# Date 2008-01-16 Time 01:32:17 PST -0800 (1200475937.31 s)
#phil __OFF__

Command line arguments: "../452.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29349
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 452

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.6339, 84.6622, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8666 1.96141
Completeness in resolution range: 0.945643
Completeness with d_max=infinity: 0.942776

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8666
                             d_min =   1.9614

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8666 1.96141
Completeness in resolution range: 0.945643
Completeness with d_max=infinity: 0.942776

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8670 -  4.1970 [2178/2207]  1960   218  10.0%
  bin  2:  4.1970 -  3.3438 [2086/2109]  1876   210  10.1%
  bin  3:  3.3438 -  2.9247 [2065/2090]  1856   209  10.1%
  bin  4:  2.9247 -  2.6590 [2039/2055]  1841   198   9.7%
  bin  5:  2.6590 -  2.4693 [2030/2074]  1821   209  10.3%
  bin  6:  2.4693 -  2.3243 [2023/2051]  1833   190   9.4%
  bin  7:  2.3243 -  2.2083 [1999/2035]  1792   207  10.4%
  bin  8:  2.2083 -  2.1125 [1988/2030]  1794   194   9.8%
  bin  9:  2.1125 -  2.0313 [2002/2048]  1805   197   9.8%
  bin 10:  2.0313 -  1.9614 [1179/2016]  1052   127  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_452/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: 0.14 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:
        1.62 -     2.27: 29
        2.27 -     2.93: 1582
        2.93 -     3.59: 4504
        3.59 -     4.24: 9280
        4.24 -     4.90: 13172
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.616 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.646 3.040 -x+1/2,-y+1,z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.725 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.753 3.040 -x+1/2,-y+1,z+1/2
  " OG  SER A  95 " - " O   SER A 271 "  1.770 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28562 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_452/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_452/model_refine_001.geo

CPU time processing inputs: 9.06


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.63395 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4890   r_free= 0.4858   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| 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: 6.288850                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6812 0.99   1409  157 0.4013 0.3972      6.6046      6.6042|
|  2:  4.6812 -  3.7350 0.99   1366  150 0.4142 0.4126      6.8023      6.8218|
|  3:  3.7350 -  3.2686 0.99   1328  152 0.4490 0.4239      6.6826      6.7254|
|  4:  3.2686 -  2.9723 0.99   1324  143 0.4638 0.4578      6.5158      6.4964|
|  5:  2.9723 -  2.7607 0.98   1325  148 0.5159 0.5400      6.3891      6.3845|
|  6:  2.7607 -  2.5989 0.99   1307  146 0.5086 0.5428      6.2737      6.2112|
|  7:  2.5989 -  2.4693 0.98   1295  148 0.5295 0.4475      6.2654      6.1686|
|  8:  2.4693 -  2.3623 0.99   1295  141 0.5339 0.5292      6.1756      6.1812|
|  9:  2.3623 -  2.2717 0.99   1300  142 0.5464 0.5726      6.1281      6.1666|
| 10:  2.2717 -  2.1935 0.98   1293  143 0.5345 0.5629      6.1174      6.1385|
| 11:  2.1935 -  2.1252 0.97   1275  139 0.5424 0.5137      6.0409       6.008|
| 12:  2.1252 -  2.0646 0.99   1277  150 0.5392 0.5901      5.9678      6.0049|
| 13:  2.0646 -  2.0104 0.94   1257  134 0.5508 0.5234       5.884      5.8571|
| 14:  2.0104 -  1.9614 0.45    579   66 0.5621 0.5026      5.8743      5.7438|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8670 -  4.6812  1409   157  0.67  37.08   0.80     0.69      80247.70|
|  2:  4.6812 -  3.7350  1366   150  0.68  37.33   0.88     0.74     114338.05|
|  3:  3.7350 -  3.2686  1328   152  0.57  46.14   0.83     0.69     122240.41|
|  4:  3.2686 -  2.9723  1324   143  0.48  53.26   0.81     0.58     106837.40|
|  5:  2.9723 -  2.7607  1325   148  0.38  61.22   0.73     0.47      89466.48|
|  6:  2.7607 -  2.5989  1307   146  0.37  62.28   0.73     0.43      74150.08|
|  7:  2.5989 -  2.4693  1295   148  0.37  62.11   0.73     0.43      65418.29|
|  8:  2.4693 -  2.3623  1295   141  0.36  62.78   0.72     0.43      58726.96|
|  9:  2.3623 -  2.2717  1300   142  0.31  67.07   0.72     0.37      57084.18|
| 10:  2.2717 -  2.1935  1293   143  0.26  70.71   0.75     0.31      55067.55|
| 11:  2.1935 -  2.1252  1275   139  0.18  76.27   0.76     0.24      53667.39|
| 12:  2.1252 -  2.0646  1277   150  0.19  76.16   0.74     0.24      50057.31|
| 13:  2.0646 -  2.0104  1257   134  0.22  73.34   0.73     0.29      40333.04|
| 14:  2.0104 -  1.9614   579    66  0.38  61.29   0.71     0.43      27496.67|
|alpha:            min =        0.24 max =            0.74 mean =         0.46|
|beta:             min =    27496.67 max =       122240.41 mean =     73377.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.95 mean =        60.13|
|phase err.(test): min =        0.00 max =           89.87 mean =        60.35|
|-----------------------------------------------------------------------------|

============================== 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 = 15.864568             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.112   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.477663              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.140   (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 |  1.046 -  1.431:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.431 -  1.817:        9 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.817 -  2.202:      108 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.202 -  2.588:      566 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.588 -  2.973:     1358 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.973 -  3.358:     2515 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.358 -  3.744:     3968 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.744 -  4.129:     5194 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.129 -  4.515:     6801 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.515 -  4.900:     8074 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.338 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.046 |       2.186 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4944   r_free= 0.4932   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.289862                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4819   r_free= 0.4783   ksol= 0.36   Bsol= 20.00   scale= 0.976   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.16,9.63,7.94,0.00,0.00,0.00); trace/3= 7.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.285642                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.799075             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.002   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.344822              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.497   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4819      final r-factor (work) = 0.4104          |
| start r-factor (free) = 0.4783      final r-factor (free) = 0.4263          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.7189 = 13.80 * 0.50 * 6.2875 + 1.00 * 53.3382                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.0063 = 13.80 * 0.50 * 6.2112 + 1.00 * 0.1520                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4104      final r-factor (work) = 0.3677          |
| start r-factor (free) = 0.4263      final r-factor (free) = 0.4081          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3673 = 1.34 * 1.00 * 6.2112 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2793 = 1.34 * 1.00 * 6.1429 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.43   14.16    None  None   None       |
|    all(noH): 2823   0      0.00    97.43   14.16    None  None   None       |
|    Sol.    : 438    0      0.00    97.43   26.78    None  None   None       |
|    Mac.    : 2385   0      0.00    75.24   11.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.743: 1317   |   5:    48.714 -  58.457:   42        |
|      1:     9.743 -  19.486:  793   |   6:    58.457 -  68.200:   13        |
|      2:    19.486 -  29.228:  366   |   7:    68.200 -  77.942:   11        |
|      3:    29.228 -  38.971:  201   |   8:    77.942 -  87.685:    2        |
|      4:    38.971 -  48.714:   77   |   9:    87.685 -  97.428:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3677 r_free = 0.4081             target_work(ml) = 6.128         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3667 r_free = 0.4082             target_work(ml) = 6.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3667   r_free= 0.4082   ksol= 0.36   Bsol= 20.00   scale= 1.094   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.16,9.63,7.94,0.00,0.00,0.00); trace/3= 7.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.127016                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3652   r_free= 0.4037   ksol= 0.33   Bsol= 34.98   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,6.25,5.45,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.127538                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.639825             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.278   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.557277              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.715  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3652      final r-factor (work) = 0.2696          |
| start r-factor (free) = 0.4037      final r-factor (free) = 0.3260          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.8096 = 10.64 * 0.50 * 6.1388 + 1.00 * 0.1520                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.0810 = 10.64 * 0.50 * 6.0119 + 1.00 * 0.0982                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2696      final r-factor (work) = 0.2416          |
| start r-factor (free) = 0.3260      final r-factor (free) = 0.2989          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3709 = 0.56 * 1.00 * 6.0119 + 1.00 * 0.0206                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2849 = 0.56 * 1.00 * 5.8420 + 1.00 * 0.0293                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.49  13.96    None  None   None       |
|    all(noH): 2823   0      0.00    110.49  13.96    None  None   None       |
|    Sol.    : 438    0      1.50    94.92   32.47    None  None   None       |
|    Mac.    : 2385   0      0.00    110.49  10.56    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 -  11.049: 1600   |   5:    55.245 -  66.294:   24        |
|      1:    11.049 -  22.098:  667   |   6:    66.294 -  77.343:   11        |
|      2:    22.098 -  33.147:  272   |   7:    77.343 -  88.391:    1        |
|      3:    33.147 -  44.196:  162   |   8:    88.391 -  99.440:    1        |
|      4:    44.196 -  55.245:   84   |   9:    99.440 - 110.489:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2416 r_free = 0.2989             target_work(ml) = 5.802         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2412 r_free = 0.2990             target_work(ml) = 5.801         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2412   r_free= 0.2990   ksol= 0.33   Bsol= 34.98   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,6.25,5.45,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.800804                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2375   r_free= 0.2954   ksol= 0.32   Bsol= 34.98   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,3.27,2.83,0.00,0.00,0.00); trace/3= 2.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.797449                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.092325              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.354   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.279560              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.918   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2375      final r-factor (work) = 0.1807          |
| start r-factor (free) = 0.2954      final r-factor (free) = 0.2273          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1400 = 3.09 * 0.50 * 5.8479 + 1.00 * 0.0982                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8589 = 3.09 * 0.50 * 5.6917 + 1.00 * 0.0587                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1807      final r-factor (work) = 0.1678          |
| start r-factor (free) = 0.2273      final r-factor (free) = 0.2140          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6049 = 0.28 * 1.00 * 5.6917 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5539 = 0.28 * 1.00 * 5.5169 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.76   13.92    None  None   None       |
|    all(noH): 2823   0      0.00    78.76   13.92    None  None   None       |
|    Sol.    : 438    0      3.43    78.76   35.51    None  None   None       |
|    Mac.    : 2385   0      0.00    76.77   9.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.876: 1247   |   5:    39.378 -  47.254:  107        |
|      1:     7.876 -  15.751:  857   |   6:    47.254 -  55.129:   69        |
|      2:    15.751 -  23.627:  243   |   7:    55.129 -  63.005:   32        |
|      3:    23.627 -  31.502:  129   |   8:    63.005 -  70.880:   13        |
|      4:    31.502 -  39.378:  119   |   9:    70.880 -  78.756:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1678 r_free = 0.2140             target_work(ml) = 5.484         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1674 r_free = 0.2140             target_work(ml) = 5.483         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1674   r_free= 0.2140   ksol= 0.32   Bsol= 34.98   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,3.27,2.83,0.00,0.00,0.00); trace/3= 2.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.483064                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1671   r_free= 0.2136   ksol= 0.32   Bsol= 35.71   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.50,2.17,1.83,0.00,0.00,0.00); trace/3= 1.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.481968                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.541321              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.728  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.433811              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.462  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1671      final r-factor (work) = 0.1346          |
| start r-factor (free) = 0.2136      final r-factor (free) = 0.1779          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0747 = 2.54 * 0.50 * 5.5216 + 1.00 * 0.0587                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9054 = 2.54 * 0.50 * 5.3879 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1346      final r-factor (work) = 0.1290          |
| start r-factor (free) = 0.1779      final r-factor (free) = 0.1722          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3601 = 0.43 * 1.00 * 5.3879 + 1.00 * 0.0228                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2964 = 0.43 * 1.00 * 5.2699 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.21   14.02    None  None   None       |
|    all(noH): 2823   0      0.00    80.21   14.02    None  None   None       |
|    Sol.    : 438    0      3.03    72.71   37.14    None  None   None       |
|    Mac.    : 2385   0      0.00    80.21   9.78     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.021: 1288   |   5:    40.105 -  48.126:  101        |
|      1:     8.021 -  16.042:  863   |   6:    48.126 -  56.147:   84        |
|      2:    16.042 -  24.063:  208   |   7:    56.147 -  64.168:   36        |
|      3:    24.063 -  32.084:  111   |   8:    64.168 -  72.189:   14        |
|      4:    32.084 -  40.105:  112   |   9:    72.189 -  80.210:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1290 r_free = 0.1722             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1289 r_free = 0.1723             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1289   r_free= 0.1723   ksol= 0.32   Bsol= 35.71   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.50,2.17,1.83,0.00,0.00,0.00); trace/3= 1.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.256016                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1729   ksol= 0.32   Bsol= 35.71   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.39,1.73,1.55,0.00,0.00,0.00); trace/3= 1.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.259423                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.340682              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.044  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.590375              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.059  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1294      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1729      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8658 = 3.34 * 0.50 * 5.2723 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7830 = 3.34 * 0.50 * 5.2143 + 1.00 * 0.0735                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0886 = 0.59 * 1.00 * 5.2143 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0649 = 0.59 * 1.00 * 5.1733 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.07   13.94    None  None   None       |
|    all(noH): 2823   0      0.00    84.07   13.94    None  None   None       |
|    Sol.    : 438    0      2.20    75.12   37.35    None  None   None       |
|    Mac.    : 2385   0      0.00    84.07   9.65     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.407: 1410   |   5:    42.037 -  50.444:   99        |
|      1:     8.407 -  16.815:  791   |   6:    50.444 -  58.851:   74        |
|      2:    16.815 -  25.222:  187   |   7:    58.851 -  67.258:   31        |
|      3:    25.222 -  33.629:  105   |   8:    67.258 -  75.666:   13        |
|      4:    33.629 -  42.037:  108   |   9:    75.666 -  84.073:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1629             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1629             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1629   ksol= 0.32   Bsol= 35.71   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.39,1.73,1.55,0.00,0.00,0.00); trace/3= 1.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171195                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6812 0.99   1409  157 0.0955 0.1280      5.3655      5.5339|
|  2:  4.6812 -  3.7350 0.99   1366  150 0.0853 0.1129      5.4396      5.6618|
|  3:  3.7350 -  3.2686 0.99   1328  152 0.1073 0.1632      5.4909      5.8917|
|  4:  3.2686 -  2.9723 0.99   1324  143 0.1268 0.1587      5.4833      5.6575|
|  5:  2.9723 -  2.7607 0.98   1325  148 0.1369 0.1684      5.3562      5.5047|
|  6:  2.7607 -  2.5989 0.99   1307  146 0.1295 0.2160      5.2677       5.554|
|  7:  2.5989 -  2.4693 0.98   1295  148 0.1246 0.1635      5.1738      5.4026|
|  8:  2.4693 -  2.3623 0.99   1295  141 0.1183 0.1684       5.095      5.3099|
|  9:  2.3623 -  2.2717 0.99   1300  142 0.1188 0.1802      5.0476      5.3413|
| 10:  2.2717 -  2.1935 0.98   1293  143 0.1173 0.1971      5.0234      5.3313|
| 11:  2.1935 -  2.1252 0.97   1275  139 0.1175 0.1818      4.9527      5.2392|
| 12:  2.1252 -  2.0646 0.99   1277  150 0.1123 0.1726       4.882      5.1412|
| 13:  2.0646 -  2.0104 0.94   1257  134 0.1153 0.1847      4.7971      5.0778|
| 14:  2.0104 -  1.9614 0.45    579   66 0.1081 0.1629      4.6797      4.8869|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8670 -  4.6812  1409   157  0.94   9.01   0.98     0.97       7338.56|
|  2:  4.6812 -  3.7350  1366   150  0.95   8.34   1.02     1.00       9384.28|
|  3:  3.7350 -  3.2686  1328   152  0.93  12.01   1.03     1.03      11204.03|
|  4:  3.2686 -  2.9723  1324   143  0.91  14.77   1.01     0.99      11132.85|
|  5:  2.9723 -  2.7607  1325   148  0.89  16.94   1.00     0.96       8901.61|
|  6:  2.7607 -  2.5989  1307   146  0.89  16.95   0.99     0.96       8037.41|
|  7:  2.5989 -  2.4693  1295   148  0.90  15.88   0.99     0.95       6350.26|
|  8:  2.4693 -  2.3623  1295   141  0.90  16.29   1.00     0.97       5916.30|
|  9:  2.3623 -  2.2717  1300   142  0.90  16.50   1.01     0.98       5379.27|
| 10:  2.2717 -  2.1935  1293   143  0.89  16.82   1.00     0.97       5188.87|
| 11:  2.1935 -  2.1252  1275   139  0.89  17.43   1.00     0.96       4618.45|
| 12:  2.1252 -  2.0646  1277   150  0.91  15.38   1.00     0.98       3983.70|
| 13:  2.0646 -  2.0104  1257   134  0.90  16.60   1.01     1.01       3434.96|
| 14:  2.0104 -  1.9614   579    66  0.90  15.63   0.99     0.96       2672.91|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2672.91 max =        11204.03 mean =      6891.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.79|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.26|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1629   ksol= 0.32   Bsol= 42.38   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,0.41,0.34,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170831                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1629   ksol= 0.32   Bsol= 42.38   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,0.41,0.34,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170831                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6812 0.99   1409  157 0.0956 0.1286      5.3673       5.538|
|  2:  4.6812 -  3.7350 0.99   1366  150 0.0858 0.1135      5.4444      5.6687|
|  3:  3.7350 -  3.2686 0.99   1328  152 0.1073 0.1634      5.4942      5.8936|
|  4:  3.2686 -  2.9723 0.99   1324  143 0.1268 0.1590      5.4831      5.6574|
|  5:  2.9723 -  2.7607 0.98   1325  148 0.1367 0.1681      5.3541      5.5023|
|  6:  2.7607 -  2.5989 0.99   1307  146 0.1292 0.2156      5.2657      5.5519|
|  7:  2.5989 -  2.4693 0.98   1295  148 0.1244 0.1637      5.1719      5.4037|
|  8:  2.4693 -  2.3623 0.99   1295  141 0.1180 0.1677      5.0936      5.3062|
|  9:  2.3623 -  2.2717 0.99   1300  142 0.1187 0.1802      5.0464      5.3411|
| 10:  2.2717 -  2.1935 0.98   1293  143 0.1171 0.1969      5.0219      5.3298|
| 11:  2.1935 -  2.1252 0.97   1275  139 0.1172 0.1813      4.9513      5.2378|
| 12:  2.1252 -  2.0646 0.99   1277  150 0.1122 0.1727      4.8808      5.1408|
| 13:  2.0646 -  2.0104 0.94   1257  134 0.1154 0.1839       4.796      5.0758|
| 14:  2.0104 -  1.9614 0.45    579   66 0.1081 0.1627      4.6774      4.8848|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8670 -  4.6812  1409   157  0.94   9.05   0.98     0.97       7392.56|
|  2:  4.6812 -  3.7350  1366   150  0.95   8.40   1.02     1.00       9481.92|
|  3:  3.7350 -  3.2686  1328   152  0.93  12.09   1.03     1.03      11314.26|
|  4:  3.2686 -  2.9723  1324   143  0.91  14.79   1.01     0.99      11139.97|
|  5:  2.9723 -  2.7607  1325   148  0.89  16.91   1.00     0.96       8869.66|
|  6:  2.7607 -  2.5989  1307   146  0.89  16.92   0.99     0.96       8003.16|
|  7:  2.5989 -  2.4693  1295   148  0.90  15.87   0.99     0.96       6332.03|
|  8:  2.4693 -  2.3623  1295   141  0.90  16.27   1.01     0.98       5902.43|
|  9:  2.3623 -  2.2717  1300   142  0.90  16.48   1.01     0.98       5367.30|
| 10:  2.2717 -  2.1935  1293   143  0.89  16.79   1.00     0.97       5172.71|
| 11:  2.1935 -  2.1252  1275   139  0.89  17.40   1.00     0.97       4604.68|
| 12:  2.1252 -  2.0646  1277   150  0.91  15.35   1.00     0.98       3973.36|
| 13:  2.0646 -  2.0104  1257   134  0.90  16.55   1.01     1.01       3419.74|
| 14:  2.0104 -  1.9614   579    66  0.90  15.56   0.99     0.96       2653.46|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2653.46 max =        11314.26 mean =      6899.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.79|
|phase err.(test): min =        0.00 max =           89.84 mean =        14.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.28    85.35   15.22    None  None   None       |
|    all(noH): 2823   0      1.28    85.35   15.22    None  None   None       |
|    Sol.    : 438    0      3.47    76.40   38.62    None  None   None       |
|    Mac.    : 2385   0      1.28    85.35   10.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.278 -   9.686: 1410   |   5:    43.315 -  51.722:   99        |
|      1:     9.686 -  18.093:  791   |   6:    51.722 -  60.129:   74        |
|      2:    18.093 -  26.500:  187   |   7:    60.129 -  68.537:   31        |
|      3:    26.500 -  34.908:  105   |   8:    68.537 -  76.944:   13        |
|      4:    34.908 -  43.315:  108   |   9:    76.944 -  85.351:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 334         
Filter by distance & map next to the model:
   mapped sites are within: 0.623 - 4.916
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 331 from: 334
   mapped sites are within: 0.744 - 4.916

peak=   10.087 closest distance to " CB  VAL A 230 " =    1.402
peak=    7.664 closest distance to " O   HOH Z 120 " =    1.250
peak=    6.778 closest distance to " CG2 VAL A 296 " =    1.101
peak=    5.889 closest distance to " CG  LEU A   5 " =    1.248
peak=    5.792 closest distance to " O   HOH Z 124 " =    1.654
peak=    5.674 closest distance to " CD1AILE A 234 " =    1.087
peak=    5.595 closest distance to " O   HOH Z 278 " =    1.326
peak=    5.537 closest distance to " NH2 ARG A  56 " =    2.228
peak=    5.367 closest distance to " CB  VAL A 296 " =    1.076
peak=    5.356 closest distance to " O   HOH Z 279 " =    1.215
peak=    4.988 closest distance to " O   HOH Z 193 " =    1.790
peak=    4.985 closest distance to " CG  PRO A  54 " =    1.165
peak=    4.955 closest distance to " CB  SER A  63 " =    1.161
peak=    4.796 closest distance to " O   HOH Z  48 " =    1.751
peak=    4.761 closest distance to " O   HOH Z 402 " =    1.514
peak=    4.739 closest distance to " O   HOH Z 126 " =    1.875
peak=    4.734 closest distance to " O   SER A  87 " =    2.352
peak=    4.720 closest distance to " O   HOH Z 403 " =    1.832
peak=    4.715 closest distance to " CB  GLN A 223 " =    1.412
peak=    4.706 closest distance to " CG  LEU A 228 " =    1.208
peak=    4.696 closest distance to " O   HOH Z 142 " =    1.677
peak=    4.667 closest distance to " O   HOH Z 272 " =    1.919
peak=    4.650 closest distance to " O   HOH Z 247 " =    1.332
peak=    4.643 closest distance to " O   HOH Z  80 " =    1.824
peak=    4.577 closest distance to " O   HOH Z 232 " =    2.312
peak=    4.561 closest distance to " CB  ARG A 275 " =    0.889
peak=    4.548 closest distance to " C   PRO A 198 " =    1.497
peak=    4.543 closest distance to " NE2 GLN A  11 " =    1.039
peak=    4.541 closest distance to " CD2 LEU A   5 " =    1.232
peak=    4.530 closest distance to " CB  GLN A 183 " =    1.338
peak=    4.503 closest distance to " O   HOH Z 316 " =    2.543
peak=    4.495 closest distance to " O   HOH Z  85 " =    1.573
peak=    4.430 closest distance to " CB  VAL A 230 " =    1.207
peak=    4.379 closest distance to " O   HOH Z 234 " =    3.737
peak=    4.377 closest distance to " O   HOH Z 346 " =    1.414
peak=    4.373 closest distance to " O   HOH Z 130 " =    2.680
peak=    4.362 closest distance to " O   HOH Z 132 " =    1.212
peak=    4.351 closest distance to " CB  SER A   3 " =    1.291
peak=    4.325 closest distance to " O   HOH Z 368 " =    2.196
peak=    4.321 closest distance to " O   HOH Z 423 " =    1.877
peak=    4.299 closest distance to " CA  ALA A  21 " =    1.247
peak=    4.298 closest distance to " O   HOH Z 411 " =    3.531
peak=    4.297 closest distance to " O   HOH Z  11 " =    1.318
peak=    4.286 closest distance to " O   HOH Z  59 " =    2.396
peak=    4.281 closest distance to " O   HOH Z 156 " =    3.274
peak=    4.261 closest distance to " O   HOH Z 154 " =    1.528
peak=    4.245 closest distance to " O   HOH Z 203 " =    1.649
peak=    4.239 closest distance to " OD1 ASN A  69 " =    2.506
peak=    4.214 closest distance to " CG  PRO A 213 " =    1.144
peak=    4.212 closest distance to " CA  TYR A  30 " =    1.032
peak=    4.175 closest distance to " O   HOH Z 345 " =    2.685
peak=    4.134 closest distance to " O   HOH Z 357 " =    2.136
peak=    4.129 closest distance to " O   HOH Z 134 " =    1.782
peak=    4.124 closest distance to " CB  GLU A 152 " =    1.096
peak=    4.112 closest distance to " CG2 THR A 221 " =    1.204
peak=    4.110 closest distance to " O   HOH Z  97 " =    1.907
peak=    4.107 closest distance to " O   HOH Z 406 " =    1.680
peak=    4.107 closest distance to " O   HOH Z 389 " =    1.857
peak=    4.102 closest distance to " O   HOH Z 394 " =    1.586
peak=    4.099 closest distance to " O   HOH Z 260 " =    1.307
peak=    4.065 closest distance to " O   HOH Z  78 " =    1.681
peak=    4.037 closest distance to " O   HOH Z 344 " =    1.843
peak=    4.021 closest distance to " CB  TYR A 169 " =    0.852
peak=    4.020 closest distance to " O   HOH Z 327 " =    1.719
peak=    4.015 closest distance to " CG1BVAL A  72 " =    1.597
peak=    4.013 closest distance to " O   HOH Z 120 " =    2.016
peak=    4.007 closest distance to " CB  GLU A 277 " =    3.583
peak=    4.003 closest distance to " CB  PRO A  54 " =    0.805
peak=    3.998 closest distance to " O   HOH Z 414 " =    1.706
peak=    3.988 closest distance to " O   HOH Z 130 " =    1.186
peak=    3.979 closest distance to " O   HOH Z 155 " =    1.615
peak=    3.970 closest distance to " CB  GLU A 128 " =    1.157
peak=    3.964 closest distance to " O   HOH Z  54 " =    1.464
peak=    3.962 closest distance to " O   HOH Z  97 " =    2.498
peak=    3.954 closest distance to " CD2 LEU A 228 " =    1.200
peak=    3.950 closest distance to " O   HOH Z  47 " =    1.510
peak=    3.946 closest distance to " CB  TRP A 179 " =    1.225
peak=    3.943 closest distance to " O   HOH Z  20 " =    1.286
peak=    3.935 closest distance to " O   HOH Z 284 " =    2.963
peak=    3.929 closest distance to " O   HOH Z 136 " =    1.315
peak=    3.925 closest distance to " O   HOH Z 126 " =    2.603
peak=    3.918 closest distance to " O   HOH Z 102 " =    1.296
peak=    3.882 closest distance to " O   HOH Z  40 " =    1.766
peak=    3.878 closest distance to " O   HOH Z 426 " =    1.465
peak=    3.875 closest distance to " O   HOH Z 128 " =    1.861
peak=    3.869 closest distance to " NZ  LYS A 117 " =    3.126
peak=    3.864 closest distance to " CB  VAL A 202 " =    1.528
peak=    3.861 closest distance to " OE1 GLU A   2 " =    2.138
peak=    3.859 closest distance to " O   HOH Z 334 " =    1.498
peak=    3.854 closest distance to " O   HOH Z 227 " =    1.557
peak=    3.853 closest distance to " O   HOH Z 419 " =    1.677
peak=    3.852 closest distance to " O   HOH Z 344 " =    2.710
peak=    3.851 closest distance to " O   HOH Z  43 " =    1.405
peak=    3.825 closest distance to " O   HOH Z 209 " =    2.529
peak=    3.823 closest distance to " O   HOH Z 108 " =    2.432
peak=    3.815 closest distance to " O   HOH Z 303 " =    2.195
peak=    3.813 closest distance to " CD2 TRP A 179 " =    1.383
peak=    3.809 closest distance to " O   HOH Z  15 " =    2.153
peak=    3.796 closest distance to " CA  LYS A 117 " =    1.303
peak=    3.791 closest distance to " O   HOH Z 345 " =    1.721
peak=    3.791 closest distance to " O   HOH Z 261 " =    2.035
peak=    3.784 closest distance to " O   HOH Z 420 " =    2.152
peak=    3.783 closest distance to " O   HOH Z 126 " =    2.086
peak=    3.782 closest distance to " O   HOH Z  61 " =    1.563
peak=    3.778 closest distance to " O   HOH Z 227 " =    1.755
peak=    3.768 closest distance to " CG1 ILE A  33 " =    1.229
peak=    3.766 closest distance to " NH2 ARG A 156 " =    1.126
peak=    3.762 closest distance to " O   HOH Z 263 " =    1.474
peak=    3.754 closest distance to " O   HOH Z 126 " =    1.571
peak=    3.753 closest distance to " O   HOH Z 298 " =    1.950
peak=    3.750 closest distance to " O   HOH Z 326 " =    1.497
peak=    3.747 closest distance to " OG BSER A 164 " =    2.185
peak=    3.746 closest distance to " O   HOH Z 408 " =    1.617
peak=    3.738 closest distance to " CA  VAL A  41 " =    0.813
peak=    3.737 closest distance to " O   HOH Z 189 " =    2.698
peak=    3.736 closest distance to " CG AARG A 275 " =    1.075
peak=    3.732 closest distance to " O   HOH Z 366 " =    2.875
peak=    3.730 closest distance to " O   HOH Z 128 " =    1.735
peak=    3.715 closest distance to " O   HOH Z  48 " =    1.982
peak=    3.707 closest distance to " O   HOH Z 245 " =    1.427
peak=    3.690 closest distance to " OD2 ASP A 286 " =    2.720
peak=    3.688 closest distance to " O   HOH Z  67 " =    1.829
peak=    3.682 closest distance to " O   HOH Z 214 " =    2.574
peak=    3.677 closest distance to " CG  PRO A 198 " =    1.325
peak=    3.677 closest distance to " CG  ARG A  66 " =    1.041
peak=    3.676 closest distance to " NH2AARG A 145 " =    2.223
peak=    3.669 closest distance to " OG1 THR A 294 " =    2.298
peak=    3.665 closest distance to " CB  SER A 141 " =    1.081
peak=    3.658 closest distance to " O   HOH Z 374 " =    2.491
peak=    3.658 closest distance to " O   HOH Z 133 " =    1.439
peak=    3.650 closest distance to " O   HOH Z  21 " =    1.903
peak=    3.642 closest distance to " CD  ARG A 269 " =    1.112
peak=    3.641 closest distance to " CA  ASP A 191 " =    0.922
peak=    3.638 closest distance to " O   HOH Z 236 " =    1.665
peak=    3.632 closest distance to " O   HOH Z 193 " =    2.167
peak=    3.631 closest distance to " O   GLY A  91 " =    1.443
peak=    3.624 closest distance to " ND2 ASN A 187 " =    1.664
peak=    3.623 closest distance to " O   HOH Z 197 " =    2.397
peak=    3.623 closest distance to " O   HOH Z  71 " =    1.926
peak=    3.616 closest distance to " CB  ALA A   9 " =    1.596
peak=    3.616 closest distance to " CB  ASN A  39 " =    0.824
peak=    3.615 closest distance to " O   HOH Z 112 " =    1.655
peak=    3.613 closest distance to " O   ALA A 158 " =    1.285
peak=    3.611 closest distance to " O   HOH Z 163 " =    1.399
peak=    3.603 closest distance to " CB  ASN A 148 " =    1.261
peak=    3.600 closest distance to " O   HOH Z  78 " =    1.882
peak=    3.592 closest distance to " O   HOH Z 155 " =    2.654
peak=    3.577 closest distance to " CB  ARG A  79 " =    1.503
peak=    3.573 closest distance to " O   HOH Z 273 " =    2.608
peak=    3.567 closest distance to " O   HOH Z 147 " =    1.806
peak=    3.565 closest distance to " CD1 ILE A  33 " =    1.593
peak=    3.564 closest distance to " O   HOH Z 251 " =    1.676
peak=    3.561 closest distance to " O   HOH Z 261 " =    1.807
peak=    3.561 closest distance to " O   HOH Z 280 " =    2.336
peak=    3.555 closest distance to " CB AVAL A  41 " =    1.112
peak=    3.553 closest distance to " O   HOH Z 369 " =    2.170
peak=    3.545 closest distance to " CA  ARG A 195 " =    1.117
peak=    3.541 closest distance to " OE1 GLN A  11 " =    1.792
peak=    3.540 closest distance to " CB  VAL A 265 " =    1.194
peak=    3.535 closest distance to " CA  ASN A 176 " =    1.057
peak=    3.533 closest distance to " O   HOH Z 210 " =    0.960
peak=    3.531 closest distance to " NH2BARG A 145 " =    2.224
peak=    3.527 closest distance to " CB  SER A  62 " =    1.124
peak=    3.526 closest distance to " N   ASN A  39 " =    1.251
peak=    3.526 closest distance to " CB  ARG A 139 " =    0.957
peak=    3.525 closest distance to " O   HOH Z 280 " =    1.503
peak=    3.524 closest distance to " O   TRP A 274 " =    1.870
peak=    3.520 closest distance to " O   HOH Z  35 " =    2.457
peak=    3.518 closest distance to " CD  ARG A 195 " =    0.929
peak=    3.517 closest distance to " O   MET A 105 " =    1.858
peak=    3.515 closest distance to " CD  ARG A 195 " =    3.445
peak=    3.508 closest distance to " CB  ALA A 100 " =    1.235
peak=    3.506 closest distance to " O   HOH Z 411 " =    1.790
peak=    3.505 closest distance to " CG2 ILE A  20 " =    1.447
peak=    3.505 closest distance to " CE  LYS A 119 " =    1.005
peak=    3.503 closest distance to " O   HOH Z  88 " =    3.223
peak=    3.495 closest distance to " CB  SER A  26 " =    1.653
peak=    3.494 closest distance to " O   HOH Z 298 " =    4.916
peak=    3.490 closest distance to " O   HOH Z 192 " =    1.762
peak=    3.488 closest distance to " NH2AARG A 275 " =    3.878
peak=    3.488 closest distance to " CA  ALA A 295 " =    1.084
peak=    3.488 closest distance to " O   HOH Z 166 " =    1.503
peak=    3.487 closest distance to " O   HOH Z 132 " =    2.881
peak=    3.477 closest distance to " CB  LEU A 228 " =    1.460
peak=    3.461 closest distance to " O   HOH Z 295 " =    1.591
peak=    3.458 closest distance to " CB  TRP A 266 " =    1.107
peak=    3.458 closest distance to " O   HOH Z 422 " =    2.526
peak=    3.454 closest distance to " O   HOH Z 145 " =    2.331
peak=    3.444 closest distance to " O   HOH Z 423 " =    3.110
peak=    3.442 closest distance to " O   HOH Z  44 " =    2.037
peak=    3.437 closest distance to " CA  ARG A  36 " =    1.066
peak=    3.432 closest distance to " O   HOH Z  54 " =    2.512
peak=    3.432 closest distance to " O   HOH Z 402 " =    2.752
peak=    3.429 closest distance to " O   HOH Z 248 " =    1.667
peak=    3.426 closest distance to " CD  ARG A 159 " =    0.782
peak=    3.424 closest distance to " OD2 ASP A 298 " =    3.990
peak=    3.421 closest distance to " CA  ASP A 140 " =    1.211
peak=    3.420 closest distance to " O   HOH Z 431 " =    1.110
peak=    3.418 closest distance to " O   HOH Z 425 " =    2.153
peak=    3.412 closest distance to " CD  LYS A 166 " =    1.384
peak=    3.410 closest distance to " O   ASP A 124 " =    1.481
peak=    3.404 closest distance to " OD1 ASP A 286 " =    1.645
peak=    3.404 closest distance to " CD  LYS A 119 " =    1.774
peak=    3.401 closest distance to " O   HOH Z 358 " =    2.254
peak=    3.387 closest distance to " O   ALA A 165 " =    1.262
peak=    3.387 closest distance to " O   HOH Z 421 " =    1.788
peak=    3.385 closest distance to " CD2 LEU A 255 " =    1.167
peak=    3.382 closest distance to " CB  ARG A 190 " =    1.704
peak=    3.379 closest distance to " CZ AARG A 102 " =    1.799
peak=    3.377 closest distance to " O   HOH Z 329 " =    3.548
peak=    3.376 closest distance to " O   HOH Z 197 " =    2.131
peak=    3.358 closest distance to " CA  ALA A  51 " =    1.006
peak=    3.351 closest distance to " CE1 TYR A 186 " =    1.202
peak=    3.345 closest distance to " O   HOH Z 279 " =    2.006
peak=    3.344 closest distance to " O   HOH Z 383 " =    1.820
peak=    3.337 closest distance to " O   HOH Z 435 " =    1.912
peak=    3.335 closest distance to " O   HOH Z 109 " =    2.354
peak=    3.333 closest distance to " OG  SER A  62 " =    3.019
peak=    3.329 closest distance to " O   HOH Z 118 " =    1.170
peak=    3.326 closest distance to " CB  ALA A 137 " =    1.273
peak=    3.326 closest distance to " O   HOH Z 214 " =    1.216
peak=    3.324 closest distance to " O   ALA A   1 " =    1.668
peak=    3.323 closest distance to " O   HOH Z 291 " =    1.472
peak=    3.318 closest distance to " CA  ALA A 291 " =    0.932
peak=    3.317 closest distance to " O   HOH Z 283 " =    1.800
peak=    3.315 closest distance to " O   HOH Z 332 " =    1.545
peak=    3.314 closest distance to " CD2 TYR A 186 " =    1.112
peak=    3.304 closest distance to " C   SER A  32 " =    1.038
peak=    3.302 closest distance to " CB  ARG A 259 " =    1.883
peak=    3.300 closest distance to " CA  GLY A  80 " =    1.073
peak=    3.298 closest distance to " OG  SER A  22 " =    2.734
peak=    3.297 closest distance to " CG  GLN A  58 " =    2.569
peak=    3.292 closest distance to " O   HOH Z 284 " =    1.425
peak=    3.288 closest distance to " CB  GLN A  88 " =    1.198
peak=    3.288 closest distance to " O   HOH Z 329 " =    2.843
peak=    3.288 closest distance to " O   HOH Z 427 " =    2.681
peak=    3.285 closest distance to " O   HOH Z 236 " =    1.792
peak=    3.283 closest distance to " OD1 ASN A  60 " =    1.549
peak=    3.282 closest distance to " O   HOH Z 412 " =    3.941
peak=    3.281 closest distance to " NH1 ARG A  14 " =    1.173
peak=    3.280 closest distance to " CG2 ILE A 120 " =    1.380
peak=    3.276 closest distance to " O   HOH Z 194 " =    1.980
peak=    3.268 closest distance to " CB  THR A  52 " =    1.100
peak=    3.264 closest distance to " CZ  PHE A  38 " =    1.455
peak=    3.262 closest distance to " O   HOH Z 271 " =    1.411
peak=    3.262 closest distance to " O   HOH Z 217 " =    1.323
peak=    3.261 closest distance to " O   HOH Z 250 " =    1.287
peak=    3.261 closest distance to " CD1 LEU A  96 " =    0.775
peak=    3.260 closest distance to " O   HOH Z 261 " =    2.029
peak=    3.260 closest distance to " O   HOH Z 362 " =    3.326
peak=    3.259 closest distance to " O   HOH Z 313 " =    1.715
peak=    3.259 closest distance to " CB  ALA A 295 " =    1.260
peak=    3.257 closest distance to " OD1 ASN A  45 " =    1.398
peak=    3.255 closest distance to " O   THR A  31 " =    1.484
peak=    3.253 closest distance to " O   HOH Z 244 " =    1.686
peak=    3.252 closest distance to " O   HOH Z 417 " =    3.086
peak=    3.249 closest distance to " CG  LYS A 166 " =    1.532
peak=    3.247 closest distance to " O   HOH Z  66 " =    1.637
peak=    3.247 closest distance to " O   HOH Z  83 " =    1.621
peak=    3.247 closest distance to " CZ2 TRP A 179 " =    1.780
peak=    3.245 closest distance to " O   SER A  26 " =    1.658
peak=    3.245 closest distance to " O   HOH Z 355 " =    1.697
peak=    3.245 closest distance to " O   HOH Z 433 " =    1.440
peak=    3.245 closest distance to " O   HOH Z  59 " =    2.309
peak=    3.243 closest distance to " CB  ALA A  71 " =    1.221
peak=    3.242 closest distance to " CD1 LEU A 228 " =    1.454
peak=    3.236 closest distance to " O   HOH Z 114 " =    1.085
peak=    3.235 closest distance to " CB  ASN A 215 " =    1.089
peak=    3.235 closest distance to " CG2 THR A 220 " =    0.744
peak=    3.234 closest distance to " CA  ASN A 215 " =    1.142
peak=    3.232 closest distance to " O   GLY A  75 " =    3.410
peak=    3.231 closest distance to " O   HOH Z 185 " =    1.609
peak=    3.231 closest distance to " O   HOH Z  50 " =    2.081
peak=    3.230 closest distance to " CG  MET A 185 " =    1.209
peak=    3.230 closest distance to " CB  ALA A 256 " =    1.004
peak=    3.228 closest distance to " CB  THR A  31 " =    1.579
peak=    3.224 closest distance to " NH2 ARG A  79 " =    1.401
peak=    3.222 closest distance to " CB  TYR A 247 " =    0.995
peak=    3.221 closest distance to " CB  PRO A  54 " =    1.258
peak=    3.221 closest distance to " CD  GLN A 194 " =    1.574
peak=    3.212 closest distance to " O   HOH Z 322 " =    2.162
peak=    3.211 closest distance to " CG2 THR A  42 " =    0.860
peak=    3.210 closest distance to " O   HOH Z 361 " =    3.230
peak=    3.210 closest distance to " O   HOH Z 156 " =    2.426
peak=    3.200 closest distance to " O   HOH Z 189 " =    2.685
peak=    3.200 closest distance to " O   HOH Z   9 " =    2.310
peak=    3.199 closest distance to " O   HOH Z 163 " =    1.928
peak=    3.199 closest distance to " CZ  TYR A 214 " =    1.434
peak=    3.198 closest distance to " CG  GLN A  77 " =    2.270
peak=    3.196 closest distance to " O   HOH Z 108 " =    1.033
peak=    3.190 closest distance to " CD BLYS A 290 " =    1.104
peak=    3.184 closest distance to " O   HOH Z 281 " =    4.179
peak=    3.183 closest distance to " O   HOH Z  43 " =    2.184
peak=    3.183 closest distance to " CB  LEU A   5 " =    1.178
peak=    3.176 closest distance to " O   HOH Z  59 " =    1.976
peak=    3.176 closest distance to " CD2 HIS A  81 " =    1.138
peak=    3.172 closest distance to " N   TYR A 247 " =    1.179
peak=    3.167 closest distance to " CA  LEU A  83 " =    1.355
peak=    3.166 closest distance to " NH1BARG A 190 " =    2.040
peak=    3.164 closest distance to " O   HOH Z 395 " =    1.380
peak=    3.161 closest distance to " O   HOH Z   4 " =    1.547
peak=    3.159 closest distance to " CB  PRO A 198 " =    1.053
peak=    3.158 closest distance to " CG2 VAL A 197 " =    1.079
peak=    3.156 closest distance to " CB  ASP A 171 " =    0.903
peak=    3.155 closest distance to " O   HOH Z  90 " =    3.392
peak=    3.155 closest distance to " O   HOH Z 248 " =    1.548
peak=    3.153 closest distance to " CA  VAL A 126 " =    0.983
peak=    3.153 closest distance to " CE BMET A  47 " =    1.236
peak=    3.152 closest distance to " O   PHE A 155 " =    1.855
peak=    3.145 closest distance to " O   HOH Z 280 " =    3.045
peak=    3.143 closest distance to " CG2AVAL A 121 " =    2.077
peak=    3.139 closest distance to " O   HOH Z 173 " =    2.317
peak=    3.132 closest distance to " CG2 THR A 294 " =    1.488
peak=    3.129 closest distance to " O   HOH Z 299 " =    4.212
peak=    3.128 closest distance to " CA  THR A 221 " =    0.877
peak=    3.125 closest distance to " O   HOH Z 280 " =    2.450
peak=    3.118 closest distance to " CA  ALA A 158 " =    1.162
peak=    3.109 closest distance to " CB  ALA A 291 " =    1.329
peak=    3.108 closest distance to " CA  THR A 246 " =    1.138
peak=    3.104 closest distance to " O   HOH Z   1 " =    2.206
peak=    3.102 closest distance to " O   HOH Z 367 " =    3.509
peak=    3.098 closest distance to " CB  MET A  47 " =    1.301
peak=    3.097 closest distance to " O   HOH Z 380 " =    2.029
peak=    3.094 closest distance to " NZ  LYS A  76 " =    1.925
peak=    3.083 closest distance to " CB  PRO A  90 " =    1.307
peak=    3.083 closest distance to " N   ASP A 162 " =    1.345
peak=    3.080 closest distance to " CD1 LEU A 101 " =    1.183
peak=    3.080 closest distance to " O   HOH Z 152 " =    1.611
peak=    3.058 closest distance to " O   HOH Z 116 " =    1.657
peak=    3.042 closest distance to " O   HOH Z 211 " =    2.540
peak=    3.014 closest distance to " CB  ARG A  79 " =    0.904

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.828 - 5.377
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 208
   mapped sites are within: 0.828 - 5.377

peak=   -5.132 closest distance to " CG2 VAL A 230 " =    0.828
peak=   -4.592 closest distance to " CD  ARG A 156 " =    2.051
peak=   -4.572 closest distance to " O   PRO A 163 " =    2.095
peak=   -4.532 closest distance to " O   HOH Z  13 " =    1.624
peak=   -4.385 closest distance to " O   HOH Z 166 " =    1.812
peak=   -4.349 closest distance to " O   HOH Z 266 " =    4.359
peak=   -4.314 closest distance to " O   VAL A  67 " =    2.759
peak=   -4.253 closest distance to " SG  CYS A 254 " =    3.193
peak=   -4.248 closest distance to " O   HOH Z 210 " =    0.939
peak=   -4.180 closest distance to " CD1 LEU A 101 " =    2.516
peak=   -4.157 closest distance to " OG ASER A 134 " =    1.150
peak=   -4.153 closest distance to " CG2 THR A   4 " =    1.845
peak=   -4.085 closest distance to " CD1 PHE A  59 " =    1.913
peak=   -4.078 closest distance to " O   HOH Z 103 " =    1.881
peak=   -4.040 closest distance to " OXT GLY A 302 " =    2.738
peak=   -4.022 closest distance to " OG BSER A 134 " =    1.337
peak=   -3.959 closest distance to " CB  ALA A 161 " =    2.551
peak=   -3.932 closest distance to " NH2 ARG A  66 " =    1.393
peak=   -3.918 closest distance to " O   HOH Z 407 " =    2.967
peak=   -3.899 closest distance to " C   HIS A 108 " =    1.176
peak=   -3.847 closest distance to " N   SER A 276 " =    1.405
peak=   -3.826 closest distance to " O   HOH Z 231 " =    2.167
peak=   -3.812 closest distance to " CD2 LEU A 300 " =    2.733
peak=   -3.804 closest distance to " CE2 TYR A  30 " =    2.746
peak=   -3.780 closest distance to " O   HOH Z 126 " =    1.830
peak=   -3.773 closest distance to " CD2 LEU A 237 " =    2.702
peak=   -3.759 closest distance to " O   HOH Z  71 " =    1.217
peak=   -3.755 closest distance to " O   HOH Z 414 " =    1.763
peak=   -3.745 closest distance to " C   THR A 279 " =    1.170
peak=   -3.734 closest distance to " O   ASN A 187 " =    1.463
peak=   -3.719 closest distance to " C   ALA A 158 " =    1.193
peak=   -3.685 closest distance to " CE BMET A  47 " =    1.538
peak=   -3.681 closest distance to " N   GLN A  58 " =    1.661
peak=   -3.676 closest distance to " O   ALA A 256 " =    1.409
peak=   -3.665 closest distance to " OG  SER A  97 " =    2.265
peak=   -3.663 closest distance to " NH2AARG A 275 " =    4.920
peak=   -3.655 closest distance to " CH2 TRP A 179 " =    1.319
peak=   -3.655 closest distance to " O   HOH Z 165 " =    2.103
peak=   -3.646 closest distance to " OG  SER A  62 " =    1.321
peak=   -3.634 closest distance to " CG  ARG A 219 " =    2.429
peak=   -3.633 closest distance to " O   VAL A  67 " =    2.636
peak=   -3.632 closest distance to " CG  LYS A 193 " =    2.458
peak=   -3.623 closest distance to " O   PHE A 218 " =    1.599
peak=   -3.622 closest distance to " CZ  TYR A 169 " =    1.888
peak=   -3.620 closest distance to " CB  ALA A 248 " =    1.928
peak=   -3.609 closest distance to " CD  LYS A 289 " =    2.491
peak=   -3.607 closest distance to " O   HOH Z 290 " =    0.900
peak=   -3.598 closest distance to " O   HOH Z 136 " =    1.996
peak=   -3.592 closest distance to " O   HOH Z  48 " =    1.257
peak=   -3.589 closest distance to " O   ALA A 161 " =    1.730
peak=   -3.589 closest distance to " N   ALA A 226 " =    1.990
peak=   -3.582 closest distance to " OD1 ASN A  39 " =    2.221
peak=   -3.581 closest distance to " N   THR A 235 " =    1.318
peak=   -3.573 closest distance to " OG BSER A 134 " =    1.693
peak=   -3.567 closest distance to " O   HOH Z 234 " =    4.272
peak=   -3.560 closest distance to " O   ALA A   1 " =    1.823
peak=   -3.546 closest distance to " CB  PRO A 163 " =    2.730
peak=   -3.543 closest distance to " O   HOH Z  52 " =    1.690
peak=   -3.529 closest distance to " O   ALA A  51 " =    1.429
peak=   -3.529 closest distance to " CG2 THR A 182 " =    2.286
peak=   -3.527 closest distance to " N   ALA A 248 " =    1.732
peak=   -3.522 closest distance to " O   LEU A 228 " =    2.366
peak=   -3.520 closest distance to " O   ALA A 160 " =    1.397
peak=   -3.510 closest distance to " CB  CYS A 254 " =    2.489
peak=   -3.509 closest distance to " CG1 VAL A 112 " =    2.494
peak=   -3.507 closest distance to " O   HOH Z  97 " =    1.389
peak=   -3.503 closest distance to " O   HOH Z  11 " =    1.610
peak=   -3.502 closest distance to " O   HOH Z 313 " =    1.318
peak=   -3.501 closest distance to " CD2 TYR A 293 " =    2.086
peak=   -3.494 closest distance to " C   GLY A  91 " =    1.336
peak=   -3.493 closest distance to " O   HOH Z 266 " =    4.511
peak=   -3.492 closest distance to " O   HOH Z 351 " =    1.466
peak=   -3.467 closest distance to " O  BHOH Z 338 " =    1.579
peak=   -3.466 closest distance to " O   HOH Z 166 " =    2.213
peak=   -3.462 closest distance to " CG  ASP A 231 " =    0.842
peak=   -3.461 closest distance to " CD  GLN A  88 " =    1.022
peak=   -3.459 closest distance to " CG2 VAL A 197 " =    2.247
peak=   -3.456 closest distance to " O   HOH Z 423 " =    2.311
peak=   -3.452 closest distance to " O   HOH Z 196 " =    2.298
peak=   -3.450 closest distance to " O   TRP A  92 " =    1.892
peak=   -3.448 closest distance to " CA  GLY A 203 " =    2.067
peak=   -3.447 closest distance to " CG2 VAL A 189 " =    1.970
peak=   -3.444 closest distance to " O   ASP A 191 " =    1.373
peak=   -3.441 closest distance to " CD  GLN A  58 " =    1.364
peak=   -3.438 closest distance to " CB  PHE A 208 " =    2.270
peak=   -3.437 closest distance to " CG  ASP A  50 " =    2.486
peak=   -3.436 closest distance to " O   HOH Z 150 " =    1.468
peak=   -3.436 closest distance to " O   HOH Z  17 " =    1.197
peak=   -3.433 closest distance to " O   HOH Z 118 " =    3.226
peak=   -3.430 closest distance to " O   SER A 271 " =    2.041
peak=   -3.429 closest distance to " N   THR A 157 " =    1.576
peak=   -3.423 closest distance to " OE2 GLU A   2 " =    1.755
peak=   -3.416 closest distance to " NH2 ARG A  79 " =    1.864
peak=   -3.416 closest distance to " O   HOH Z 377 " =    1.916
peak=   -3.411 closest distance to " CG  GLU A  53 " =    1.474
peak=   -3.411 closest distance to " O   HOH Z 292 " =    4.374
peak=   -3.410 closest distance to " ND2 ASN A  45 " =    1.129
peak=   -3.406 closest distance to " OG BSER A 210 " =    1.320
peak=   -3.400 closest distance to " O   HOH Z 120 " =    1.202
peak=   -3.395 closest distance to " O   HOH Z 311 " =    3.393
peak=   -3.393 closest distance to " O   PRO A 198 " =    1.287
peak=   -3.391 closest distance to " CB  SER A 210 " =    1.407
peak=   -3.390 closest distance to " CD  ARG A 139 " =    1.648
peak=   -3.389 closest distance to " O   HOH Z 431 " =    2.253
peak=   -3.388 closest distance to " OD1 ASN A 148 " =    1.626
peak=   -3.387 closest distance to " O   HOH Z 426 " =    2.365
peak=   -3.385 closest distance to " CD1 LEU A 228 " =    2.243
peak=   -3.383 closest distance to " CG  GLU A 277 " =    1.120
peak=   -3.380 closest distance to " CE3 TRP A 150 " =    2.267
peak=   -3.369 closest distance to " O   VAL A 197 " =    1.379
peak=   -3.360 closest distance to " N   HIS A 115 " =    1.971
peak=   -3.359 closest distance to " O   HOH Z 166 " =    1.452
peak=   -3.357 closest distance to " O   HOH Z 191 " =    5.377
peak=   -3.355 closest distance to " O   HOH Z 198 " =    2.253
peak=   -3.352 closest distance to " ND2 ASN A  69 " =    1.555
peak=   -3.348 closest distance to " OG1 THR A  82 " =    1.284
peak=   -3.348 closest distance to " CG  MET A 105 " =    0.882
peak=   -3.347 closest distance to " O   ALA A   8 " =    1.923
peak=   -3.344 closest distance to " CD1 TYR A 247 " =    2.280
peak=   -3.344 closest distance to " CB  ALA A  51 " =    1.851
peak=   -3.342 closest distance to " O   SER A 146 " =    0.931
peak=   -3.340 closest distance to " OXT GLY A 302 " =    3.502
peak=   -3.329 closest distance to " O   HOH Z 313 " =    2.156
peak=   -3.320 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.318 closest distance to " O   HOH Z  43 " =    1.888
peak=   -3.318 closest distance to " O   HOH Z  92 " =    1.525
peak=   -3.307 closest distance to " ND2 ASN A  60 " =    1.310
peak=   -3.307 closest distance to " CA  GLY A 133 " =    1.981
peak=   -3.304 closest distance to " CA  ASP A 298 " =    1.057
peak=   -3.304 closest distance to " CB  ALA A 248 " =    2.149
peak=   -3.301 closest distance to " O   GLY A 196 " =    0.966
peak=   -3.300 closest distance to " CA  GLY A 133 " =    2.221
peak=   -3.299 closest distance to " ND2 ASN A  39 " =    1.152
peak=   -3.299 closest distance to " O   HOH Z 250 " =    1.387
peak=   -3.295 closest distance to " CG2 VAL A 112 " =    2.512
peak=   -3.292 closest distance to " O   VAL A 174 " =    1.990
peak=   -3.286 closest distance to " O   HOH Z 166 " =    1.446
peak=   -3.283 closest distance to " N   ALA A  43 " =    2.554
peak=   -3.268 closest distance to " CD  ARG A 195 " =    5.080
peak=   -3.264 closest distance to " O   HOH Z 427 " =    1.394
peak=   -3.262 closest distance to " CE  MET A 105 " =    1.920
peak=   -3.261 closest distance to " O   HOH Z 388 " =    2.121
peak=   -3.255 closest distance to " O   HOH Z 423 " =    0.989
peak=   -3.249 closest distance to " O   HOH Z 171 " =    2.118
peak=   -3.247 closest distance to " CD  GLN A  88 " =    2.183
peak=   -3.246 closest distance to " CA  PRO A 243 " =    2.680
peak=   -3.237 closest distance to " O   SER A  95 " =    1.551
peak=   -3.237 closest distance to " O   HOH Z  10 " =    1.415
peak=   -3.234 closest distance to " O   HOH Z  60 " =    2.128
peak=   -3.231 closest distance to " CG2 ILE A 263 " =    2.280
peak=   -3.227 closest distance to " O   HOH Z  15 " =    1.526
peak=   -3.226 closest distance to " O   HOH Z 435 " =    2.530
peak=   -3.221 closest distance to " CG  ARG A 269 " =    2.243
peak=   -3.220 closest distance to " O   MET A  40 " =    2.745
peak=   -3.219 closest distance to " O   HOH Z 265 " =    2.021
peak=   -3.218 closest distance to " CB  ASP A 162 " =    2.767
peak=   -3.217 closest distance to " O   VAL A 125 " =    2.142
peak=   -3.215 closest distance to " O   HOH Z 139 " =    3.265
peak=   -3.214 closest distance to " O   HOH Z 185 " =    2.119
peak=   -3.211 closest distance to " O   HOH Z 151 " =    1.493
peak=   -3.210 closest distance to " O   ALA A 100 " =    2.392
peak=   -3.210 closest distance to " O   HOH Z 292 " =    2.652
peak=   -3.209 closest distance to " CB  ASN A  39 " =    2.280
peak=   -3.194 closest distance to " CB  ASP A 132 " =    2.312
peak=   -3.193 closest distance to " O   HOH Z 301 " =    2.193
peak=   -3.189 closest distance to " O   HOH Z 189 " =    1.639
peak=   -3.178 closest distance to " C   GLY A  80 " =    2.407
peak=   -3.174 closest distance to " N   SER A 206 " =    1.881
peak=   -3.172 closest distance to " N   ARG A  66 " =    1.762
peak=   -3.170 closest distance to " N   THR A 220 " =    2.328
peak=   -3.164 closest distance to " O   HOH Z 193 " =    1.803
peak=   -3.161 closest distance to " O   HOH Z  56 " =    2.267
peak=   -3.160 closest distance to " N   GLN A 122 " =    1.495
peak=   -3.157 closest distance to " CG  GLU A 152 " =    1.218
peak=   -3.156 closest distance to " O   HOH Z 283 " =    1.943
peak=   -3.152 closest distance to " O   HOH Z 361 " =    3.422
peak=   -3.151 closest distance to " OD1 ASP A 200 " =    1.226
peak=   -3.150 closest distance to " O   HOH Z 424 " =    2.909
peak=   -3.144 closest distance to " CD2 LEU A 237 " =    2.806
peak=   -3.140 closest distance to " O   HOH Z 108 " =    2.101
peak=   -3.138 closest distance to " CE  LYS A 166 " =    3.052
peak=   -3.135 closest distance to " CB  SER A 146 " =    2.102
peak=   -3.127 closest distance to " O   HOH Z  78 " =    1.718
peak=   -3.125 closest distance to " O   HOH Z 310 " =    1.573
peak=   -3.120 closest distance to " OG  SER A  26 " =    1.330
peak=   -3.119 closest distance to " O   HOH Z 297 " =    2.792
peak=   -3.119 closest distance to " CZ2 TRP A  92 " =    2.727
peak=   -3.116 closest distance to " O   HOH Z 350 " =    2.011
peak=   -3.107 closest distance to " OD1 ASP A 171 " =    1.564
peak=   -3.105 closest distance to " O   HOH Z 208 " =    1.296
peak=   -3.104 closest distance to " CA  ASP A  27 " =    2.432
peak=   -3.101 closest distance to " OD1 ASN A 249 " =    1.089
peak=   -3.093 closest distance to " CB  ALA A 291 " =    2.139
peak=   -3.091 closest distance to " CZ  ARG A  66 " =    1.493
peak=   -3.084 closest distance to " O   HOH Z 414 " =    2.044
peak=   -3.083 closest distance to " CG2 VAL A 296 " =    1.559
peak=   -3.082 closest distance to " NH1 ARG A 195 " =    2.557
peak=   -3.080 closest distance to " CB  SER A 245 " =    2.446
peak=   -3.071 closest distance to " O   HOH Z   6 " =    1.999
peak=   -3.065 closest distance to " O   HOH Z  44 " =    2.139
peak=   -3.059 closest distance to " N   ALA A 248 " =    2.246
peak=   -3.057 closest distance to " O   HOH Z 174 " =    2.126
peak=   -3.050 closest distance to " CE1 HIS A  81 " =    1.389
peak=   -3.043 closest distance to " NH2 ARG A  79 " =    1.768
peak=   -3.034 closest distance to " O   ASN A 301 " =    1.334
peak=   -3.022 closest distance to " CG  GLU A 152 " =    2.153

================= 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    :  0.4890 0.4858   6.288850e+00   6.279150e+00
   1_bss:  0.4819 0.4783   6.285642e+00   6.269964e+00
   1_xyz:  0.4104 0.4263   6.191824e+00   6.220122e+00
   1_adp:  0.3677 0.4081   6.127902e+00   6.200713e+00
   1_occ:  0.3667 0.4082   6.127016e+00   6.200306e+00
   2_bss:  0.3652 0.4037   6.127538e+00   6.198324e+00
   2_xyz:  0.2696 0.3260   5.889632e+00   6.035733e+00
   2_adp:  0.2416 0.2989   5.801710e+00   5.963282e+00
   2_occ:  0.2412 0.2990   5.800804e+00   5.962538e+00
   3_bss:  0.2375 0.2954   5.797449e+00   5.958083e+00
   3_xyz:  0.1807 0.2273   5.553314e+00   5.743549e+00
   3_adp:  0.1678 0.2140   5.483824e+00   5.676324e+00
   3_occ:  0.1674 0.2140   5.483064e+00   5.676261e+00
   4_bss:  0.1671 0.2136   5.481968e+00   5.674506e+00
   4_xyz:  0.1346 0.1779   5.290366e+00   5.504143e+00
   4_adp:  0.1290 0.1722   5.255985e+00   5.476129e+00
   4_occ:  0.1289 0.1723   5.256016e+00   5.476649e+00
   5_bss:  0.1294 0.1729   5.259423e+00   5.479777e+00
   5_xyz:  0.1159 0.1632   5.182024e+00   5.424885e+00
   5_adp:  0.1138 0.1629   5.171399e+00   5.420863e+00
   5_occ:  0.1137 0.1629   5.171195e+00   5.420991e+00
   5_bss:  0.1136 0.1629   5.170831e+00   5.421020e+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:  0.360  20.001   6.158   9.626   7.941   0.000   0.000   0.000
   1_xyz:  0.360  20.001   6.158   9.626   7.941   0.000   0.000   0.000
   1_adp:  0.360  20.001   6.158   9.626   7.941   0.000   0.000   0.000
   1_occ:  0.360  20.001   6.158   9.626   7.941   0.000   0.000   0.000
   2_bss:  0.333  34.978   3.138   6.252   5.448   0.000   0.000   0.000
   2_xyz:  0.333  34.978   3.138   6.252   5.448   0.000   0.000   0.000
   2_adp:  0.333  34.978   3.138   6.252   5.448   0.000   0.000   0.000
   2_occ:  0.333  34.978   3.138   6.252   5.448   0.000   0.000   0.000
   3_bss:  0.315  34.978   1.366   3.269   2.834   0.000   0.000   0.000
   3_xyz:  0.315  34.978   1.366   3.269   2.834   0.000   0.000   0.000
   3_adp:  0.315  34.978   1.366   3.269   2.834   0.000   0.000   0.000
   3_occ:  0.315  34.978   1.366   3.269   2.834   0.000   0.000   0.000
   4_bss:  0.317  35.708   0.501   2.172   1.834   0.000   0.000   0.000
   4_xyz:  0.317  35.708   0.501   2.172   1.834   0.000   0.000   0.000
   4_adp:  0.317  35.708   0.501   2.172   1.834   0.000   0.000   0.000
   4_occ:  0.317  35.708   0.501   2.172   1.834   0.000   0.000   0.000
   5_bss:  0.317  35.708   0.390   1.730   1.547   0.000   0.000   0.000
   5_xyz:  0.317  35.708   0.390   1.730   1.547   0.000   0.000   0.000
   5_adp:  0.317  35.708   0.390   1.730   1.547   0.000   0.000   0.000
   5_occ:  0.317  35.708   0.390   1.730   1.547   0.000   0.000   0.000
   5_bss:  0.322  42.377  -0.755   0.411   0.344   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.151 0.3917  0.4586    73380.663
   1_bss:  59.874 0.3931  0.5735    70354.928
   1_xyz:  52.069 0.4918  0.7090    55450.427
   1_adp:  48.478 0.5377  0.8322    50759.554
   1_occ:  48.412 0.5385  0.8323    50630.783
   2_bss:  48.049 0.5430  0.7591    50064.763
   2_xyz:  35.158 0.6983  0.9609    29225.260
   2_adp:  31.129 0.7450  1.0073    24138.252
   2_occ:  31.102 0.7453  1.0074    24096.036
   3_bss:  30.869 0.7477  0.9242    23752.845
   3_xyz:  22.673 0.8350  0.9904    13734.444
   3_adp:  20.590 0.8563  1.0030    11875.431
   3_occ:  20.580 0.8564  1.0031    11882.916
   4_bss:  20.492 0.8572  0.9680    11768.107
   4_xyz:  16.611 0.8927  0.9881     8106.172
   4_adp:  15.974 0.8985  0.9888     7686.850
   4_occ:  15.982 0.8985  0.9887     7696.117
   5_bss:  16.025 0.8982  0.9786     7772.453
   5_xyz:  14.873 0.9079  0.9822     6960.610
   5_adp:  14.743 0.9091  0.9784     6888.910
   5_occ:  14.741 0.9091  0.9783     6892.015
   5_bss:  14.735 0.9092  0.9807     6899.912
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3338e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3338e+01
   1_xyz:   1.767  0.014  0.111 18.273  0.007  4.108   1.5195e-01
   1_adp:   1.767  0.014  0.111 18.273  0.007  4.108   1.5195e-01
   1_occ:   1.767  0.014  0.111 18.273  0.007  4.108   1.5195e-01
   2_bss:   1.767  0.014  0.111 18.273  0.007  4.108   1.5195e-01
   2_xyz:   1.292  0.010  0.087 16.503  0.006  4.111   9.8188e-02
   2_adp:   1.292  0.010  0.087 16.503  0.006  4.111   9.8188e-02
   2_occ:   1.292  0.010  0.087 16.503  0.006  4.111   9.8188e-02
   3_bss:   1.292  0.010  0.087 16.503  0.006  4.111   9.8188e-02
   3_xyz:   0.994  0.006  0.070 15.246  0.004  4.128   5.8671e-02
   3_adp:   0.994  0.006  0.070 15.246  0.004  4.128   5.8671e-02
   3_occ:   0.994  0.006  0.070 15.246  0.004  4.128   5.8671e-02
   4_bss:   0.994  0.006  0.070 15.246  0.004  4.128   5.8671e-02
   4_xyz:   0.991  0.006  0.075 15.304  0.003  4.121   5.9190e-02
   4_adp:   0.991  0.006  0.075 15.304  0.003  4.121   5.9190e-02
   4_occ:   0.991  0.006  0.075 15.304  0.003  4.121   5.9190e-02
   5_bss:   0.991  0.006  0.075 15.304  0.003  4.121   5.9190e-02
   5_xyz:   1.137  0.008  0.089 15.739  0.004  4.126   7.3461e-02
   5_adp:   1.137  0.008  0.089 15.739  0.004  4.126   7.3461e-02
   5_occ:   1.137  0.008  0.089 15.739  0.004  4.126   7.3461e-02
   5_bss:   1.137  0.008  0.089 15.739  0.004  4.126   7.3461e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.046   6.9119e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.046   6.9119e+00
   1_xyz:  15.738  0.175  0.528 86.952  0.057  2.175   1.0540e-01
   1_adp:  15.738  0.175  0.528 86.952  0.057  2.175   1.0540e-01
   1_occ:  15.738  0.175  0.528 86.952  0.057  2.175   1.0540e-01
   2_bss:  15.738  0.175  0.528 86.952  0.057  2.175   1.0540e-01
   2_xyz:   9.027  0.144  0.365 88.616  0.061  2.195   9.5906e-02
   2_adp:   9.027  0.144  0.365 88.616  0.061  2.195   9.5906e-02
   2_occ:   9.027  0.144  0.365 88.616  0.061  2.195   9.5906e-02
   3_bss:   9.027  0.144  0.365 88.616  0.061  2.195   9.5906e-02
   3_xyz:   7.358  0.053  0.335 80.203  0.050  2.308   4.2264e-02
   3_adp:   7.358  0.053  0.335 80.203  0.050  2.308   4.2264e-02
   3_occ:   7.358  0.053  0.335 80.203  0.050  2.308   4.2264e-02
   4_bss:   7.358  0.053  0.335 80.203  0.050  2.308   4.2264e-02
   4_xyz:   6.653  0.040  0.462 80.156  0.028  2.331   4.0153e-02
   4_adp:   6.653  0.040  0.462 80.156  0.028  2.331   4.0153e-02
   4_occ:   6.653  0.040  0.462 80.156  0.028  2.331   4.0153e-02
   5_bss:   6.653  0.040  0.462 80.156  0.028  2.331   4.0153e-02
   5_xyz:   7.595  0.046  0.676 81.833  0.032  2.300   5.4357e-02
   5_adp:   7.595  0.046  0.676 81.833  0.032  2.300   5.4357e-02
   5_occ:   7.595  0.046  0.676 81.833  0.032  2.300   5.4357e-02
   5_bss:   7.595  0.046  0.676 81.833  0.032  2.300   5.4357e-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:  97.43   0.00  14.16  75.24   0.00  11.85  97.43   0.00  26.78
   1_occ:  97.43   0.00  14.16  75.24   0.00  11.85  97.43   0.00  26.78
   2_bss:  97.43   0.00  14.16  75.24   0.00  11.85  97.43   0.00  26.78
   2_xyz:  97.43   0.00  14.16  75.24   0.00  11.85  97.43   0.00  26.78
   2_adp: 110.49   0.00  13.96 110.49   0.00  10.56  94.92   1.50  32.47
   2_occ: 110.49   0.00  13.96 110.49   0.00  10.56  94.92   1.50  32.47
   3_bss: 110.49   0.00  13.96 110.49   0.00  10.56  94.92   1.50  32.47
   3_xyz: 110.49   0.00  13.96 110.49   0.00  10.56  94.92   1.50  32.47
   3_adp:  78.76   0.00  13.92  76.77   0.00   9.95  78.76   3.43  35.51
   3_occ:  78.76   0.00  13.92  76.77   0.00   9.95  78.76   3.43  35.51
   4_bss:  78.76   0.00  13.92  76.77   0.00   9.95  78.76   3.43  35.51
   4_xyz:  78.76   0.00  13.92  76.77   0.00   9.95  78.76   3.43  35.51
   4_adp:  80.21   0.00  14.02  80.21   0.00   9.78  72.71   3.03  37.14
   4_occ:  80.21   0.00  14.02  80.21   0.00   9.78  72.71   3.03  37.14
   5_bss:  80.21   0.00  14.02  80.21   0.00   9.78  72.71   3.03  37.14
   5_xyz:  80.21   0.00  14.02  80.21   0.00   9.78  72.71   3.03  37.14
   5_adp:  84.07   0.00  13.94  84.07   0.00   9.65  75.12   2.20  37.35
   5_occ:  84.07   0.00  13.94  84.07   0.00   9.65  75.12   2.20  37.35
   5_bss:  85.35   1.28  15.22  85.35   1.28  10.92  76.40   3.47  38.62
------------------------------------------------------------------------
 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:    1.185    0.017    0.416
   1_adp:    1.185    0.017    0.416
   1_occ:    1.185    0.017    0.416
   2_bss:    1.185    0.017    0.416
   2_xyz:    1.907    0.025    0.636
   2_adp:    1.907    0.025    0.636
   2_occ:    1.907    0.025    0.636
   3_bss:    1.907    0.025    0.636
   3_xyz:    1.574    0.034    0.694
   3_adp:    1.574    0.034    0.694
   3_occ:    1.574    0.034    0.694
   4_bss:    1.574    0.034    0.694
   4_xyz:    1.739    0.073    0.757
   4_adp:    1.739    0.073    0.757
   4_occ:    1.739    0.073    0.757
   5_bss:    1.739    0.073    0.757
   5_xyz:    1.792    0.077    0.788
   5_adp:    1.792    0.077    0.788
   5_occ:    1.792    0.077    0.788
   5_bss:    1.792    0.077    0.788
------------------------------------------------------------------------

CPU time actual refinement: 348.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_452/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_452/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_452/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_452/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_452/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.36 
  Macro-tasks:
    bulk solvent and scale       = 41.38  
    individual site refinement   = 147.15 
    weights calculation          = 32.32  
    collect and process          = 6.55   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 227.51 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 109.79 
    alpha_beta                      = 8.41   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 120.36 
    fmodel                         = 7.21   
    r_factors                      = 0.21   
    phase_errors                   = 10.48  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 260.42 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.872 micro seconds
Total CPU time: 6.03 minutes
from_scatterers_fft:    652 calls, 109.42 s
gradients_fft:          596 calls, 106.83 s

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

# Date 2008-01-16 Time 01:38:17 PST -0800 (1200476297.96 s)
Start R-work = 0.4890, R-free = 0.4858 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1796 (no bulk solvent and anisotropic scale)

Start R-work = 0.4819, R-free = 0.4783
Final R-work = 0.1136, R-free = 0.1629