " O   HOH Z 209 " =    2.425
peak=    3.532 closest distance to " O   HOH Z 166 " =    1.422
peak=    3.528 closest distance to " O   THR A  82 " =    1.895
peak=    3.522 closest distance to " O   HOH Z 162 " =    1.673
peak=    3.522 closest distance to " O   HOH Z 369 " =    2.606
peak=    3.517 closest distance to " O   HOH Z 404 " =    1.340
peak=    3.509 closest distance to " O   HOH Z 238 " =    0.944
peak=    3.503 closest distance to " CB  TYR A 247 " =    1.088
peak=    3.503 closest distance to " CD ALYS A 290 " =    1.069
peak=    3.502 closest distance to " CB  SER A  63 " =    1.213
peak=    3.490 closest distance to " O   HOH Z 282 " =    1.390
peak=    3.489 closest distance to " O   HOH Z 368 " =    2.053
peak=    3.484 closest distance to " O   HOH Z  60 " =    1.306
peak=    3.481 closest distance to " N   ASN A  39 " =    1.325
peak=    3.480 closest distance to " O   HOH Z 383 " =    2.107
peak=    3.473 closest distance to " O   HOH Z 284 " =    2.825
peak=    3.471 closest distance to " O   HOH Z 113 " =    1.700
peak=    3.471 closest distance to " O   HOH Z 381 " =    1.522
peak=    3.468 closest distance to " O   HOH Z 428 " =    3.528
peak=    3.462 closest distance to " OD1 ASP A 286 " =    1.425
peak=    3.459 closest distance to " O   HOH Z 350 " =    2.041
peak=    3.459 closest distance to " CA  VAL A 126 " =    0.981
peak=    3.458 closest distance to " NE2 HIS A 115 " =    1.035
peak=    3.452 closest distance to " CD2 LEU A 255 " =    1.181
peak=    3.445 closest distance to " O   HOH Z 142 " =    1.957
peak=    3.438 closest distance to " O   HOH Z 343 " =    2.405
peak=    3.438 closest distance to " O   HOH Z   9 " =    2.368
peak=    3.430 closest distance to " CA  ARG A 195 " =    1.128
peak=    3.427 closest distance to " O   HOH Z 174 " =    2.281
peak=    3.427 closest distance to " O   SER A 164 " =    0.978
peak=    3.420 closest distance to " CG2 ILE A 234 " =    0.951
peak=    3.417 closest distance to " CB  VAL A 202 " =    1.795
peak=    3.414 closest distance to " O   HOH Z 364 " =    1.984
peak=    3.409 closest distance to " O   HOH Z   3 " =    1.567
peak=    3.408 closest distance to " CD  PRO A  54 " =    0.860
peak=    3.407 closest distance to " O   HOH Z 345 " =    2.339
peak=    3.405 closest distance to " CG  PRO A 280 " =    0.917
peak=    3.402 closest distance to " NZ  LYS A  76 " =    1.329
peak=    3.399 closest distance to " CB  ASP A 132 " =    3.894
peak=    3.396 closest distance to " O   HOH Z 173 " =    1.846
peak=    3.396 closest distance to " O   HOH Z 215 " =    1.490
peak=    3.394 closest distance to " O   HOH Z  50 " =    1.703
peak=    3.385 closest distance to " O   HOH Z  20 " =    1.781
peak=    3.381 closest distance to " CB  GLN A  58 " =    1.036
peak=    3.381 closest distance to " O   HOH Z 152 " =    1.986
peak=    3.379 closest distance to " O   HOH Z 130 " =    2.809
peak=    3.376 closest distance to " CG  PRO A 243 " =    1.276
peak=    3.374 closest distance to " CB  PHE A 225 " =    1.508
peak=    3.373 closest distance to " OG1 THR A 294 " =    2.305
peak=    3.364 closest distance to " O   HOH Z 194 " =    2.096
peak=    3.361 closest distance to " O   HOH Z 195 " =    4.104
peak=    3.361 closest distance to " CG  MET A  93 " =    1.078
peak=    3.361 closest distance to " NH2 ARG A 219 " =    1.892
peak=    3.358 closest distance to " O   HOH Z 253 " =    1.622
peak=    3.351 closest distance to " ND2 ASN A  60 " =    2.694
peak=    3.349 closest distance to " O   HOH Z 342 " =    0.925
peak=    3.339 closest distance to " O   HOH Z 280 " =    2.177
peak=    3.328 closest distance to " O   HOH Z 368 " =    1.130
peak=    3.328 closest distance to " NZ  LYS A 119 " =    1.561
peak=    3.324 closest distance to " O   HOH Z 267 " =    2.069
peak=    3.321 closest distance to " O   HOH Z 271 " =    1.689
peak=    3.315 closest distance to " O   HOH Z 409 " =    1.946
peak=    3.313 closest distance to " CG  ARG A 269 " =    0.951
peak=    3.301 closest distance to " CG  GLN A  88 " =    1.066
peak=    3.301 closest distance to " NH1 ARG A  14 " =    1.029
peak=    3.298 closest distance to " O   HOH Z 280 " =    1.394
peak=    3.292 closest distance to " CD2 TYR A  30 " =    0.845
peak=    3.292 closest distance to " O   HOH Z 150 " =    1.550
peak=    3.288 closest distance to " O   HOH Z 217 " =    1.828
peak=    3.286 closest distance to " O   HOH Z  96 " =    1.913
peak=    3.282 closest distance to " CE BLYS A 290 " =    0.822
peak=    3.281 closest distance to " O   HOH Z 334 " =    1.477
peak=    3.279 closest distance to " CB  TYR A 169 " =    0.806
peak=    3.273 closest distance to " O   HOH Z 109 " =    2.027
peak=    3.272 closest distance to " CB  ARG A 259 " =    1.858
peak=    3.271 closest distance to " O   HOH Z 207 " =    1.694
peak=    3.269 closest distance to " O   HOH Z 128 " =    1.436
peak=    3.268 closest distance to " O   HOH Z 283 " =    1.853
peak=    3.262 closest distance to " O   HOH Z 331 " =    1.320
peak=    3.259 closest distance to " CG2 THR A 221 " =    1.055
peak=    3.256 closest distance to " CD2 PHE A 218 " =    0.844
peak=    3.255 closest distance to " O   HOH Z 173 " =    2.265
peak=    3.239 closest distance to " O   ARG A 102 " =    2.234
peak=    3.235 closest distance to " OG BSER A 210 " =    1.340
peak=    3.226 closest distance to " O   HOH Z 143 " =    1.143
peak=    3.224 closest distance to " ND1 HIS A  81 " =    1.217
peak=    3.223 closest distance to " CG  MET A 185 " =    1.326
peak=    3.218 closest distance to " CA  LEU A  83 " =    1.344
peak=    3.212 closest distance to " CB  LEU A 228 " =    1.530
peak=    3.212 closest distance to " O   HOH Z 285 " =    1.449
peak=    3.207 closest distance to " OG ASER A 134 " =    1.867
peak=    3.206 closest distance to " O   HOH Z 425 " =    2.045
peak=    3.204 closest distance to " NH1 ARG A 138 " =    1.247
peak=    3.204 closest distance to " CZ AARG A 102 " =    1.522
peak=    3.202 closest distance to " NE2 GLN A  89 " =    1.092
peak=    3.202 closest distance to " CG  GLN A  77 " =    2.144
peak=    3.200 closest distance to " O   HOH Z 375 " =    2.193
peak=    3.198 closest distance to " O   HOH Z 420 " =    2.372
peak=    3.197 closest distance to " O   THR A  31 " =    1.754
peak=    3.193 closest distance to " CD  LYS A 193 " =    1.246
peak=    3.192 closest distance to " CB  ALA A 256 " =    0.996
peak=    3.190 closest distance to " O   HOH Z 197 " =    2.208
peak=    3.187 closest distance to " OG  SER A  62 " =    2.906
peak=    3.187 closest distance to " CB  GLN A  73 " =    1.443
peak=    3.185 closest distance to " CG2 VAL A  67 " =    1.189
peak=    3.185 closest distance to " CA  ASN A 284 " =    1.179
peak=    3.182 closest distance to " CG2 VAL A  78 " =    0.868
peak=    3.181 closest distance to " O   HOH Z 273 " =    2.635
peak=    3.180 closest distance to " OD1 ASN A  45 " =    1.196
peak=    3.180 closest distance to " O   HOH Z 197 " =    1.877
peak=    3.178 closest distance to " O   HOH Z 436 " =    1.551
peak=    3.177 closest distance to " CB  MET A  47 " =    1.284
peak=    3.176 closest distance to " CD2 LEU A  83 " =    1.604
peak=    3.176 closest distance to " O   HOH Z 423 " =    3.018
peak=    3.174 closest distance to " O   HOH Z 408 " =    2.079
peak=    3.173 closest distance to " O   ASN A 301 " =    2.841
peak=    3.173 closest distance to " O   HOH Z 114 " =    1.249
peak=    3.172 closest distance to " O   HOH Z  11 " =    1.274
peak=    3.169 closest distance to " O   HOH Z  61 " =    1.463
peak=    3.169 closest distance to " O   HOH Z  89 " =    1.789
peak=    3.168 closest distance to " CG2AVAL A  41 " =    0.860
peak=    3.167 closest distance to " O   HOH Z 337 " =    1.516
peak=    3.161 closest distance to " CG2 VAL A 197 " =    1.176
peak=    3.159 closest distance to " CA  THR A 221 " =    0.929
peak=    3.155 closest distance to " CB  ASN A 110 " =    1.108
peak=    3.150 closest distance to " CG2 THR A 251 " =    1.153
peak=    3.146 closest distance to " O   HOH Z 278 " =    1.167
peak=    3.144 closest distance to " NE BARG A 190 " =    1.680
peak=    3.143 closest distance to " O   HOH Z  39 " =    2.223
peak=    3.133 closest distance to " CA  LEU A 282 " =    1.150
peak=    3.132 closest distance to " O   HOH Z  48 " =    2.491
peak=    3.131 closest distance to " CA  LYS A 117 " =    1.257
peak=    3.130 closest distance to " O   ASP A 124 " =    1.837
peak=    3.125 closest distance to " ND1 HIS A  81 " =    1.300
peak=    3.108 closest distance to " O   HOH Z  32 " =    1.726
peak=    3.108 closest distance to " OD1 ASP A 238 " =    0.931
peak=    3.101 closest distance to " CB  TRP A 266 " =    1.141
peak=    3.100 closest distance to " CB  ASN A 142 " =    1.270
peak=    3.099 closest distance to " O   HOH Z 380 " =    2.006
peak=    3.093 closest distance to " O   HOH Z 144 " =    1.914
peak=    3.091 closest distance to " O   HOH Z 183 " =    1.858
peak=    3.088 closest distance to " CA  THR A 264 " =    1.107
peak=    3.087 closest distance to " O   HOH Z 139 " =    4.219
peak=    3.063 closest distance to " O   HOH Z 186 " =    2.371
peak=    3.050 closest distance to " OG BSER A 258 " =    2.670
peak=    3.048 closest distance to " CA  ASN A 176 " =    1.032
peak=    3.024 closest distance to " CA  ALA A 299 " =    0.889
peak=    3.003 closest distance to " NH2BARG A 190 " =    1.909

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.817 - 5.674
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.817 - 5.674

peak=   -4.619 closest distance to " O   HOH Z 169 " =    0.817
peak=   -4.367 closest distance to " CG2 VAL A 230 " =    0.830
peak=   -4.188 closest distance to " C   HIS A 108 " =    1.238
peak=   -4.176 closest distance to " O   PRO A 163 " =    2.037
peak=   -4.168 closest distance to " O   SER A 146 " =    0.865
peak=   -4.154 closest distance to " CD1 TRP A 179 " =    1.083
peak=   -4.144 closest distance to " O   HOH Z 362 " =    5.426
peak=   -4.140 closest distance to " OG ASER A 134 " =    1.346
peak=   -4.114 closest distance to " O   ASN A 187 " =    1.453
peak=   -4.105 closest distance to " CG  ARG A 219 " =    2.363
peak=   -4.088 closest distance to " O   HOH Z 166 " =    2.208
peak=   -4.064 closest distance to " N   GLN A 122 " =    1.509
peak=   -4.047 closest distance to " O   HOH Z  11 " =    1.524
peak=   -3.964 closest distance to " N   ALA A 248 " =    2.001
peak=   -3.962 closest distance to " OG BSER A 134 " =    1.370
peak=   -3.950 closest distance to " O   HOH Z  13 " =    1.331
peak=   -3.927 closest distance to " O   HOH Z  56 " =    2.002
peak=   -3.919 closest distance to " O   SER A 273 " =    1.191
peak=   -3.897 closest distance to " O   VAL A 197 " =    1.070
peak=   -3.877 closest distance to " OG  SER A  63 " =    1.117
peak=   -3.856 closest distance to " OD1 ASP A 200 " =    1.219
peak=   -3.842 closest distance to " CG1 VAL A 296 " =    0.915
peak=   -3.840 closest distance to " CD  ARG A  14 " =    3.037
peak=   -3.835 closest distance to " O   HOH Z 423 " =    2.451
peak=   -3.827 closest distance to " N   GLN A  58 " =    1.057
peak=   -3.823 closest distance to " O   HOH Z  92 " =    1.680
peak=   -3.822 closest distance to " ND2 ASN A  45 " =    1.000
peak=   -3.822 closest distance to " O   HOH Z 103 " =    1.789
peak=   -3.819 closest distance to " CG2 THR A  18 " =    2.714
peak=   -3.791 closest distance to " O   HOH Z 215 " =    3.308
peak=   -3.790 closest distance to " O   HOH Z 266 " =    4.286
peak=   -3.788 closest distance to " CB  ALA A 244 " =    2.000
peak=   -3.764 closest distance to " N   GLY A  17 " =    1.333
peak=   -3.759 closest distance to " CD  ARG A 139 " =    1.512
peak=   -3.758 closest distance to " O   ALA A 161 " =    1.385
peak=   -3.742 closest distance to " O   HOH Z 250 " =    1.483
peak=   -3.703 closest distance to " O   HOH Z 435 " =    2.222
peak=   -3.689 closest distance to " O   HOH Z 274 " =    2.732
peak=   -3.681 closest distance to " CD2 LEU A 300 " =    2.567
peak=   -3.672 closest distance to " CD  LYS A 289 " =    2.460
peak=   -3.661 closest distance to " O   HOH Z 407 " =    2.412
peak=   -3.643 closest distance to " CE2 TYR A  30 " =    2.873
peak=   -3.639 closest distance to " CG  ARG A 138 " =    0.893
peak=   -3.632 closest distance to " CD1 PHE A  59 " =    1.784
peak=   -3.629 closest distance to " O   HOH Z  60 " =    1.815
peak=   -3.626 closest distance to " NH2 ARG A  79 " =    1.904
peak=   -3.617 closest distance to " O   HOH Z 234 " =    3.948
peak=   -3.617 closest distance to " O   VAL A  67 " =    2.476
peak=   -3.613 closest distance to " NE2 GLN A  55 " =    2.104
peak=   -3.613 closest distance to " C   THR A 279 " =    1.285
peak=   -3.609 closest distance to " N   ARG A  66 " =    1.750
peak=   -3.602 closest distance to " OD2 ASP A 191 " =    1.604
peak=   -3.592 closest distance to " O   HOH Z 281 " =    3.110
peak=   -3.550 closest distance to " O   LEU A 143 " =    1.526
peak=   -3.541 closest distance to " CD  ARG A 156 " =    2.001
peak=   -3.539 closest distance to " CB  ALA A 248 " =    1.999
peak=   -3.532 closest distance to " OD2 ASP A  50 " =    1.418
peak=   -3.529 closest distance to " C   ALA A 158 " =    1.131
peak=   -3.525 closest distance to " O   HOH Z 388 " =    2.115
peak=   -3.524 closest distance to " O   HOH Z 125 " =    3.101
peak=   -3.521 closest distance to " OG  SER A  26 " =    1.307
peak=   -3.508 closest distance to " O   HOH Z 222 " =    2.967
peak=   -3.502 closest distance to " C   GLY A  91 " =    1.336
peak=   -3.501 closest distance to " O   HOH Z 198 " =    1.104
peak=   -3.486 closest distance to " CG  GLU A   2 " =    1.918
peak=   -3.480 closest distance to " CB  PRO A 163 " =    2.903
peak=   -3.460 closest distance to " O   HOH Z 227 " =    1.046
peak=   -3.459 closest distance to " O   HOH Z 208 " =    1.144
peak=   -3.459 closest distance to " CG2BVAL A  41 " =    2.806
peak=   -3.457 closest distance to " CD2 LEU A 237 " =    2.838
peak=   -3.454 closest distance to " O   HOH Z 426 " =    2.183
peak=   -3.447 closest distance to " C   GLN A 144 " =    0.835
peak=   -3.441 closest distance to " O   HOH Z 427 " =    1.433
peak=   -3.440 closest distance to " O   HOH Z 290 " =    0.964
peak=   -3.438 closest distance to " CZ2 TRP A  92 " =    2.587
peak=   -3.431 closest distance to " OG  SER A  97 " =    2.107
peak=   -3.429 closest distance to " N   THR A 235 " =    1.272
peak=   -3.427 closest distance to " O   HOH Z 210 " =    0.924
peak=   -3.420 closest distance to " O   LEU A 228 " =    2.352
peak=   -3.411 closest distance to " O   HOH Z 183 " =    1.554
peak=   -3.410 closest distance to " O   ALA A 160 " =    1.205
peak=   -3.409 closest distance to " O   ALA A  51 " =    1.534
peak=   -3.409 closest distance to " O   HOH Z  97 " =    1.171
peak=   -3.406 closest distance to " CZ  TYR A 169 " =    1.813
peak=   -3.406 closest distance to " CD1 TYR A 247 " =    2.186
peak=   -3.394 closest distance to " O   HOH Z 345 " =    2.434
peak=   -3.393 closest distance to " CG2 VAL A 296 " =    1.494
peak=   -3.389 closest distance to " ND2 ASN A 142 " =    1.773
peak=   -3.378 closest distance to " CG BARG A 275 " =    0.992
peak=   -3.373 closest distance to " O   HOH Z 166 " =    1.277
peak=   -3.372 closest distance to " OG BSER A 210 " =    1.446
peak=   -3.367 closest distance to " OG ASER A 258 " =    2.772
peak=   -3.365 closest distance to " OD1 ASN A 301 " =    1.984
peak=   -3.364 closest distance to " O   HOH Z 392 " =    4.919
peak=   -3.363 closest distance to " O   HOH Z 131 " =    4.167
peak=   -3.361 closest distance to " CG  GLN A  88 " =    1.077
peak=   -3.355 closest distance to " O   HOH Z 346 " =    2.018
peak=   -3.352 closest distance to " OE1 GLN A 223 " =    4.591
peak=   -3.350 closest distance to " OG  SER A 206 " =    1.357
peak=   -3.350 closest distance to " CB  ALA A 100 " =    1.767
peak=   -3.344 closest distance to " O   HOH Z  63 " =    0.902
peak=   -3.323 closest distance to " O   GLY A 118 " =    2.091
peak=   -3.320 closest distance to " N   HIS A 115 " =    1.894
peak=   -3.312 closest distance to " O   VAL A 174 " =    2.193
peak=   -3.308 closest distance to " CB  ALA A  51 " =    1.806
peak=   -3.306 closest distance to " CA  GLN A  58 " =    1.149
peak=   -3.304 closest distance to " O   HOH Z 316 " =    1.532
peak=   -3.302 closest distance to " O   HOH Z 126 " =    1.983
peak=   -3.299 closest distance to " CA  GLY A  98 " =    2.062
peak=   -3.299 closest distance to " O   HOH Z 147 " =    0.863
peak=   -3.293 closest distance to " O   HOH Z 231 " =    2.200
peak=   -3.293 closest distance to " NE2 GLN A  88 " =    1.905
peak=   -3.292 closest distance to " O   HOH Z  37 " =    0.872
peak=   -3.291 closest distance to " O   HOH Z 435 " =    2.429
peak=   -3.286 closest distance to " O   HOH Z 172 " =    5.674
peak=   -3.286 closest distance to " CB  PHE A 208 " =    2.292
peak=   -3.282 closest distance to " CD1 LEU A  96 " =    2.057
peak=   -3.281 closest distance to " O   HOH Z 249 " =    1.661
peak=   -3.279 closest distance to " O   GLY A  80 " =    2.466
peak=   -3.270 closest distance to " N   GLN A  58 " =    2.152
peak=   -3.268 closest distance to " CG  ASP A  50 " =    2.075
peak=   -3.266 closest distance to " CE1 PHE A 204 " =    2.493
peak=   -3.263 closest distance to " ND2 ASN A  39 " =    1.163
peak=   -3.261 closest distance to " CE3 TRP A 150 " =    1.988
peak=   -3.260 closest distance to " O   HOH Z 145 " =    1.736
peak=   -3.256 closest distance to " OD2 ASP A 286 " =    2.206
peak=   -3.255 closest distance to " O   HOH Z 377 " =    2.266
peak=   -3.253 closest distance to " O   HOH Z 340 " =    1.094
peak=   -3.250 closest distance to " ND2 ASN A  60 " =    2.078
peak=   -3.247 closest distance to " O   PRO A 198 " =    1.348
peak=   -3.246 closest distance to " CD  ARG A 138 " =    1.599
peak=   -3.245 closest distance to " O   HOH Z 236 " =    4.889
peak=   -3.244 closest distance to " CA  VAL A 296 " =    1.056
peak=   -3.244 closest distance to " CG  LEU A 228 " =    1.012
peak=   -3.240 closest distance to " O   HOH Z 395 " =    4.938
peak=   -3.239 closest distance to " O   PHE A 218 " =    1.634
peak=   -3.231 closest distance to " O   HOH Z 165 " =    2.113
peak=   -3.229 closest distance to " O   HOH Z 280 " =    1.812
peak=   -3.228 closest distance to " CD2 LEU A 143 " =    2.400
peak=   -3.226 closest distance to " O   HOH Z 118 " =    2.362
peak=   -3.219 closest distance to " NH2 ARG A  66 " =    1.645
peak=   -3.218 closest distance to " CG1 ILE A 199 " =    1.785
peak=   -3.218 closest distance to " O   PRO A  54 " =    1.264
peak=   -3.216 closest distance to " O   HOH Z  55 " =    2.376
peak=   -3.211 closest distance to " O   PRO A 198 " =    1.357
peak=   -3.208 closest distance to " NE2 GLN A 240 " =    1.789
peak=   -3.207 closest distance to " CG1AVAL A  72 " =    2.036
peak=   -3.207 closest distance to " CD2 TYR A 293 " =    2.041
peak=   -3.201 closest distance to " CG  LYS A 193 " =    2.137
peak=   -3.197 closest distance to " CE  MET A 105 " =    1.954
peak=   -3.196 closest distance to " C   TYR A  30 " =    0.980
peak=   -3.196 closest distance to " CG2 VAL A 230 " =    1.412
peak=   -3.195 closest distance to " NE2 GLN A  58 " =    2.412
peak=   -3.193 closest distance to " O   ARG A 275 " =    2.108
peak=   -3.193 closest distance to " OG  SER A  62 " =    1.264
peak=   -3.193 closest distance to " O   HOH Z 111 " =    4.195
peak=   -3.190 closest distance to " O   HOH Z 179 " =    1.810
peak=   -3.184 closest distance to " O   ALA A 184 " =    1.497
peak=   -3.181 closest distance to " N   PHE A 192 " =    1.661
peak=   -3.171 closest distance to " O   HOH Z 137 " =    1.779
peak=   -3.168 closest distance to " CG1 VAL A 296 " =    1.942
peak=   -3.167 closest distance to " O   HOH Z 134 " =    2.544
peak=   -3.165 closest distance to " O   HOH Z 108 " =    2.369
peak=   -3.164 closest distance to " O   HOH Z 424 " =    3.158
peak=   -3.163 closest distance to " O   HOH Z 368 " =    2.440
peak=   -3.161 closest distance to " O   HOH Z 292 " =    2.549
peak=   -3.159 closest distance to " CB  GLN A  58 " =    1.262
peak=   -3.156 closest distance to " O   HOH Z 174 " =    2.178
peak=   -3.156 closest distance to " O   ARG A  66 " =    1.167
peak=   -3.156 closest distance to " OE1 GLN A 223 " =    2.144
peak=   -3.156 closest distance to " NE BARG A 275 " =    1.189
peak=   -3.152 closest distance to " O   HOH Z 107 " =    1.712
peak=   -3.150 closest distance to " CE BMET A  47 " =    1.223
peak=   -3.150 closest distance to " O   HOH Z 138 " =    1.014
peak=   -3.149 closest distance to " CD1 LEU A 101 " =    2.393
peak=   -3.146 closest distance to " O   HOH Z 116 " =    0.939
peak=   -3.145 closest distance to " O   HOH Z 198 " =    1.570
peak=   -3.145 closest distance to " CA  ASP A 298 " =    1.145
peak=   -3.142 closest distance to " O   HOH Z 221 " =    1.469
peak=   -3.141 closest distance to " N   GLY A 302 " =    1.719
peak=   -3.137 closest distance to " NE1 TRP A 274 " =    1.256
peak=   -3.135 closest distance to " CD1 LEU A 228 " =    2.187
peak=   -3.131 closest distance to " NE2 GLN A 194 " =    1.752
peak=   -3.130 closest distance to " CG  ASN A  45 " =    1.708
peak=   -3.123 closest distance to " O   HOH Z 150 " =    1.326
peak=   -3.122 closest distance to " O   HOH Z 416 " =    0.817
peak=   -3.121 closest distance to " CG  ASP A 286 " =    1.273
peak=   -3.120 closest distance to " O   HOH Z  52 " =    1.988
peak=   -3.116 closest distance to " O   HOH Z 310 " =    3.548
peak=   -3.114 closest distance to " N   ALA A  43 " =    2.548
peak=   -3.109 closest distance to " O   ALA A  34 " =    2.517
peak=   -3.104 closest distance to " O   HOH Z  34 " =    2.025
peak=   -3.100 closest distance to " NE2 GLN A  58 " =    2.239
peak=   -3.099 closest distance to " O   HOH Z 348 " =    1.678
peak=   -3.097 closest distance to " N   THR A  52 " =    1.672
peak=   -3.092 closest distance to " C   ARG A 269 " =    1.385
peak=   -3.092 closest distance to " CD2 TYR A  15 " =    2.187
peak=   -3.091 closest distance to " O   HOH Z 128 " =    1.665
peak=   -3.090 closest distance to " O   HOH Z 138 " =    1.773
peak=   -3.089 closest distance to " OD1 ASN A 176 " =    1.125
peak=   -3.084 closest distance to " CB  CYS A 254 " =    2.598
peak=   -3.084 closest distance to " O   HOH Z 117 " =    0.971
peak=   -3.081 closest distance to " O   HOH Z 385 " =    3.364
peak=   -3.079 closest distance to " CB  ALA A   9 " =    2.539
peak=   -3.074 closest distance to " CG  TYR A 169 " =    1.847
peak=   -3.050 closest distance to " CD2 LEU A 300 " =    2.718
peak=   -3.043 closest distance to " CG2 THR A 279 " =    1.658
peak=   -3.032 closest distance to " CB  THR A  42 " =    1.957

================= 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    :  0.5092 0.5038   6.304969e+00   6.297261e+00
   1_bss:  0.5007 0.4959   6.302718e+00   6.289886e+00
   1_xyz:  0.4297 0.4571   6.221914e+00   6.256990e+00
   1_adp:  0.3917 0.4507   6.175505e+00   6.247286e+00
   1_occ:  0.3910 0.4512   6.174473e+00   6.246550e+00
   2_bss:  0.3897 0.4469   6.174474e+00   6.245227e+00
   2_xyz:  0.3166 0.3787   6.012473e+00   6.135251e+00
   2_adp:  0.2916 0.3584   5.955205e+00   6.098258e+00
   2_occ:  0.2915 0.3584   5.954974e+00   6.098079e+00
   3_bss:  0.2893 0.3552   5.951857e+00   6.094915e+00
   3_xyz:  0.2289 0.2908   5.759531e+00   5.940848e+00
   3_adp:  0.2163 0.2730   5.706370e+00   5.885865e+00
   3_occ:  0.2159 0.2733   5.705886e+00   5.886485e+00
   4_bss:  0.2148 0.2713   5.702896e+00   5.883054e+00
   4_xyz:  0.1760 0.2323   5.543024e+00   5.748068e+00
   4_adp:  0.1590 0.2133   5.449932e+00   5.664858e+00
   4_occ:  0.1589 0.2133   5.449685e+00   5.664646e+00
   5_bss:  0.1589 0.2124   5.448099e+00   5.662510e+00
   5_xyz:  0.1329 0.1825   5.290764e+00   5.524158e+00
   5_adp:  0.1264 0.1757   5.247917e+00   5.483896e+00
   5_occ:  0.1263 0.1755   5.247249e+00   5.483373e+00
   5_bss:  0.1265 0.1760   5.248122e+00   5.484594e+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:  0.358   2.659   7.468   8.443   8.715   0.000   0.000   0.000
   1_xyz:  0.358   2.659   7.468   8.443   8.715   0.000   0.000   0.000
   1_adp:  0.358   2.659   7.468   8.443   8.715   0.000   0.000   0.000
   1_occ:  0.358   2.659   7.468   8.443   8.715   0.000   0.000   0.000
   2_bss:  0.333  32.772   4.036   4.999   5.871   0.000   0.000   0.000
   2_xyz:  0.333  32.772   4.036   4.999   5.871   0.000   0.000   0.000
   2_adp:  0.333  32.772   4.036   4.999   5.871   0.000   0.000   0.000
   2_occ:  0.333  32.772   4.036   4.999   5.871   0.000   0.000   0.000
   3_bss:  0.319  32.772   1.994   3.193   3.709   0.000   0.000   0.000
   3_xyz:  0.319  32.772   1.994   3.193   3.709   0.000   0.000   0.000
   3_adp:  0.319  32.772   1.994   3.193   3.709   0.000   0.000   0.000
   3_occ:  0.319  32.772   1.994   3.193   3.709   0.000   0.000   0.000
   4_bss:  0.324  30.982   0.681   2.189   2.233   0.000   0.000   0.000
   4_xyz:  0.324  30.982   0.681   2.189   2.233   0.000   0.000   0.000
   4_adp:  0.324  30.982   0.681   2.189   2.233   0.000   0.000   0.000
   4_occ:  0.324  30.982   0.681   2.189   2.233   0.000   0.000   0.000
   5_bss:  0.313  30.932  -0.001   1.480   1.431   0.000   0.000   0.000
   5_xyz:  0.313  30.932  -0.001   1.480   1.431   0.000   0.000   0.000
   5_adp:  0.313  30.932  -0.001   1.480   1.431   0.000   0.000   0.000
   5_occ:  0.313  30.932  -0.001   1.480   1.431   0.000   0.000   0.000
   5_bss:  0.313  33.685  -0.971   0.510   0.461   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.146 0.3401  0.4046    81573.230
   1_bss:  63.598 0.3454  0.5153    78388.599
   1_xyz:  58.836 0.4054  0.5933    65794.308
   1_adp:  55.173 0.4534  0.7259    62562.629
   1_occ:  55.166 0.4534  0.7244    62441.561
   2_bss:  54.642 0.4600  0.6644    61658.395
   2_xyz:  42.031 0.6170  0.8867    39916.945
   2_adp:  38.935 0.6541  0.9375    35069.188
   2_occ:  38.925 0.6542  0.9377    35083.854
   3_bss:  38.647 0.6572  0.8746    34477.852
   3_xyz:  29.804 0.7590  0.9794    22108.373
   3_adp:  27.098 0.7894  1.0111    19379.894
   3_occ:  27.102 0.7893  1.0109    19382.706
   4_bss:  26.890 0.7913  0.9652    19039.913
   4_xyz:  22.640 0.8359  0.9952    13990.939
   4_adp:  20.290 0.8597  1.0048    11722.830
   4_occ:  20.284 0.8597  1.0048    11715.649
   5_bss:  20.207 0.8603  0.9784    11592.867
   5_xyz:  17.032 0.8891  0.9917     8479.968
   5_adp:  16.105 0.8976  0.9882     7882.026
   5_occ:  16.085 0.8977  0.9882     7866.278
   5_bss:  16.100 0.8977  0.9885     7909.193
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2806e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2806e+01
   1_xyz:   2.070  0.017  0.127 18.745  0.008  4.105   2.0686e-01
   1_adp:   2.070  0.017  0.127 18.745  0.008  4.105   2.0686e-01
   1_occ:   2.070  0.017  0.127 18.745  0.008  4.105   2.0686e-01
   2_bss:   2.070  0.017  0.127 18.745  0.008  4.105   2.0686e-01
   2_xyz:   1.327  0.010  0.088 17.274  0.006  4.103   1.0954e-01
   2_adp:   1.327  0.010  0.088 17.274  0.006  4.103   1.0954e-01
   2_occ:   1.327  0.010  0.088 17.274  0.006  4.103   1.0954e-01
   3_bss:   1.327  0.010  0.088 17.274  0.006  4.103   1.0954e-01
   3_xyz:   1.103  0.008  0.077 16.064  0.004  4.120   7.3684e-02
   3_adp:   1.103  0.008  0.077 16.064  0.004  4.120   7.3684e-02
   3_occ:   1.103  0.008  0.077 16.064  0.004  4.120   7.3684e-02
   4_bss:   1.103  0.008  0.077 16.064  0.004  4.120   7.3684e-02
   4_xyz:   0.979  0.006  0.070 15.536  0.004  4.113   6.0101e-02
   4_adp:   0.979  0.006  0.070 15.536  0.004  4.113   6.0101e-02
   4_occ:   0.979  0.006  0.070 15.536  0.004  4.113   6.0101e-02
   5_bss:   0.979  0.006  0.070 15.536  0.004  4.113   6.0101e-02
   5_xyz:   1.100  0.007  0.079 15.915  0.004  4.107   6.8951e-02
   5_adp:   1.100  0.007  0.079 15.915  0.004  4.107   6.8951e-02
   5_occ:   1.100  0.007  0.079 15.915  0.004  4.107   6.8951e-02
   5_bss:   1.100  0.007  0.079 15.915  0.004  4.107   6.8951e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.822   6.8320e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.822   6.8320e+00
   1_xyz:  17.858  0.231  0.620 88.031  0.063  2.128   1.2902e-01
   1_adp:  17.858  0.231  0.620 88.031  0.063  2.128   1.2902e-01
   1_occ:  17.858  0.231  0.620 88.031  0.063  2.128   1.2902e-01
   2_bss:  17.858  0.231  0.620 88.031  0.063  2.128   1.2902e-01
   2_xyz:   8.937  0.132  0.336 85.646  0.069  2.141   8.6761e-02
   2_adp:   8.937  0.132  0.336 85.646  0.069  2.141   8.6761e-02
   2_occ:   8.937  0.132  0.336 85.646  0.069  2.141   8.6761e-02
   3_bss:   8.937  0.132  0.336 85.646  0.069  2.141   8.6761e-02
   3_xyz:   7.940  0.052  0.279 81.439  0.033  2.327   7.9594e-02
   3_adp:   7.940  0.052  0.279 81.439  0.033  2.327   7.9594e-02
   3_occ:   7.940  0.052  0.279 81.439  0.033  2.327   7.9594e-02
   4_bss:   7.940  0.052  0.279 81.439  0.033  2.327   7.9594e-02
   4_xyz:   6.984  0.035  0.253 77.713  0.028  2.333   4.5559e-02
   4_adp:   6.984  0.035  0.253 77.713  0.028  2.333   4.5559e-02
   4_occ:   6.984  0.035  0.253 77.713  0.028  2.333   4.5559e-02
   5_bss:   6.984  0.035  0.253 77.713  0.028  2.333   4.5559e-02
   5_xyz:   7.125  0.049  0.382 84.460  0.035  2.252   5.9644e-02
   5_adp:   7.125  0.049  0.382 84.460  0.035  2.252   5.9644e-02
   5_occ:   7.125  0.049  0.382 84.460  0.035  2.252   5.9644e-02
   5_bss:   7.125  0.049  0.382 84.460  0.035  2.252   5.9644e-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:  83.99   0.00  14.86  73.00   0.00  13.06  83.99   0.00  24.67
   1_occ:  83.99   0.00  14.86  73.00   0.00  13.06  83.99   0.00  24.67
   2_bss:  83.99   0.00  14.86  73.00   0.00  13.06  83.99   0.00  24.67
   2_xyz:  83.99   0.00  14.86  73.00   0.00  13.06  83.99   0.00  24.67
   2_adp:  93.49   0.00  15.20  73.68   0.00  12.15  93.49   0.00  31.79
   2_occ:  93.49   0.00  15.20  73.68   0.00  12.15  93.49   0.00  31.79
   3_bss:  93.49   0.00  15.20  73.68   0.00  12.15  93.49   0.00  31.79
   3_xyz:  93.49   0.00  15.20  73.68   0.00  12.15  93.49   0.00  31.79
   3_adp: 126.17   0.00  14.98 126.17   0.00  11.65  91.54   1.68  33.12
   3_occ: 126.17   0.00  14.98 126.17   0.00  11.65  91.54   1.68  33.12
   4_bss: 126.17   0.00  14.98 126.17   0.00  11.65  91.54   1.68  33.12
   4_xyz: 126.17   0.00  14.98 126.17   0.00  11.65  91.54   1.68  33.12
   4_adp:  95.38   0.00  15.12  85.95   0.00  10.67  95.38   2.92  39.36
   4_occ:  95.38   0.00  15.12  85.95   0.00  10.67  95.38   2.92  39.36
   5_bss:  95.38   0.00  15.12  85.95   0.00  10.67  95.38   2.92  39.36
   5_xyz:  95.38   0.00  15.12  85.95   0.00  10.67  95.38   2.92  39.36
   5_adp:  96.61   0.00  14.88  91.27   0.00  10.20  96.61   3.69  40.38
   5_occ:  96.61   0.00  14.88  91.27   0.00  10.20  96.61   3.69  40.38
   5_bss:  97.58   0.97  15.85  92.24   0.97  11.17  97.58   4.66  41.35
------------------------------------------------------------------------
 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:    1.299    0.042    0.449
   1_adp:    1.299    0.042    0.449
   1_occ:    1.299    0.042    0.449
   2_bss:    1.299    0.042    0.449
   2_xyz:    1.885    0.018    0.639
   2_adp:    1.885    0.018    0.639
   2_occ:    1.885    0.018    0.639
   3_bss:    1.885    0.018    0.639
   3_xyz:    1.748    0.057    0.732
   3_adp:    1.748    0.057    0.732
   3_occ:    1.748    0.057    0.732
   4_bss:    1.748    0.057    0.732
   4_xyz:    1.896    0.038    0.812
   4_adp:    1.896    0.038    0.812
   4_occ:    1.896    0.038    0.812
   5_bss:    1.896    0.038    0.812
   5_xyz:    2.017    0.063    0.858
   5_adp:    2.017    0.063    0.858
   5_occ:    2.017    0.063    0.858
   5_bss:    2.017    0.063    0.858
------------------------------------------------------------------------

CPU time actual refinement: 337.08


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_77/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_77/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_77/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_77/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_77/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.93 
  Macro-tasks:
    bulk solvent and scale       = 39.07  
    individual site refinement   = 139.84 
    weights calculation          = 32.06  
    collect and process          = 6.36   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 217.46 
  Micro-tasks:
    mask                            = 3.03   
    f_calc                          = 105.95 
    alpha_beta                      = 8.36   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 115.75 
    fmodel                         = 6.95   
    r_factors                      = 0.21   
    phase_errors                   = 10.07  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 251.72 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.786 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    633 calls, 105.71 s
gradients_fft:          579 calls, 102.96 s

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

# Date 2008-01-16 Time 00:39:35 PST -0800 (1200472775.86 s)
Start R-work = 0.5092, R-free = 0.5038 (no bulk solvent and anisotropic scale)
Final R-work = 0.1439, R-free = 0.1926 (no bulk solvent and anisotropic scale)

Start R-work = 0.5007, R-free = 0.4959
Final R-work = 0.1265, R-free = 0.1760