# Date 2008-01-16 Time 03:02:00 PST -0800 (1200481320.27 s)
#phil __OFF__

Command line arguments: "../1073.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20081
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1073

-------------------------------------------------------------------------------
  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: (71.3037, 47.8686, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.8686, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.01117
Completeness in resolution range: 0.963599
Completeness with d_max=infinity: 0.960575

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1778
                             d_min =   2.0112

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: (71.3037, 47.8686, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.01117
Completeness in resolution range: 0.963599
Completeness with d_max=infinity: 0.960575

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1782 -  4.3031 [2127/2154]  1915   212  10.0%
  bin  2:  4.3031 -  3.4284 [2044/2060]  1838   206  10.1%
  bin  3:  3.4284 -  2.9989 [2032/2051]  1827   205  10.1%
  bin  4:  2.9989 -  2.7264 [2006/2036]  1809   197   9.8%
  bin  5:  2.7264 -  2.5319 [1995/2014]  1798   197   9.9%
  bin  6:  2.5319 -  2.3833 [1965/2001]  1770   195   9.9%
  bin  7:  2.3833 -  2.2643 [1976/2009]  1776   200  10.1%
  bin  8:  2.2643 -  2.1660 [1967/2000]  1768   199  10.1%
  bin  9:  2.1660 -  2.0829 [1963/1992]  1770   193   9.8%
  bin 10:  2.0829 -  2.0112 [1514/2012]  1359   155  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1073/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:
        1.43 -     2.13: 6
        2.13 -     2.82: 831
        2.82 -     3.51: 4347
        3.51 -     4.21: 9116
        4.21 -     4.90: 13475
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.432 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.920 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  1.920 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.939 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27770 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_1073/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1073/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 = 71.30375 47.8686 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4882   r_free= 0.4699   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.289408                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7993 0.99   1380  154 0.3968 0.3892      6.5969      6.5424|
|  2:  4.7993 -  3.8295 0.99   1346  146 0.4073 0.4433      6.8151      6.8973|
|  3:  3.8295 -  3.3514 0.99   1306  149 0.4586 0.3970      6.7151      6.6462|
|  4:  3.3514 -  3.0476 0.99   1295  143 0.4779 0.4268      6.5507      6.4609|
|  5:  3.0476 -  2.8307 0.99   1292  142 0.5210 0.4866      6.3881      6.3986|
|  6:  2.8307 -  2.6648 0.99   1288  144 0.5256 0.5248      6.3084       6.236|
|  7:  2.6648 -  2.5319 0.99   1280  139 0.5016 0.4775      6.2399      6.2025|
|  8:  2.5319 -  2.4222 0.98   1274  147 0.5315 0.4724      6.1908      6.1451|
|  9:  2.4222 -  2.3293 0.98   1276  140 0.5318 0.5783      6.1203      6.1786|
| 10:  2.3293 -  2.2492 0.98   1244  138 0.5343 0.5193      6.1176      6.1409|
| 11:  2.2492 -  2.1791 1.00   1283  143 0.5322 0.4921      6.0471      6.0592|
| 12:  2.1791 -  2.1169 0.97   1243  136 0.5408 0.5134      5.9945       6.021|
| 13:  2.1169 -  2.0613 0.98   1257  144 0.5357 0.5063      5.8915      5.8349|
| 14:  2.0613 -  2.0112 0.67    866   94 0.5433 0.5391      5.8482      5.7793|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7993  1380   154  0.68  35.87   0.79     0.71      76519.63|
|  2:  4.7993 -  3.8295  1346   146  0.70  35.62   0.87     0.74     107622.42|
|  3:  3.8295 -  3.3514  1306   149  0.60  43.78   0.80     0.69     113712.68|
|  4:  3.3514 -  3.0476  1295   143  0.52  50.39   0.79     0.60      98758.64|
|  5:  3.0476 -  2.8307  1292   142  0.45  56.21   0.72     0.52      78543.45|
|  6:  2.8307 -  2.6648  1288   144  0.44  56.70   0.71     0.50      66406.87|
|  7:  2.6648 -  2.5319  1280   139  0.41  58.99   0.74     0.45      61632.53|
|  8:  2.5319 -  2.4222  1274   147  0.32  65.76   0.72     0.38      62637.98|
|  9:  2.4222 -  2.3293  1276   140  0.25  71.12   0.69     0.29      60742.54|
| 10:  2.3293 -  2.2492  1244   138  0.25  71.33   0.72     0.29      56450.59|
| 11:  2.2492 -  2.1791  1283   143  0.29  68.15   0.74     0.34      48349.85|
| 12:  2.1791 -  2.1169  1243   136  0.32  66.10   0.74     0.39      43971.73|
| 13:  2.1169 -  2.0613  1257   144  0.30  67.78   0.70     0.36      37799.22|
| 14:  2.0613 -  2.0112   866    94  0.25  71.35   0.70     0.27      32455.05|
|alpha:            min =        0.27 max =            0.74 mean =         0.47|
|beta:             min =    32455.05 max =       113712.68 mean =     68780.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.91|
|phase err.(test): min =        0.00 max =           89.91 mean =        57.91|
|-----------------------------------------------------------------------------|

============================== 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 = 14.787802             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.359   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.418168              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.546   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1462 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2578 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3820 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4969 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6478 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7597 |
|-----------------------------------------------------------------------------|
|-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 |       54.559 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.721 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    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 = 12.373)------------------------------------------|
|    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: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4930   r_free= 0.4751   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.290802                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4820   r_free= 0.4609   ksol= 0.30   Bsol= 20.00   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.18,11.21,7.50,0.00,0.00,0.00); trace/3= 8.63                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.285432                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.521945             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.462   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.206358              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.027   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4820      final r-factor (work) = 0.4024          |
| start r-factor (free) = 0.4609      final r-factor (free) = 0.4173          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 97.0832 = 13.52 * 0.50 * 6.2897 + 1.00 * 54.5588                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.1097 = 13.52 * 0.50 * 6.2067 + 1.00 * 0.1463                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4024      final r-factor (work) = 0.3597          |
| start r-factor (free) = 0.4173      final r-factor (free) = 0.3986          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5023 = 1.21 * 1.00 * 6.2067 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4164 = 1.21 * 1.00 * 6.1318 + 1.00 * 0.0192                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    118.87  13.85    None  None   None       |
|    all(noH): 2823   0      0.00    118.87  13.85    None  None   None       |
|    Sol.    : 438    0      0.00    118.87  26.89    None  None   None       |
|    Mac.    : 2385   0      0.00    77.53   11.46    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 -  11.887: 1601   |   5:    59.436 -  71.324:   22        |
|      1:    11.887 -  23.775:  725   |   6:    71.324 -  83.211:   10        |
|      2:    23.775 -  35.662:  303   |   7:    83.211 -  95.098:    2        |
|      3:    35.662 -  47.549:  108   |   8:    95.098 - 106.985:    1        |
|      4:    47.549 -  59.436:   49   |   9:   106.985 - 118.873:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3597 r_free = 0.3986             target_work(ml) = 6.114         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3591 r_free = 0.3978             target_work(ml) = 6.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3591   r_free= 0.3978   ksol= 0.30   Bsol= 20.00   scale= 1.075   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.18,11.21,7.50,0.00,0.00,0.00); trace/3= 8.63                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.113348                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3572   r_free= 0.3948   ksol= 0.31   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.30,7.50,4.80,0.00,0.00,0.00); trace/3= 5.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.114307                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.324016             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.099  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.561280              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.399  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3572      final r-factor (work) = 0.2767          |
| start r-factor (free) = 0.3948      final r-factor (free) = 0.3350          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.7690 = 10.32 * 0.50 * 6.1261 + 1.00 * 0.1461                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.0628 = 10.32 * 0.50 * 5.9971 + 1.00 * 0.1056                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2767      final r-factor (work) = 0.2553          |
| start r-factor (free) = 0.3350      final r-factor (free) = 0.3116          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3857 = 0.56 * 1.00 * 5.9971 + 1.00 * 0.0196                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3154 = 0.56 * 1.00 * 5.8787 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.84  13.20    None  None   None       |
|    all(noH): 2823   0      0.00    113.84  13.20    None  None   None       |
|    Sol.    : 438    0      0.00    113.84  31.51    None  None   None       |
|    Mac.    : 2385   0      0.00    76.15   9.84     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 -  11.384: 1718   |   5:    56.922 -  68.306:   30        |
|      1:    11.384 -  22.769:  618   |   6:    68.306 -  79.690:   11        |
|      2:    22.769 -  34.153:  252   |   7:    79.690 -  91.075:    1        |
|      3:    34.153 -  45.537:  125   |   8:    91.075 - 102.459:    0        |
|      4:    45.537 -  56.922:   66   |   9:   102.459 - 113.843:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2553 r_free = 0.3116             target_work(ml) = 5.855         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2550 r_free = 0.3113             target_work(ml) = 5.854         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2550   r_free= 0.3113   ksol= 0.31   Bsol= 50.00   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.30,7.50,4.80,0.00,0.00,0.00); trace/3= 5.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.854436                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2536   r_free= 0.3094   ksol= 0.32   Bsol= 65.48   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.78,4.70,3.48,0.00,0.00,0.00); trace/3= 3.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.854181                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.667396              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.096  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.333934              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.331  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2536      final r-factor (work) = 0.2028          |
| start r-factor (free) = 0.3094      final r-factor (free) = 0.2480          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8879 = 3.67 * 0.50 * 5.8801 + 1.00 * 0.1056                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6287 = 3.67 * 0.50 * 5.7597 + 1.00 * 0.0670                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2028      final r-factor (work) = 0.1886          |
| start r-factor (free) = 0.2480      final r-factor (free) = 0.2322          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9382 = 0.33 * 1.00 * 5.7597 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8847 = 0.33 * 1.00 * 5.6101 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.98  13.31    None  None   None       |
|    all(noH): 2823   0      0.00    104.98  13.31    None  None   None       |
|    Sol.    : 438    0      0.00    104.98  35.12    None  None   None       |
|    Mac.    : 2385   0      0.00    79.07   9.31     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 -  10.498: 1720   |   5:    52.490 -  62.989:   59        |
|      1:    10.498 -  20.996:  577   |   6:    62.989 -  73.487:   18        |
|      2:    20.996 -  31.494:  195   |   7:    73.487 -  83.985:    4        |
|      3:    31.494 -  41.992:  138   |   8:    83.985 -  94.483:    1        |
|      4:    41.992 -  52.490:  109   |   9:    94.483 - 104.981:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1886 r_free = 0.2322             target_work(ml) = 5.587         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1882 r_free = 0.2322             target_work(ml) = 5.586         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1882   r_free= 0.2322   ksol= 0.32   Bsol= 65.48   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.78,4.70,3.48,0.00,0.00,0.00); trace/3= 3.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.586180                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1881   r_free= 0.2328   ksol= 0.32   Bsol= 65.48   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.96,3.27,2.94,0.00,0.00,0.00); trace/3= 2.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.587078                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.532517              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.171  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.236496              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.985  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1881      final r-factor (work) = 0.1521          |
| start r-factor (free) = 0.2328      final r-factor (free) = 0.1974          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1725 = 2.53 * 0.50 * 5.6113 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0142 = 2.53 * 0.50 * 5.4857 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1521      final r-factor (work) = 0.1461          |
| start r-factor (free) = 0.1974      final r-factor (free) = 0.1939          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3086 = 0.24 * 1.00 * 5.4857 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3749 = 0.24 * 1.00 * 5.3809 + 1.00 * 0.1024                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.05  13.26    None  None   None       |
|    all(noH): 2823   0      0.00    101.05  13.26    None  None   None       |
|    Sol.    : 438    0      1.50    101.05  35.86    None  None   None       |
|    Mac.    : 2385   0      0.00    80.20   9.11     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 -  10.105: 1719   |   5:    50.524 -  60.629:   76        |
|      1:    10.105 -  20.210:  590   |   6:    60.629 -  70.733:   21        |
|      2:    20.210 -  30.314:  162   |   7:    70.733 -  80.838:    5        |
|      3:    30.314 -  40.419:  135   |   8:    80.838 -  90.943:    2        |
|      4:    40.419 -  50.524:  111   |   9:    90.943 - 101.048:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1461 r_free = 0.1939             target_work(ml) = 5.369         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1458 r_free = 0.1939             target_work(ml) = 5.369         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1458   r_free= 0.1939   ksol= 0.32   Bsol= 65.48   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.96,3.27,2.94,0.00,0.00,0.00); trace/3= 2.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.368832                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1458   r_free= 0.1943   ksol= 0.33   Bsol= 64.84   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,2.48,2.75,0.00,0.00,0.00); trace/3= 2.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.368785                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.298849              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.498  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.585380              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.930   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1458      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.1943      final r-factor (free) = 0.1783          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2515 = 2.30 * 0.50 * 5.3797 + 1.00 * 0.0679                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1885 = 2.30 * 0.50 * 5.3223 + 1.00 * 0.0709                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1315      final r-factor (work) = 0.1267          |
| start r-factor (free) = 0.1783      final r-factor (free) = 0.1783          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.7787 = 2.59 * 1.00 * 5.3223 + 1.00 * 0.0185                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.6720 = 2.59 * 1.00 * 5.2627 + 1.00 * 0.0659                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.51  13.95    None  None   None       |
|    all(noH): 2823   0      0.00    116.51  13.95    None  None   None       |
|    Sol.    : 438    0      1.60    97.47   40.20    None  None   None       |
|    Mac.    : 2385   0      0.00    116.51  9.13     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 -  11.651: 1886   |   5:    58.255 -  69.906:   60        |
|      1:    11.651 -  23.302:  461   |   6:    69.906 -  81.557:   28        |
|      2:    23.302 -  34.953:  150   |   7:    81.557 -  93.208:    9        |
|      3:    34.953 -  46.604:  114   |   8:    93.208 - 104.860:    2        |
|      4:    46.604 -  58.255:  112   |   9:   104.860 - 116.511:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1267 r_free = 0.1783             target_work(ml) = 5.264         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1267 r_free = 0.1783             target_work(ml) = 5.264         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1783   ksol= 0.33   Bsol= 64.84   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,2.48,2.75,0.00,0.00,0.00); trace/3= 2.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.263822                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7993 0.99   1380  154 0.1041 0.1395      5.4288      5.5788|
|  2:  4.7993 -  3.8295 0.99   1346  146 0.0909 0.1136      5.4934      5.6625|
|  3:  3.8295 -  3.3514 0.99   1306  149 0.1167 0.1649      5.5671      5.9302|
|  4:  3.3514 -  3.0476 0.99   1295  143 0.1351 0.1780      5.5602      5.7492|
|  5:  3.0476 -  2.8307 0.99   1292  142 0.1555 0.1963      5.4819       5.644|
|  6:  2.8307 -  2.6648 0.99   1288  144 0.1437 0.2201      5.3603      5.6073|
|  7:  2.6648 -  2.5319 0.99   1280  139 0.1419 0.1859      5.2842      5.4777|
|  8:  2.5319 -  2.4222 0.98   1274  147 0.1364 0.1930      5.2069      5.4499|
|  9:  2.4222 -  2.3293 0.98   1276  140 0.1369 0.2077      5.1542      5.4434|
| 10:  2.3293 -  2.2492 0.98   1244  138 0.1356 0.1920      5.1293      5.3058|
| 11:  2.2492 -  2.1791 1.00   1283  143 0.1351 0.2105      5.0814      5.4147|
| 12:  2.1791 -  2.1169 0.97   1243  136 0.1281 0.1900      5.0132      5.2818|
| 13:  2.1169 -  2.0613 0.98   1257  144 0.1310 0.2042      4.9267      5.2096|
| 14:  2.0613 -  2.0112 0.67    866   94 0.1207 0.2015      4.8025      5.0825|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7993  1380   154  0.93   9.90   0.96     0.94       8247.42|
|  2:  4.7993 -  3.8295  1346   146  0.95   8.65   1.00     0.98       9973.35|
|  3:  3.8295 -  3.3514  1306   149  0.92  12.60   1.01     1.01      12328.09|
|  4:  3.3514 -  3.0476  1295   143  0.91  15.46   1.00     0.98      12773.99|
|  5:  3.0476 -  2.8307  1292   142  0.87  19.02   0.99     0.98      11505.42|
|  6:  2.8307 -  2.6648  1288   144  0.88  18.50   0.97     0.93       9349.64|
|  7:  2.6648 -  2.5319  1280   139  0.89  17.85   0.98     0.96       7925.02|
|  8:  2.5319 -  2.4222  1274   147  0.89  17.89   0.98     0.93       6974.21|
|  9:  2.4222 -  2.3293  1276   140  0.89  18.06   0.98     0.93       6351.58|
| 10:  2.3293 -  2.2492  1244   138  0.88  18.64   0.98     0.93       6139.73|
| 11:  2.2492 -  2.1791  1283   143  0.87  19.24   0.97     0.92       5689.90|
| 12:  2.1791 -  2.1169  1243   136  0.89  17.81   0.97     0.94       5244.20|
| 13:  2.1169 -  2.0613  1257   144  0.87  19.24   0.98     0.96       4572.10|
| 14:  2.0613 -  2.0112   866    94  0.88  17.95   0.94     0.90       3455.90|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     3455.90 max =        12773.99 mean =      8036.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.37|
|phase err.(test): min =        0.00 max =           89.91 mean =        15.70|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1783   ksol= 0.32   Bsol= 68.75   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,0.08,0.52,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.263632                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1783   ksol= 0.32   Bsol= 68.75   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,0.08,0.52,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.263632                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7993 0.99   1380  154 0.1040 0.1394      5.4286      5.5798|
|  2:  4.7993 -  3.8295 0.99   1346  146 0.0911 0.1138      5.4953      5.6655|
|  3:  3.8295 -  3.3514 0.99   1306  149 0.1169 0.1649      5.5684      5.9308|
|  4:  3.3514 -  3.0476 0.99   1295  143 0.1350 0.1780      5.5598      5.7497|
|  5:  3.0476 -  2.8307 0.99   1292  142 0.1553 0.1962       5.481      5.6428|
|  6:  2.8307 -  2.6648 0.99   1288  144 0.1435 0.2197      5.3593      5.6057|
|  7:  2.6648 -  2.5319 0.99   1280  139 0.1419 0.1861      5.2837      5.4785|
|  8:  2.5319 -  2.4222 0.98   1274  147 0.1364 0.1930      5.2066      5.4488|
|  9:  2.4222 -  2.3293 0.98   1276  140 0.1367 0.2077      5.1538      5.4435|
| 10:  2.3293 -  2.2492 0.98   1244  138 0.1355 0.1924       5.129      5.3059|
| 11:  2.2492 -  2.1791 1.00   1283  143 0.1351 0.2102      5.0807      5.4135|
| 12:  2.1791 -  2.1169 0.97   1243  136 0.1281 0.1902      5.0128       5.282|
| 13:  2.1169 -  2.0613 0.98   1257  144 0.1310 0.2039      4.9261      5.2087|
| 14:  2.0613 -  2.0112 0.67    866   94 0.1208 0.2011      4.8016      5.0813|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7993  1380   154  0.93   9.90   0.96     0.94       8257.52|
|  2:  4.7993 -  3.8295  1346   146  0.95   8.68   1.00     0.98      10012.58|
|  3:  3.8295 -  3.3514  1306   149  0.92  12.65   1.02     1.01      12387.31|
|  4:  3.3514 -  3.0476  1295   143  0.91  15.46   1.00     0.98      12770.05|
|  5:  3.0476 -  2.8307  1292   142  0.87  19.00   1.00     0.98      11484.66|
|  6:  2.8307 -  2.6648  1288   144  0.88  18.48   0.98     0.93       9329.32|
|  7:  2.6648 -  2.5319  1280   139  0.89  17.84   0.99     0.96       7914.94|
|  8:  2.5319 -  2.4222  1274   147  0.89  17.89   0.98     0.94       6970.92|
|  9:  2.4222 -  2.3293  1276   140  0.89  18.06   0.99     0.94       6349.13|
| 10:  2.3293 -  2.2492  1244   138  0.88  18.63   0.98     0.94       6134.32|
| 11:  2.2492 -  2.1791  1283   143  0.87  19.23   0.98     0.93       5682.46|
| 12:  2.1791 -  2.1169  1243   136  0.89  17.80   0.98     0.95       5241.07|
| 13:  2.1169 -  2.0613  1257   144  0.88  19.22   0.99     0.97       4562.80|
| 14:  2.0613 -  2.0112   866    94  0.88  17.92   0.95     0.91       3444.34|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3444.34 max =        12770.05 mean =      8037.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.37|
|phase err.(test): min =        0.00 max =           89.90 mean =        15.70|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.45    118.96  16.40    None  None   None       |
|    all(noH): 2823   0      2.45    118.96  16.40    None  None   None       |
|    Sol.    : 438    0      4.05    99.92   42.64    None  None   None       |
|    Mac.    : 2385   0      2.45    118.96  11.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.448 -  14.099: 1886   |   5:    60.703 -  72.354:   60        |
|      1:    14.099 -  25.750:  461   |   6:    72.354 -  84.005:   28        |
|      2:    25.750 -  37.401:  150   |   7:    84.005 -  95.656:    9        |
|      3:    37.401 -  49.052:  114   |   8:    95.656 - 107.307:    2        |
|      4:    49.052 -  60.703:  112   |   9:   107.307 - 118.958:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.287 - 5.687
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 336
   mapped sites are within: 0.707 - 5.687

peak=    8.318 closest distance to " CG2 VAL A 230 " =    1.311
peak=    6.992 closest distance to " CG2 VAL A 296 " =    1.174
peak=    6.783 closest distance to " O   HOH Z 120 " =    1.299
peak=    6.479 closest distance to " CD1AILE A 234 " =    1.238
peak=    6.422 closest distance to " CG  ARG A 138 " =    1.133
peak=    6.032 closest distance to " CG  LEU A   5 " =    1.187
peak=    5.860 closest distance to " O   HOH Z 210 " =    1.281
peak=    5.637 closest distance to " O   HOH Z 111 " =    2.283
peak=    5.434 closest distance to " CB  VAL A 230 " =    1.267
peak=    5.300 closest distance to " CG  PRO A 280 " =    0.904
peak=    5.034 closest distance to " CG  PRO A 198 " =    1.257
peak=    5.001 closest distance to " O   HOH Z 400 " =    0.892
peak=    4.952 closest distance to " CB  GLN A 223 " =    1.379
peak=    4.946 closest distance to " CB  SER A  63 " =    1.289
peak=    4.907 closest distance to " CG  PRO A  54 " =    1.268
peak=    4.824 closest distance to " NH1 ARG A 138 " =    0.980
peak=    4.719 closest distance to " CG  LEU A 228 " =    1.214
peak=    4.604 closest distance to " O   HOH Z 433 " =    1.930
peak=    4.603 closest distance to " CA  TYR A  30 " =    0.970
peak=    4.581 closest distance to " O   HOH Z 102 " =    1.552
peak=    4.515 closest distance to " CG  PRO A 213 " =    1.257
peak=    4.503 closest distance to " CB  PRO A  54 " =    0.906
peak=    4.502 closest distance to " O   HOH Z  49 " =    1.314
peak=    4.487 closest distance to " O   HOH Z 412 " =    3.599
peak=    4.364 closest distance to " O   PRO A 198 " =    1.575
peak=    4.341 closest distance to " CB  ARG A 275 " =    0.870
peak=    4.314 closest distance to " CZ  PHE A 218 " =    1.141
peak=    4.302 closest distance to " O  BHOH Z 338 " =    0.992
peak=    4.258 closest distance to " O   HOH Z 425 " =    1.582
peak=    4.227 closest distance to " CD2 LEU A 228 " =    1.186
peak=    4.219 closest distance to " CD  ARG A  66 " =    2.765
peak=    4.218 closest distance to " O   HOH Z 369 " =    2.135
peak=    4.204 closest distance to " O   HOH Z 232 " =    2.272
peak=    4.187 closest distance to " O   HOH Z 402 " =    1.619
peak=    4.184 closest distance to " N   SER A 164 " =    1.008
peak=    4.179 closest distance to " CG2 THR A 221 " =    1.130
peak=    4.176 closest distance to " NE2 GLN A  11 " =    1.048
peak=    4.170 closest distance to " CD  ARG A 269 " =    0.938
peak=    4.161 closest distance to " O   HOH Z 234 " =    3.608
peak=    4.156 closest distance to " O   HOH Z  44 " =    2.160
peak=    4.154 closest distance to " O   HOH Z 394 " =    1.665
peak=    4.112 closest distance to " O   HOH Z 184 " =    1.639
peak=    4.103 closest distance to " O   HOH Z 134 " =    1.988
peak=    4.099 closest distance to " CB  GLN A 183 " =    1.260
peak=    4.064 closest distance to " O   HOH Z 431 " =    1.370
peak=    4.056 closest distance to " O   HOH Z 359 " =    1.531
peak=    4.052 closest distance to " CB  TRP A 266 " =    1.025
peak=    4.047 closest distance to " CA  ALA A  51 " =    1.085
peak=    4.044 closest distance to " CA  ARG A 195 " =    1.204
peak=    4.038 closest distance to " O   HOH Z  48 " =    1.876
peak=    4.033 closest distance to " O   ASP A 124 " =    1.216
peak=    4.026 closest distance to " CB  VAL A 296 " =    1.012
peak=    4.020 closest distance to " O   HOH Z  20 " =    1.978
peak=    4.003 closest distance to " O   HOH Z  67 " =    1.954
peak=    4.002 closest distance to " O   HOH Z 247 " =    1.614
peak=    3.989 closest distance to " CB AVAL A  41 " =    1.133
peak=    3.987 closest distance to " O   HOH Z  47 " =    1.431
peak=    3.980 closest distance to " CE1 TYR A 186 " =    1.395
peak=    3.967 closest distance to " CD  ARG A 159 " =    0.777
peak=    3.965 closest distance to " O   HOH Z 403 " =    1.845
peak=    3.957 closest distance to " O   SER A  87 " =    2.299
peak=    3.953 closest distance to " CB  ASP A 124 " =    0.710
peak=    3.944 closest distance to " O   HOH Z  40 " =    1.989
peak=    3.917 closest distance to " O   HOH Z  43 " =    2.353
peak=    3.895 closest distance to " CB  GLU A 128 " =    1.231
peak=    3.870 closest distance to " CB  TYR A 169 " =    0.707
peak=    3.862 closest distance to " O   HOH Z 316 " =    3.085
peak=    3.850 closest distance to " O   HOH Z 130 " =    1.155
peak=    3.849 closest distance to " CG2 ILE A 234 " =    0.982
peak=    3.846 closest distance to " O   HOH Z 303 " =    2.425
peak=    3.823 closest distance to " O   HOH Z  63 " =    1.736
peak=    3.822 closest distance to " CB  PRO A 198 " =    1.034
peak=    3.816 closest distance to " CD1 LEU A   5 " =    1.356
peak=    3.810 closest distance to " O   HOH Z 128 " =    1.563
peak=    3.795 closest distance to " CD BLYS A 290 " =    1.105
peak=    3.789 closest distance to " O   HOH Z 395 " =    1.407
peak=    3.780 closest distance to " CG1 ILE A  33 " =    1.220
peak=    3.778 closest distance to " O   HOH Z 357 " =    2.169
peak=    3.772 closest distance to " CB  ASN A 148 " =    1.322
peak=    3.762 closest distance to " O   HOH Z   4 " =    1.746
peak=    3.755 closest distance to " N   ILE A  33 " =    1.010
peak=    3.751 closest distance to " O   HOH Z 196 " =    1.567
peak=    3.737 closest distance to " O   HOH Z 298 " =    1.882
peak=    3.736 closest distance to " O   HOH Z  80 " =    2.048
peak=    3.735 closest distance to " CD  LYS A 166 " =    1.467
peak=    3.734 closest distance to " O   HOH Z 426 " =    1.381
peak=    3.726 closest distance to " O   HOH Z  57 " =    1.834
peak=    3.723 closest distance to " OD1 ASN A 301 " =    1.277
peak=    3.719 closest distance to " CA  ASP A 191 " =    0.802
peak=    3.713 closest distance to " CB  GLN A  88 " =    1.257
peak=    3.712 closest distance to " CA  ALA A 160 " =    0.938
peak=    3.706 closest distance to " O   HOH Z 265 " =    2.082
peak=    3.702 closest distance to " O   HOH Z   9 " =    2.374
peak=    3.702 closest distance to " NH1AARG A 145 " =    1.208
peak=    3.700 closest distance to " CA  MET A  40 " =    1.228
peak=    3.696 closest distance to " NE2 HIS A 115 " =    1.018
peak=    3.696 closest distance to " CB  TRP A 179 " =    1.348
peak=    3.693 closest distance to " CE3 TRP A  85 " =    1.344
peak=    3.690 closest distance to " CG1BVAL A 121 " =    1.181
peak=    3.689 closest distance to " O   HOH Z 245 " =    1.297
peak=    3.687 closest distance to " O   HOH Z 383 " =    2.240
peak=    3.680 closest distance to " CB  GLU A 277 " =    3.842
peak=    3.678 closest distance to " CB  ALA A 100 " =    1.496
peak=    3.678 closest distance to " O   HOH Z  63 " =    2.416
peak=    3.676 closest distance to " CA  ASP A 140 " =    1.310
peak=    3.671 closest distance to " O   HOH Z 332 " =    1.611
peak=    3.671 closest distance to " O   HOH Z 393 " =    3.698
peak=    3.668 closest distance to " CB  VAL A 202 " =    1.508
peak=    3.666 closest distance to " CG1 VAL A 153 " =    1.123
peak=    3.665 closest distance to " CB  ARG A 190 " =    1.720
peak=    3.663 closest distance to " C   VAL A 265 " =    1.146
peak=    3.662 closest distance to " O   HOH Z 261 " =    1.775
peak=    3.662 closest distance to " O   HOH Z 423 " =    1.680
peak=    3.661 closest distance to " CG  PRO A 243 " =    1.163
peak=    3.661 closest distance to " CG2 VAL A  78 " =    1.020
peak=    3.658 closest distance to " O   HOH Z 285 " =    3.073
peak=    3.650 closest distance to " CA  GLN A  88 " =    1.223
peak=    3.648 closest distance to " CB  MET A  40 " =    0.907
peak=    3.647 closest distance to " O   HOH Z 368 " =    3.427
peak=    3.631 closest distance to " CA  THR A 246 " =    1.132
peak=    3.630 closest distance to " CA  ALA A  21 " =    1.394
peak=    3.620 closest distance to " O   MET A 105 " =    1.909
peak=    3.613 closest distance to " O   HOH Z 280 " =    2.857
peak=    3.610 closest distance to " CB  ASN A  39 " =    0.803
peak=    3.610 closest distance to " O   HOH Z 301 " =    1.528
peak=    3.609 closest distance to " CG AARG A 275 " =    1.217
peak=    3.599 closest distance to " OD1 ASN A 217 " =    1.695
peak=    3.592 closest distance to " O   HOH Z 301 " =    2.031
peak=    3.588 closest distance to " O   ALA A 165 " =    1.360
peak=    3.588 closest distance to " CD  ARG A 138 " =    1.271
peak=    3.588 closest distance to " CB  ARG A  79 " =    1.279
peak=    3.587 closest distance to " CB  LEU A 228 " =    1.294
peak=    3.586 closest distance to " O   HOH Z 388 " =    1.254
peak=    3.585 closest distance to " O   HOH Z 185 " =    1.748
peak=    3.581 closest distance to " CA  ILE A 106 " =    0.768
peak=    3.573 closest distance to " CB  ASP A 140 " =    0.823
peak=    3.569 closest distance to " O   HOH Z 139 " =    4.907
peak=    3.563 closest distance to " O   HOH Z  38 " =    2.868
peak=    3.553 closest distance to " CB  SER A 141 " =    1.038
peak=    3.553 closest distance to " OG  SER A  22 " =    2.876
peak=    3.551 closest distance to " CB  GLU A  46 " =    0.996
peak=    3.549 closest distance to " CZ3 TRP A  85 " =    0.887
peak=    3.549 closest distance to " CB  GLN A  89 " =    1.157
peak=    3.544 closest distance to " OG  SER A 245 " =    1.575
peak=    3.544 closest distance to " O   HOH Z 133 " =    2.106
peak=    3.540 closest distance to " O   HOH Z 248 " =    1.943
peak=    3.537 closest distance to " CB  SER A  62 " =    0.856
peak=    3.535 closest distance to " O   HOH Z 155 " =    1.504
peak=    3.533 closest distance to " CD2 LEU A   5 " =    1.014
peak=    3.528 closest distance to " O   HOH Z  88 " =    3.266
peak=    3.523 closest distance to " CG  GLN A  77 " =    0.845
peak=    3.523 closest distance to " CZ  PHE A 192 " =    1.015
peak=    3.522 closest distance to " CB  ALA A   9 " =    1.640
peak=    3.522 closest distance to " O   HOH Z 437 " =    2.143
peak=    3.515 closest distance to " O   HOH Z 403 " =    1.411
peak=    3.512 closest distance to " CA  VAL A  41 " =    0.881
peak=    3.511 closest distance to " CA  ASN A 217 " =    1.365
peak=    3.511 closest distance to " OE1 GLU A   2 " =    1.774
peak=    3.509 closest distance to " O   HOH Z 146 " =    1.526
peak=    3.508 closest distance to " O   HOH Z 344 " =    2.986
peak=    3.502 closest distance to " CE1 HIS A 108 " =    1.086
peak=    3.502 closest distance to " CG  LEU A 167 " =    1.082
peak=    3.501 closest distance to " CB  ALA A 295 " =    1.456
peak=    3.500 closest distance to " N   ALA A 256 " =    1.073
peak=    3.500 closest distance to " O   HOH Z 193 " =    2.302
peak=    3.495 closest distance to " N   TYR A  15 " =    0.873
peak=    3.493 closest distance to " CA  ASP A 162 " =    1.152
peak=    3.487 closest distance to " C   GLY A  80 " =    1.126
peak=    3.485 closest distance to " CD1 LEU A 300 " =    1.240
peak=    3.483 closest distance to " O   HOH Z 261 " =    1.518
peak=    3.483 closest distance to " O   HOH Z  61 " =    1.459
peak=    3.479 closest distance to " O   GLN A 278 " =    1.323
peak=    3.479 closest distance to " CD1 LEU A  96 " =    0.769
peak=    3.476 closest distance to " O   HOH Z 435 " =    2.029
peak=    3.473 closest distance to " O   HOH Z 389 " =    2.032
peak=    3.472 closest distance to " CB  LEU A 143 " =    1.192
peak=    3.469 closest distance to " O   HOH Z 227 " =    1.663
peak=    3.467 closest distance to " O   HOH Z 371 " =    3.295
peak=    3.455 closest distance to " CA  ALA A 295 " =    1.085
peak=    3.454 closest distance to " O   HOH Z 327 " =    2.497
peak=    3.452 closest distance to " O   PRO A 213 " =    1.494
peak=    3.450 closest distance to " O   HOH Z 214 " =    3.111
peak=    3.448 closest distance to " O   GLY A  91 " =    1.176
peak=    3.445 closest distance to " O   HOH Z 420 " =    5.687
peak=    3.445 closest distance to " CA  SER A  87 " =    0.979
peak=    3.443 closest distance to " O   HOH Z 189 " =    2.904
peak=    3.442 closest distance to " CB  ASN A 142 " =    1.029
peak=    3.439 closest distance to " O   HOH Z 387 " =    2.887
peak=    3.438 closest distance to " O   THR A 220 " =    1.188
peak=    3.436 closest distance to " O   HOH Z 368 " =    2.099
peak=    3.435 closest distance to " O   HOH Z 189 " =    3.079
peak=    3.433 closest distance to " O   HOH Z 148 " =    1.960
peak=    3.432 closest distance to " O   HOH Z 258 " =    2.261
peak=    3.432 closest distance to " O   HOH Z  78 " =    2.247
peak=    3.431 closest distance to " CA  TYR A 116 " =    1.448
peak=    3.430 closest distance to " O   HOH Z 271 " =    2.443
peak=    3.429 closest distance to " O   HOH Z 126 " =    1.677
peak=    3.426 closest distance to " O   HOH Z 163 " =    1.700
peak=    3.422 closest distance to " O   HOH Z 404 " =    1.546
peak=    3.419 closest distance to " O   HOH Z 158 " =    3.121
peak=    3.417 closest distance to " O   HOH Z 427 " =    3.291
peak=    3.414 closest distance to " NZ  LYS A  76 " =    1.614
peak=    3.414 closest distance to " O   HOH Z  56 " =    1.633
peak=    3.413 closest distance to " OE1 GLN A  11 " =    1.969
peak=    3.412 closest distance to " CA  GLY A 267 " =    0.785
peak=    3.405 closest distance to " CA  ALA A 291 " =    0.916
peak=    3.401 closest distance to " O   HOH Z 418 " =    1.538
peak=    3.398 closest distance to " CD  ARG A 195 " =    1.049
peak=    3.394 closest distance to " O   HOH Z  19 " =    1.658
peak=    3.383 closest distance to " OH  TYR A 116 " =    1.283
peak=    3.381 closest distance to " O   HOH Z  78 " =    1.788
peak=    3.380 closest distance to " CA  PRO A  54 " =    1.393
peak=    3.378 closest distance to " O   HOH Z  32 " =    1.871
peak=    3.377 closest distance to " O   HOH Z 236 " =    1.916
peak=    3.377 closest distance to " CA  THR A 264 " =    0.815
peak=    3.376 closest distance to " NH2 ARG A 156 " =    1.125
peak=    3.374 closest distance to " O   HOH Z 131 " =    2.285
peak=    3.373 closest distance to " O   HOH Z 132 " =    2.644
peak=    3.372 closest distance to " OE1 GLN A  88 " =    0.925
peak=    3.370 closest distance to " O   HOH Z 166 " =    1.779
peak=    3.366 closest distance to " CB  SER A 273 " =    0.829
peak=    3.366 closest distance to " NH1 ARG A  14 " =    1.119
peak=    3.365 closest distance to " CB  SER A  28 " =    1.018
peak=    3.364 closest distance to " O   HOH Z  99 " =    2.452
peak=    3.357 closest distance to " O   HOH Z 214 " =    1.345
peak=    3.355 closest distance to " CG  GLU A  37 " =    0.946
peak=    3.354 closest distance to " CB  PRO A 243 " =    1.235
peak=    3.352 closest distance to " O   HOH Z 346 " =    1.626
peak=    3.352 closest distance to " CG2 THR A  42 " =    0.886
peak=    3.348 closest distance to " O   HOH Z 109 " =    2.252
peak=    3.344 closest distance to " CD1 LEU A 101 " =    1.235
peak=    3.335 closest distance to " CB  ASN A 187 " =    1.096
peak=    3.331 closest distance to " NH1 ARG A  56 " =    1.061
peak=    3.330 closest distance to " CB  ASN A 285 " =    0.827
peak=    3.326 closest distance to " O   HOH Z 187 " =    2.280
peak=    3.325 closest distance to " CA  ALA A 100 " =    1.208
peak=    3.323 closest distance to " OD2 ASP A 286 " =    2.939
peak=    3.323 closest distance to " CA  ILE A  33 " =    1.662
peak=    3.322 closest distance to " O   ASP A 200 " =    1.602
peak=    3.322 closest distance to " CB  ALA A 291 " =    1.337
peak=    3.320 closest distance to " CA  GLU A 152 " =    0.896
peak=    3.319 closest distance to " CA  SER A  12 " =    1.521
peak=    3.318 closest distance to " CG  MET A 185 " =    1.333
peak=    3.316 closest distance to " O   HOH Z 392 " =    1.356
peak=    3.315 closest distance to " CG2 THR A 220 " =    0.757
peak=    3.314 closest distance to " O   HOH Z  54 " =    1.164
peak=    3.312 closest distance to " O   HOH Z 154 " =    1.237
peak=    3.312 closest distance to " CG2 ILE A  20 " =    1.376
peak=    3.311 closest distance to " OD1 ASN A  69 " =    2.464
peak=    3.309 closest distance to " O   HOH Z 141 " =    1.642
peak=    3.308 closest distance to " O   HOH Z 174 " =    1.991
peak=    3.305 closest distance to " CA  VAL A 125 " =    1.456
peak=    3.302 closest distance to " O   HOH Z 421 " =    2.657
peak=    3.301 closest distance to " O   HOH Z 125 " =    3.753
peak=    3.300 closest distance to " O   HOH Z 417 " =    3.072
peak=    3.294 closest distance to " O   HOH Z 423 " =    3.126
peak=    3.294 closest distance to " O   PRO A  90 " =    1.287
peak=    3.288 closest distance to " O   HOH Z 368 " =    4.204
peak=    3.284 closest distance to " CZ3 TRP A 266 " =    1.072
peak=    3.283 closest distance to " CB  ILE A 199 " =    1.003
peak=    3.280 closest distance to " O   HOH Z 155 " =    3.075
peak=    3.279 closest distance to " O   HOH Z 176 " =    1.663
peak=    3.272 closest distance to " OG  SER A 206 " =    1.187
peak=    3.271 closest distance to " CB  ALA A 104 " =    0.875
peak=    3.271 closest distance to " O   HOH Z 126 " =    2.235
peak=    3.270 closest distance to " OH  TYR A 186 " =    1.024
peak=    3.268 closest distance to " CA  ASN A 127 " =    1.126
peak=    3.267 closest distance to " OD2 ASP A 298 " =    3.444
peak=    3.266 closest distance to " O   HOH Z 151 " =    1.786
peak=    3.264 closest distance to " CA  LEU A 282 " =    1.124
peak=    3.259 closest distance to " CG  MET A 188 " =    0.878
peak=    3.255 closest distance to " N   ASN A 127 " =    1.087
peak=    3.254 closest distance to " O   ALA A 158 " =    1.256
peak=    3.250 closest distance to " O   GLU A   2 " =    1.793
peak=    3.250 closest distance to " CA  TRP A 274 " =    0.930
peak=    3.249 closest distance to " O   HOH Z 438 " =    3.055
peak=    3.243 closest distance to " CG1 VAL A 257 " =    0.945
peak=    3.243 closest distance to " CZ3 TRP A  92 " =    1.316
peak=    3.240 closest distance to " O   HOH Z 422 " =    2.535
peak=    3.238 closest distance to " CB  TYR A 247 " =    0.983
peak=    3.233 closest distance to " CB  GLU A 152 " =    1.137
peak=    3.231 closest distance to " N   GLU A  44 " =    1.030
peak=    3.231 closest distance to " O   HOH Z 424 " =    3.381
peak=    3.231 closest distance to " O   HOH Z  20 " =    1.718
peak=    3.226 closest distance to " CB  ASP A 107 " =    1.177
peak=    3.223 closest distance to " O   HOH Z 343 " =    2.723
peak=    3.216 closest distance to " CB  ALA A 256 " =    1.357
peak=    3.213 closest distance to " CB  ALA A  84 " =    0.907
peak=    3.211 closest distance to " O   HOH Z 272 " =    1.994
peak=    3.208 closest distance to " O   HOH Z 432 " =    1.709
peak=    3.207 closest distance to " O   HOH Z  21 " =    1.774
peak=    3.207 closest distance to " O   HOH Z 357 " =    2.472
peak=    3.197 closest distance to " CG2 ILE A 106 " =    0.919
peak=    3.196 closest distance to " CB  VAL A 265 " =    1.265
peak=    3.191 closest distance to " CB  ARG A 219 " =    1.653
peak=    3.188 closest distance to " CA  LYS A 117 " =    1.316
peak=    3.187 closest distance to " CB  THR A  82 " =    1.440
peak=    3.186 closest distance to " NZ  LYS A 117 " =    3.504
peak=    3.185 closest distance to " CG1 ILE A  49 " =    1.698
peak=    3.184 closest distance to " CE2 PHE A 204 " =    0.982
peak=    3.180 closest distance to " CA  MET A 105 " =    1.098
peak=    3.177 closest distance to " N   ASN A  39 " =    1.329
peak=    3.172 closest distance to " CA  ARG A 156 " =    1.061
peak=    3.170 closest distance to " O   HOH Z 352 " =    1.897
peak=    3.166 closest distance to " CA  ASP A 132 " =    1.135
peak=    3.164 closest distance to " O   HOH Z 374 " =    2.963
peak=    3.162 closest distance to " O   HOH Z 128 " =    2.064
peak=    3.162 closest distance to " CA  GLY A 196 " =    0.970
peak=    3.161 closest distance to " NE2 GLN A 278 " =    2.504
peak=    3.156 closest distance to " CA  SER A 210 " =    1.481
peak=    3.149 closest distance to " O   HOH Z 199 " =    1.633
peak=    3.148 closest distance to " O   HOH Z 365 " =    3.027
peak=    3.148 closest distance to " CA  ARG A 139 " =    1.504
peak=    3.146 closest distance to " OG BSER A 164 " =    2.015
peak=    3.117 closest distance to " N   PHE A 130 " =    1.175
peak=    3.113 closest distance to " O   HOH Z 162 " =    1.684
peak=    3.106 closest distance to " ND1 HIS A  81 " =    1.657
peak=    3.100 closest distance to " OG  SER A  62 " =    3.010
peak=    3.098 closest distance to " CG  GLN A 205 " =    1.049
peak=    3.096 closest distance to " CD1 ILE A 199 " =    0.861
peak=    3.085 closest distance to " CB  ALA A 242 " =    0.922
peak=    3.078 closest distance to " CD  PRO A  54 " =    1.118
peak=    3.075 closest distance to " CB  ILE A 120 " =    1.411
peak=    3.068 closest distance to " O   HOH Z 117 " =    1.977
peak=    3.051 closest distance to " O   THR A  31 " =    1.620
peak=    3.049 closest distance to " O   HOH Z 298 " =    5.250
peak=    3.041 closest distance to " CA  ARG A  36 " =    1.079
peak=    3.033 closest distance to " O   HOH Z  68 " =    2.479
peak=    3.030 closest distance to " CB  ASP A 140 " =    0.737

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.812 - 5.617
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 221 from: 221
   mapped sites are within: 0.812 - 5.617

peak=   -5.053 closest distance to " CG2 VAL A 230 " =    0.934
peak=   -4.616 closest distance to " O   HOH Z 166 " =    1.480
peak=   -4.335 closest distance to " CB  ALA A 291 " =    2.568
peak=   -4.334 closest distance to " CD  ARG A 138 " =    1.354
peak=   -4.302 closest distance to " OE1 GLN A  58 " =    1.098
peak=   -4.288 closest distance to " CG1 VAL A 250 " =    2.666
peak=   -4.285 closest distance to " O   HOH Z  19 " =    2.222
peak=   -4.245 closest distance to " CD1 PHE A  59 " =    1.909
peak=   -4.225 closest distance to " O   HOH Z 411 " =    5.228
peak=   -4.180 closest distance to " NH2 ARG A  66 " =    1.408
peak=   -4.178 closest distance to " CD  GLN A  88 " =    0.980
peak=   -4.158 closest distance to " CG  ARG A 269 " =    2.421
peak=   -4.135 closest distance to " CA  TYR A  68 " =    2.892
peak=   -4.070 closest distance to " OXT GLY A 302 " =    3.032
peak=   -4.069 closest distance to " O   HOH Z  52 " =    1.961
peak=   -4.016 closest distance to " CD  GLN A 223 " =    1.495
peak=   -3.981 closest distance to " CA  ASP A 298 " =    1.009
peak=   -3.981 closest distance to " O   HOH Z 351 " =    1.488
peak=   -3.958 closest distance to " CG  ARG A 138 " =    0.989
peak=   -3.948 closest distance to " O   HOH Z  13 " =    1.723
peak=   -3.930 closest distance to " C   ASN A 285 " =    2.488
peak=   -3.900 closest distance to " CG  ASP A 231 " =    0.822
peak=   -3.889 closest distance to " OG  SER A  26 " =    1.383
peak=   -3.882 closest distance to " O   HOH Z 103 " =    2.071
peak=   -3.873 closest distance to " O   HOH Z  10 " =    1.630
peak=   -3.825 closest distance to " CD2 PHE A  61 " =    1.999
peak=   -3.821 closest distance to " O   HOH Z 400 " =    1.202
peak=   -3.817 closest distance to " O   SER A 271 " =    2.155
peak=   -3.811 closest distance to " CG2 VAL A 112 " =    2.542
peak=   -3.762 closest distance to " O   PRO A 198 " =    1.286
peak=   -3.747 closest distance to " CD1 LEU A  25 " =    2.442
peak=   -3.709 closest distance to " OE1 GLN A  88 " =    0.961
peak=   -3.700 closest distance to " OD1 ASN A 148 " =    1.377
peak=   -3.698 closest distance to " OH  TYR A 169 " =    1.016
peak=   -3.698 closest distance to " O   HOH Z 407 " =    3.348
peak=   -3.690 closest distance to " OG  SER A  97 " =    2.315
peak=   -3.683 closest distance to " O   HOH Z 184 " =    1.222
peak=   -3.677 closest distance to " CE3 TRP A 150 " =    2.167
peak=   -3.672 closest distance to " O   HOH Z 165 " =    1.841
peak=   -3.666 closest distance to " O   HOH Z 396 " =    1.636
peak=   -3.666 closest distance to " N   ALA A 226 " =    2.127
peak=   -3.663 closest distance to " O   ILE A 109 " =    2.708
peak=   -3.654 closest distance to " CA  SER A 164 " =    2.119
peak=   -3.649 closest distance to " CB  GLU A 277 " =    1.346
peak=   -3.645 closest distance to " O   HOH Z 151 " =    1.295
peak=   -3.636 closest distance to " O   HOH Z  43 " =    1.499
peak=   -3.632 closest distance to " O   HOH Z 113 " =    2.345
peak=   -3.623 closest distance to " CE2 TYR A  30 " =    2.677
peak=   -3.616 closest distance to " CG1 VAL A 296 " =    1.256
peak=   -3.610 closest distance to " CA  GLY A 203 " =    2.396
peak=   -3.604 closest distance to " CD1 TYR A 247 " =    2.297
peak=   -3.603 closest distance to " O   SER A 276 " =    1.726
peak=   -3.596 closest distance to " O   HOH Z  73 " =    2.122
peak=   -3.593 closest distance to " OG1 THR A  82 " =    2.126
peak=   -3.591 closest distance to " O   HOH Z   6 " =    1.868
peak=   -3.589 closest distance to " CG  TRP A 266 " =    1.893
peak=   -3.578 closest distance to " ND2BASN A 224 " =    1.895
peak=   -3.561 closest distance to " O   HOH Z 388 " =    1.802
peak=   -3.535 closest distance to " O   HOH Z 231 " =    1.770
peak=   -3.532 closest distance to " CD1 LEU A 101 " =    2.495
peak=   -3.524 closest distance to " CB  ALA A  10 " =    2.104
peak=   -3.523 closest distance to " OG  SER A  87 " =    1.664
peak=   -3.522 closest distance to " O   HOH Z 231 " =    2.069
peak=   -3.519 closest distance to " CG2 ILE A  49 " =    2.717
peak=   -3.516 closest distance to " O   HOH Z 292 " =    4.556
peak=   -3.498 closest distance to " C   ALA A 158 " =    1.235
peak=   -3.497 closest distance to " O   HOH Z 394 " =    1.682
peak=   -3.496 closest distance to " O   HOH Z 216 " =    1.894
peak=   -3.494 closest distance to " O   HOH Z 234 " =    4.239
peak=   -3.492 closest distance to " CG1 VAL A 112 " =    2.637
peak=   -3.490 closest distance to " CA  ASN A 127 " =    0.964
peak=   -3.488 closest distance to " CA  VAL A 197 " =    1.068
peak=   -3.482 closest distance to " O   HOH Z 252 " =    3.879
peak=   -3.479 closest distance to " O   HOH Z 120 " =    0.937
peak=   -3.478 closest distance to " CD  ARG A 156 " =    2.204
peak=   -3.472 closest distance to " O   HOH Z 196 " =    2.026
peak=   -3.470 closest distance to " O   HOH Z 275 " =    1.832
peak=   -3.464 closest distance to " O   HOH Z 385 " =    3.910
peak=   -3.463 closest distance to " O   HOH Z 136 " =    2.519
peak=   -3.459 closest distance to " O   HOH Z 109 " =    3.581
peak=   -3.458 closest distance to " OD2 ASP A 171 " =    1.996
peak=   -3.451 closest distance to " C   THR A 279 " =    1.198
peak=   -3.450 closest distance to " CG1 VAL A 112 " =    2.772
peak=   -3.445 closest distance to " O   HOH Z 200 " =    1.422
peak=   -3.441 closest distance to " O   HOH Z  60 " =    2.142
peak=   -3.427 closest distance to " CD  PRO A 213 " =    2.282
peak=   -3.420 closest distance to " CD  GLU A 236 " =    1.021
peak=   -3.419 closest distance to " CD  ARG A 139 " =    1.479
peak=   -3.419 closest distance to " OD2 ASP A  50 " =    2.325
peak=   -3.407 closest distance to " NE2 HIS A  86 " =    1.103
peak=   -3.405 closest distance to " O   VAL A  67 " =    2.550
peak=   -3.403 closest distance to " OD2 ASP A 298 " =    0.969
peak=   -3.402 closest distance to " O   HOH Z 350 " =    1.589
peak=   -3.402 closest distance to " SG  CYS A 254 " =    3.510
peak=   -3.395 closest distance to " OG ASER A 134 " =    1.178
peak=   -3.394 closest distance to " O   HOH Z 166 " =    1.544
peak=   -3.394 closest distance to " C   HIS A 108 " =    1.150
peak=   -3.384 closest distance to " C   GLY A  17 " =    1.261
peak=   -3.378 closest distance to " O   HOH Z 384 " =    2.075
peak=   -3.378 closest distance to " O   HOH Z 189 " =    1.985
peak=   -3.374 closest distance to " O   HOH Z 183 " =    1.546
peak=   -3.371 closest distance to " O   SER A 135 " =    2.007
peak=   -3.370 closest distance to " N   THR A 235 " =    1.255
peak=   -3.369 closest distance to " O   HOH Z 246 " =    1.431
peak=   -3.369 closest distance to " O   HOH Z 198 " =    1.535
peak=   -3.366 closest distance to " O   HOH Z 111 " =    1.340
peak=   -3.364 closest distance to " CH2 TRP A 179 " =    1.211
peak=   -3.359 closest distance to " CA  HIS A  86 " =    2.288
peak=   -3.355 closest distance to " CB  PRO A 243 " =    2.838
peak=   -3.345 closest distance to " CG1 VAL A 197 " =    2.419
peak=   -3.342 closest distance to " O   HOH Z 423 " =    1.216
peak=   -3.338 closest distance to " CA  GLY A 133 " =    2.437
peak=   -3.337 closest distance to " CB  SER A 146 " =    2.219
peak=   -3.337 closest distance to " O   GLU A  44 " =    1.652
peak=   -3.336 closest distance to " CA  ALA A 165 " =    1.938
peak=   -3.331 closest distance to " O   HOH Z 120 " =    1.598
peak=   -3.331 closest distance to " O   HOH Z 348 " =    2.281
peak=   -3.324 closest distance to " O   HOH Z  58 " =    0.991
peak=   -3.322 closest distance to " O   HOH Z 198 " =    2.277
peak=   -3.320 closest distance to " CG  PRO A 243 " =    1.734
peak=   -3.317 closest distance to " O   HOH Z 301 " =    2.297
peak=   -3.316 closest distance to " O   ALA A 100 " =    2.061
peak=   -3.315 closest distance to " OG1 THR A  82 " =    1.391
peak=   -3.315 closest distance to " O   HOH Z 308 " =    1.520
peak=   -3.314 closest distance to " O   HOH Z 275 " =    1.692
peak=   -3.313 closest distance to " O   HOH Z  91 " =    2.047
peak=   -3.312 closest distance to " N   SER A   3 " =    2.451
peak=   -3.310 closest distance to " N   SER A 134 " =    1.212
peak=   -3.300 closest distance to " CA  GLY A 241 " =    3.240
peak=   -3.299 closest distance to " N   ARG A 275 " =    1.213
peak=   -3.298 closest distance to " CG  MET A 105 " =    0.893
peak=   -3.298 closest distance to " CA  GLY A 241 " =    2.196
peak=   -3.296 closest distance to " CB  TRP A  85 " =    2.541
peak=   -3.295 closest distance to " CG2 THR A   4 " =    1.810
peak=   -3.292 closest distance to " O   HOH Z 118 " =    4.760
peak=   -3.290 closest distance to " O   HOH Z 174 " =    2.048
peak=   -3.286 closest distance to " O   HOH Z  49 " =    0.847
peak=   -3.285 closest distance to " O   HOH Z 222 " =    1.508
peak=   -3.283 closest distance to " CE3 TRP A  70 " =    1.768
peak=   -3.283 closest distance to " CD  PRO A 243 " =    1.877
peak=   -3.282 closest distance to " O   VAL A 121 " =    1.157
peak=   -3.281 closest distance to " CB  LEU A   5 " =    1.856
peak=   -3.279 closest distance to " O   HOH Z 285 " =    1.450
peak=   -3.270 closest distance to " C   LEU A 143 " =    1.221
peak=   -3.263 closest distance to " OE1 GLN A 223 " =    2.369
peak=   -3.262 closest distance to " O   HOH Z 210 " =    1.469
peak=   -3.260 closest distance to " O   HOH Z 105 " =    2.073
peak=   -3.260 closest distance to " CG2 VAL A 296 " =    0.862
peak=   -3.251 closest distance to " O   HOH Z  17 " =    1.406
peak=   -3.250 closest distance to " O   HOH Z 150 " =    1.889
peak=   -3.249 closest distance to " O   HOH Z 414 " =    1.991
peak=   -3.245 closest distance to " O   HOH Z 191 " =    5.617
peak=   -3.245 closest distance to " O   HOH Z 359 " =    2.881
peak=   -3.244 closest distance to " CB  ALA A  43 " =    2.671
peak=   -3.243 closest distance to " O   HOH Z 185 " =    2.418
peak=   -3.243 closest distance to " O   HOH Z  39 " =    0.812
peak=   -3.242 closest distance to " O   THR A  18 " =    1.694
peak=   -3.240 closest distance to " CG2 THR A 221 " =    2.408
peak=   -3.235 closest distance to " CG  GLN A  11 " =    1.426
peak=   -3.235 closest distance to " O   SER A 206 " =    1.426
peak=   -3.230 closest distance to " O   HOH Z 171 " =    2.409
peak=   -3.228 closest distance to " ND2 ASN A  60 " =    1.873
peak=   -3.226 closest distance to " O   ALA A   7 " =    1.679
peak=   -3.225 closest distance to " O   HOH Z 259 " =    4.228
peak=   -3.224 closest distance to " O   HOH Z 108 " =    1.989
peak=   -3.222 closest distance to " O   HOH Z 256 " =    1.169
peak=   -3.221 closest distance to " CH2 TRP A 177 " =    2.114
peak=   -3.217 closest distance to " O   HOH Z 111 " =    2.450
peak=   -3.215 closest distance to " O   HOH Z 353 " =    2.415
peak=   -3.212 closest distance to " CA  ALA A   8 " =    1.471
peak=   -3.206 closest distance to " OE2 GLU A  53 " =    1.272
peak=   -3.206 closest distance to " CG2 VAL A 197 " =    2.386
peak=   -3.205 closest distance to " CD1 LEU A   5 " =    2.523
peak=   -3.203 closest distance to " O   HOH Z  71 " =    1.536
peak=   -3.201 closest distance to " CD2 TYR A 293 " =    1.916
peak=   -3.195 closest distance to " O   HOH Z 292 " =    1.781
peak=   -3.194 closest distance to " O   HOH Z 418 " =    1.545
peak=   -3.192 closest distance to " O   HOH Z 264 " =    1.905
peak=   -3.191 closest distance to " NH2BARG A 145 " =    2.598
peak=   -3.189 closest distance to " N   GLN A  58 " =    1.458
peak=   -3.183 closest distance to " CB  PRO A 213 " =    2.253
peak=   -3.183 closest distance to " O   ASN A 187 " =    1.689
peak=   -3.178 closest distance to " O   HOH Z 409 " =    5.346
peak=   -3.178 closest distance to " O   HOH Z 110 " =    1.461
peak=   -3.172 closest distance to " O   HOH Z 157 " =    3.688
peak=   -3.168 closest distance to " O   HOH Z 136 " =    1.139
peak=   -3.166 closest distance to " NH2AARG A 275 " =    5.192
peak=   -3.163 closest distance to " ND2 ASN A  45 " =    1.058
peak=   -3.162 closest distance to " C   GLY A 229 " =    1.150
peak=   -3.157 closest distance to " CG  ARG A 259 " =    2.595
peak=   -3.155 closest distance to " N   ALA A  43 " =    2.627
peak=   -3.154 closest distance to " ND2 ASN A  45 " =    2.178
peak=   -3.153 closest distance to " CD1 LEU A 101 " =    2.667
peak=   -3.153 closest distance to " N   ILE A 120 " =    1.020
peak=   -3.149 closest distance to " N   ASP A 272 " =    1.194
peak=   -3.147 closest distance to " OD1 ASN A 173 " =    1.667
peak=   -3.145 closest distance to " NH2 ARG A 159 " =    2.405
peak=   -3.144 closest distance to " O   HOH Z  38 " =    1.180
peak=   -3.141 closest distance to " O   HOH Z 118 " =    1.582
peak=   -3.141 closest distance to " CD1 LEU A 228 " =    2.436
peak=   -3.139 closest distance to " O   HOH Z 177 " =    1.753
peak=   -3.138 closest distance to " O   HOH Z 380 " =    4.576
peak=   -3.135 closest distance to " O   HOH Z 402 " =    1.320
peak=   -3.132 closest distance to " O   HOH Z  30 " =    0.839
peak=   -3.130 closest distance to " CE  MET A 105 " =    2.280
peak=   -3.130 closest distance to " C   LEU A 255 " =    1.699
peak=   -3.128 closest distance to " O   VAL A 174 " =    2.026
peak=   -3.127 closest distance to " OE2 GLU A 277 " =    2.769
peak=   -3.124 closest distance to " OD1 ASP A 298 " =    2.039
peak=   -3.118 closest distance to " CB  ALA A   9 " =    2.590
peak=   -3.108 closest distance to " C   THR A  18 " =    1.326
peak=   -3.100 closest distance to " CA  SER A 276 " =    1.454
peak=   -3.099 closest distance to " O   HOH Z  90 " =    1.665
peak=   -3.096 closest distance to " C   VAL A 265 " =    0.912
peak=   -3.095 closest distance to " CB  ARG A  79 " =    2.562
peak=   -3.089 closest distance to " O   HOH Z 259 " =    1.829
peak=   -3.083 closest distance to " CD1 LEU A 167 " =    2.097
peak=   -3.083 closest distance to " O   HOH Z 422 " =    1.597
peak=   -3.081 closest distance to " CG1 VAL A  78 " =    2.587
peak=   -3.078 closest distance to " OD1 ASN A 173 " =    1.332
peak=   -3.045 closest distance to " O   HOH Z 164 " =    4.856

================= 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    :  0.4882 0.4699   6.289408e+00   6.269557e+00
   1_bss:  0.4820 0.4609   6.285432e+00   6.262977e+00
   1_xyz:  0.4024 0.4173   6.187880e+00   6.206940e+00
   1_adp:  0.3597 0.3986   6.114190e+00   6.181838e+00
   1_occ:  0.3591 0.3978   6.113348e+00   6.182418e+00
   2_bss:  0.3572 0.3948   6.114307e+00   6.181447e+00
   2_xyz:  0.2767 0.3350   5.913469e+00   6.050550e+00
   2_adp:  0.2553 0.3116   5.855017e+00   6.003254e+00
   2_occ:  0.2550 0.3113   5.854436e+00   6.002667e+00
   3_bss:  0.2536 0.3094   5.854181e+00   6.001793e+00
   3_xyz:  0.2028 0.2480   5.645062e+00   5.807902e+00
   3_adp:  0.1886 0.2322   5.586602e+00   5.753509e+00
   3_occ:  0.1882 0.2322   5.586180e+00   5.754542e+00
   4_bss:  0.1881 0.2328   5.587078e+00   5.754738e+00
   4_xyz:  0.1521 0.1974   5.399354e+00   5.601303e+00
   4_adp:  0.1461 0.1939   5.369443e+00   5.578385e+00
   4_occ:  0.1458 0.1939   5.368832e+00   5.578523e+00
   5_bss:  0.1458 0.1943   5.368785e+00   5.578563e+00
   5_xyz:  0.1315 0.1783   5.281674e+00   5.504271e+00
   5_adp:  0.1267 0.1783   5.263875e+00   5.501689e+00
   5_occ:  0.1267 0.1783   5.263822e+00   5.501710e+00
   5_bss:  0.1265 0.1783   5.263632e+00   5.501701e+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:  0.297  20.001   7.185  11.212   7.503   0.000   0.000   0.000
   1_xyz:  0.297  20.001   7.185  11.212   7.503   0.000   0.000   0.000
   1_adp:  0.297  20.001   7.185  11.212   7.503   0.000   0.000   0.000
   1_occ:  0.297  20.001   7.185  11.212   7.503   0.000   0.000   0.000
   2_bss:  0.315  50.001   4.305   7.497   4.796   0.000   0.000   0.000
   2_xyz:  0.315  50.001   4.305   7.497   4.796   0.000   0.000   0.000
   2_adp:  0.315  50.001   4.305   7.497   4.796   0.000   0.000   0.000
   2_occ:  0.315  50.001   4.305   7.497   4.796   0.000   0.000   0.000
   3_bss:  0.322  65.478   2.783   4.700   3.478   0.000   0.000   0.000
   3_xyz:  0.322  65.478   2.783   4.700   3.478   0.000   0.000   0.000
   3_adp:  0.322  65.478   2.783   4.700   3.478   0.000   0.000   0.000
   3_occ:  0.322  65.478   2.783   4.700   3.478   0.000   0.000   0.000
   4_bss:  0.324  65.478   1.957   3.268   2.944   0.000   0.000   0.000
   4_xyz:  0.324  65.478   1.957   3.268   2.944   0.000   0.000   0.000
   4_adp:  0.324  65.478   1.957   3.268   2.944   0.000   0.000   0.000
   4_occ:  0.324  65.478   1.957   3.268   2.944   0.000   0.000   0.000
   5_bss:  0.325  64.838   1.581   2.484   2.745   0.000   0.000   0.000
   5_xyz:  0.325  64.838   1.581   2.484   2.745   0.000   0.000   0.000
   5_adp:  0.325  64.838   1.581   2.484   2.745   0.000   0.000   0.000
   5_occ:  0.325  64.838   1.581   2.484   2.745   0.000   0.000   0.000
   5_bss:  0.322  68.746  -0.597   0.079   0.518   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.906 0.4206  0.4746    68780.198
   1_bss:  57.577 0.4236  0.6135    67217.751
   1_xyz:  48.874 0.5332  0.7535    51274.563
   1_adp:  45.106 0.5805  0.8633    46082.238
   1_occ:  45.139 0.5801  0.8617    46183.356
   2_bss:  44.893 0.5831  0.7800    45836.217
   2_xyz:  36.019 0.6884  0.9133    30669.438
   2_adp:  32.977 0.7243  0.9403    26704.318
   2_occ:  32.945 0.7247  0.9404    26662.743
   3_bss:  32.811 0.7262  0.8828    26507.922
   3_xyz:  24.602 0.8158  0.9559    15831.738
   3_adp:  22.670 0.8362  0.9664    13986.179
   3_occ:  22.680 0.8361  0.9659    14023.751
   4_bss:  22.664 0.8363  0.9352    14019.745
   4_xyz:  18.691 0.8742  0.9616     9805.243
   4_adp:  18.026 0.8808  0.9653     9424.089
   4_occ:  18.024 0.8808  0.9650     9430.427
   5_bss:  18.005 0.8810  0.9498     9422.528
   5_xyz:  16.349 0.8958  0.9572     8107.619
   5_adp:  16.301 0.8962  0.9498     8039.091
   5_occ:  16.303 0.8961  0.9496     8036.615
   5_bss:  16.299 0.8962  0.9557     8037.976
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4559e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4559e+01
   1_xyz:   1.717  0.013  0.109 18.072  0.007  4.127   1.4630e-01
   1_adp:   1.717  0.013  0.109 18.072  0.007  4.127   1.4630e-01
   1_occ:   1.717  0.013  0.109 18.072  0.007  4.127   1.4630e-01
   2_bss:   1.717  0.013  0.109 18.072  0.007  4.127   1.4630e-01
   2_xyz:   1.370  0.011  0.090 16.504  0.005  4.111   1.0561e-01
   2_adp:   1.370  0.011  0.090 16.504  0.005  4.111   1.0561e-01
   2_occ:   1.370  0.011  0.090 16.504  0.005  4.111   1.0561e-01
   3_bss:   1.370  0.011  0.090 16.504  0.005  4.111   1.0561e-01
   3_xyz:   1.053  0.007  0.076 15.508  0.004  4.132   6.7034e-02
   3_adp:   1.053  0.007  0.076 15.508  0.004  4.132   6.7034e-02
   3_occ:   1.053  0.007  0.076 15.508  0.004  4.132   6.7034e-02
   4_bss:   1.053  0.007  0.076 15.508  0.004  4.132   6.7034e-02
   4_xyz:   1.076  0.008  0.082 15.468  0.003  4.136   6.7906e-02
   4_adp:   1.076  0.008  0.082 15.468  0.003  4.136   6.7906e-02
   4_occ:   1.076  0.008  0.082 15.468  0.003  4.136   6.7906e-02
   5_bss:   1.076  0.008  0.082 15.468  0.003  4.136   6.7906e-02
   5_xyz:   1.091  0.009  0.084 15.589  0.004  4.145   7.0861e-02
   5_adp:   1.091  0.009  0.084 15.589  0.004  4.145   7.0861e-02
   5_occ:   1.091  0.009  0.084 15.589  0.004  4.145   7.0861e-02
   5_bss:   1.091  0.009  0.084 15.589  0.004  4.145   7.0861e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0737e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0737e+00
   1_xyz:  14.691  0.132  0.463 88.205  0.049  2.168   1.0581e-01
   1_adp:  14.691  0.132  0.463 88.205  0.049  2.168   1.0581e-01
   1_occ:  14.691  0.132  0.463 88.205  0.049  2.168   1.0581e-01
   2_bss:  14.691  0.132  0.463 88.205  0.049  2.168   1.0581e-01
   2_xyz:   8.843  0.114  0.318 84.818  0.030  2.054   7.9664e-02
   2_adp:   8.843  0.114  0.318 84.818  0.030  2.054   7.9664e-02
   2_occ:   8.843  0.114  0.318 84.818  0.030  2.054   7.9664e-02
   3_bss:   8.843  0.114  0.318 84.818  0.030  2.054   7.9664e-02
   3_xyz:   7.902  0.073  0.276 89.195  0.058  2.236   5.3023e-02
   3_adp:   7.902  0.073  0.276 89.195  0.058  2.236   5.3023e-02
   3_occ:   7.902  0.073  0.276 89.195  0.058  2.236   5.3023e-02
   4_bss:   7.902  0.073  0.276 89.195  0.058  2.236   5.3023e-02
   4_xyz:   7.183  0.053  0.362 80.276  0.034  2.321   4.1106e-02
   4_adp:   7.183  0.053  0.362 80.276  0.034  2.321   4.1106e-02
   4_occ:   7.183  0.053  0.362 80.276  0.034  2.321   4.1106e-02
   5_bss:   7.183  0.053  0.362 80.276  0.034  2.321   4.1106e-02
   5_xyz:   8.739  0.059  0.518 83.179  0.038  2.288   4.3772e-02
   5_adp:   8.739  0.059  0.518 83.179  0.038  2.288   4.3772e-02
   5_occ:   8.739  0.059  0.518 83.179  0.038  2.288   4.3772e-02
   5_bss:   8.739  0.059  0.518 83.179  0.038  2.288   4.3772e-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: 118.87   0.00  13.85  77.53   0.00  11.46 118.87   0.00  26.89
   1_occ: 118.87   0.00  13.85  77.53   0.00  11.46 118.87   0.00  26.89
   2_bss: 118.87   0.00  13.85  77.53   0.00  11.46 118.87   0.00  26.89
   2_xyz: 118.87   0.00  13.85  77.53   0.00  11.46 118.87   0.00  26.89
   2_adp: 113.84   0.00  13.20  76.15   0.00   9.84 113.84   0.00  31.51
   2_occ: 113.84   0.00  13.20  76.15   0.00   9.84 113.84   0.00  31.51
   3_bss: 113.84   0.00  13.20  76.15   0.00   9.84 113.84   0.00  31.51
   3_xyz: 113.84   0.00  13.20  76.15   0.00   9.84 113.84   0.00  31.51
   3_adp: 104.98   0.00  13.31  79.07   0.00   9.31 104.98   0.00  35.12
   3_occ: 104.98   0.00  13.31  79.07   0.00   9.31 104.98   0.00  35.12
   4_bss: 104.98   0.00  13.31  79.07   0.00   9.31 104.98   0.00  35.12
   4_xyz: 104.98   0.00  13.31  79.07   0.00   9.31 104.98   0.00  35.12
   4_adp: 101.05   0.00  13.26  80.20   0.00   9.11 101.05   1.50  35.86
   4_occ: 101.05   0.00  13.26  80.20   0.00   9.11 101.05   1.50  35.86
   5_bss: 101.05   0.00  13.26  80.20   0.00   9.11 101.05   1.50  35.86
   5_xyz: 101.05   0.00  13.26  80.20   0.00   9.11 101.05   1.50  35.86
   5_adp: 116.51   0.00  13.95 116.51   0.00   9.13  97.47   1.60  40.20
   5_occ: 116.51   0.00  13.95 116.51   0.00   9.13  97.47   1.60  40.20
   5_bss: 118.96   2.45  16.40 118.96   2.45  11.58  99.92   4.05  42.64
------------------------------------------------------------------------
 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:    1.151    0.020    0.412
   1_adp:    1.151    0.020    0.412
   1_occ:    1.151    0.020    0.412
   2_bss:    1.151    0.020    0.412
   2_xyz:    1.624    0.018    0.609
   2_adp:    1.624    0.018    0.609
   2_occ:    1.624    0.018    0.609
   3_bss:    1.624    0.018    0.609
   3_xyz:    1.652    0.055    0.688
   3_adp:    1.652    0.055    0.688
   3_occ:    1.652    0.055    0.688
   4_bss:    1.652    0.055    0.688
   4_xyz:    1.749    0.078    0.764
   4_adp:    1.749    0.078    0.764
   4_occ:    1.749    0.078    0.764
   5_bss:    1.749    0.078    0.764
   5_xyz:    1.801    0.059    0.796
   5_adp:    1.801    0.059    0.796
   5_occ:    1.801    0.059    0.796
   5_bss:    1.801    0.059    0.796
------------------------------------------------------------------------

CPU time actual refinement: 336.94


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1073/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_1073/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1073/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1073/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1073/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.79 
  Macro-tasks:
    bulk solvent and scale       = 41.70  
    individual site refinement   = 137.50 
    weights calculation          = 32.56  
    collect and process          = 6.49   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 218.36 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 104.28 
    alpha_beta                      = 8.42   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 114.66 
    fmodel                         = 7.30   
    r_factors                      = 0.32   
    phase_errors                   = 10.43  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 249.13 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.784 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    640 calls, 103.91 s
gradients_fft:          584 calls, 101.82 s

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

# Date 2008-01-16 Time 03:07:51 PST -0800 (1200481671.03 s)
Start R-work = 0.4882, R-free = 0.4699 (no bulk solvent and anisotropic scale)
Final R-work = 0.1422, R-free = 0.1928 (no bulk solvent and anisotropic scale)

Start R-work = 0.4820, R-free = 0.4609
Final R-work = 0.1265, R-free = 0.1783