# Date 2008-01-16 Time 01:58:39 PST -0800 (1200477519.21 s)
#phil __OFF__

Command line arguments: "../646.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14864
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 646

-------------------------------------------------------------------------------
  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: (70.25, 46.4607, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.98246
Completeness in resolution range: 0.95463
Completeness with d_max=infinity: 0.951708

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   1.9825

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: (70.25, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.98246
Completeness in resolution range: 0.95463
Completeness with d_max=infinity: 0.951708

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2422 [2155/2179]  1936   219  10.2%
  bin  2:  4.2422 -  3.3797 [2062/2082]  1857   205   9.9%
  bin  3:  3.3797 -  2.9562 [2046/2065]  1843   203   9.9%
  bin  4:  2.9562 -  2.6876 [2022/2052]  1820   202  10.0%
  bin  5:  2.6876 -  2.4958 [2009/2028]  1808   201  10.0%
  bin  6:  2.4958 -  2.3493 [2002/2027]  1798   204  10.2%
  bin  7:  2.3493 -  2.2320 [2005/2033]  1806   199   9.9%
  bin  8:  2.2320 -  2.1351 [1970/2006]  1773   197  10.0%
  bin  9:  2.1351 -  2.0532 [1961/2003]  1771   190   9.7%
  bin 10:  2.0532 -  1.9825 [1357/2045]  1218   139  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_646/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 23
        2.42 -     3.04: 2183
        3.04 -     3.66: 4685
        3.66 -     4.28: 9007
        4.28 -     4.90: 12342
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.857 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.889 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.989 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.136 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28235 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_646/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_646/model_refine_001.geo

CPU time processing inputs: 9.15


============================ 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 = 70.25 46.4607 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  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: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4579   r_free= 0.4398   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.256973                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7317 0.99   1396  154 0.3813 0.3554      6.5708      6.4987|
|  2:  4.7317 -  3.7752 0.99   1348  153 0.3534 0.3519      6.6952      6.7155|
|  3:  3.7752 -  3.3037 0.99   1316  141 0.3986 0.3590       6.612      6.5658|
|  4:  3.3037 -  3.0043 0.99   1312  151 0.4475 0.4136      6.5082      6.4421|
|  5:  3.0043 -  2.7904 0.99   1306  145 0.4849 0.4498      6.3439      6.3348|
|  6:  2.7904 -  2.6268 0.99   1301  142 0.4806 0.5197      6.2548      6.2047|
|  7:  2.6268 -  2.4958 0.99   1285  144 0.5039 0.5030      6.2152      6.1981|
|  8:  2.4958 -  2.3876 0.98   1279  142 0.5126 0.4550      6.1877      6.1576|
|  9:  2.3876 -  2.2961 0.98   1284  144 0.4894 0.5298       6.089      6.1573|
| 10:  2.2961 -  2.2171 1.00   1290  141 0.5351 0.4631      6.1255      6.0567|
| 11:  2.2171 -  2.1480 0.98   1281  139 0.5114 0.4930      6.0309      6.0256|
| 12:  2.1480 -  2.0867 0.98   1254  144 0.5183 0.4933      5.9715      5.9628|
| 13:  2.0867 -  2.0319 0.99   1287  141 0.5078 0.4966      5.8631      5.8248|
| 14:  2.0319 -  1.9825 0.53    691   78 0.5384 0.5240      5.8888      5.7766|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7317  1396   154  0.73  31.67   0.80     0.77      61962.63|
|  2:  4.7317 -  3.7752  1348   153  0.76  30.00   0.89     0.82      81671.26|
|  3:  3.7752 -  3.3037  1316   141  0.68  36.79   0.87     0.78      86245.82|
|  4:  3.3037 -  3.0043  1312   151  0.61  43.36   0.80     0.68      78793.58|
|  5:  3.0043 -  2.7904  1306   145  0.51  51.40   0.77     0.59      68720.43|
|  6:  2.7904 -  2.6268  1301   142  0.47  54.65   0.73     0.53      63260.43|
|  7:  2.6268 -  2.4958  1285   144  0.42  58.40   0.74     0.49      60654.20|
|  8:  2.4958 -  2.3876  1279   142  0.42  58.62   0.73     0.48      54909.92|
|  9:  2.3876 -  2.2961  1284   144  0.44  56.88   0.75     0.51      48505.68|
| 10:  2.2961 -  2.2171  1290   141  0.45  56.17   0.74     0.53      42177.62|
| 11:  2.2171 -  2.1480  1281   139  0.44  56.97   0.76     0.54      40212.06|
| 12:  2.1480 -  2.0867  1254   144  0.42  58.87   0.76     0.51      37941.43|
| 13:  2.0867 -  2.0319  1287   141  0.39  61.07   0.72     0.47      33569.57|
| 14:  2.0319 -  1.9825   691    78  0.41  58.92   0.74     0.45      28092.98|
|alpha:            min =        0.45 max =            0.82 mean =         0.59|
|beta:             min =    28092.98 max =        86245.82 mean =     57407.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.47|
|phase err.(test): min =        0.00 max =           89.71 mean =        50.73|
|-----------------------------------------------------------------------------|

============================== 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 = 9.426054              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.232   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.818864              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.251   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      179 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      680 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1485 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2626 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3916 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5072 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6560 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7676 |
|-----------------------------------------------------------------------------|
|-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 |       53.878 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.763 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    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 = 11.926)------------------------------------------|
|    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: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4661   r_free= 0.4410   ksol= 0.00   Bsol= 0.00   scale= 0.775    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.261501                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4496   r_free= 0.4268   ksol= 0.35   Bsol= 20.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.88,8.68,10.45,0.00,0.00,0.00); trace/3= 8.67                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.251697                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.973305              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.827   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.763257              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.700   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4496      final r-factor (work) = 0.3503          |
| start r-factor (free) = 0.4268      final r-factor (free) = 0.3684          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 78.8291 = 7.97 * 0.50 * 6.2586 + 1.00 * 53.8784                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5523 = 7.97 * 0.50 * 6.1267 + 1.00 * 0.1273                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3503      final r-factor (work) = 0.2963          |
| start r-factor (free) = 0.3684      final r-factor (free) = 0.3419          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6906 = 0.76 * 1.00 * 6.1267 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5869 = 0.76 * 1.00 * 5.9921 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.80   11.98    None  None   None       |
|    all(noH): 2823   0      0.00    69.80   11.98    None  None   None       |
|    Sol.    : 438    0      0.00    69.80   27.35    None  None   None       |
|    Mac.    : 2385   0      0.00    58.60   9.16     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 -   6.980: 1204   |   5:    34.900 -  41.879:   84        |
|      1:     6.980 -  13.960:  769   |   6:    41.879 -  48.859:   56        |
|      2:    13.960 -  20.940:  387   |   7:    48.859 -  55.839:   24        |
|      3:    20.940 -  27.920:  176   |   8:    55.839 -  62.819:    6        |
|      4:    27.920 -  34.900:  115   |   9:    62.819 -  69.799:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2963 r_free = 0.3419             target_work(ml) = 5.960         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2958 r_free = 0.3418             target_work(ml) = 5.959         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2958   r_free= 0.3418   ksol= 0.35   Bsol= 20.00   scale= 1.109   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.88,8.68,10.45,0.00,0.00,0.00); trace/3= 8.67                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.959201                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2906   r_free= 0.3361   ksol= 0.34   Bsol= 42.91   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,4.46,6.64,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.958398                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.182037              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.909   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.395617              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.287  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2906      final r-factor (work) = 0.1932          |
| start r-factor (free) = 0.3361      final r-factor (free) = 0.2424          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6566 = 5.18 * 0.50 * 5.9935 + 1.00 * 0.1273                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0590 = 5.18 * 0.50 * 5.7841 + 1.00 * 0.0723                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1932      final r-factor (work) = 0.1706          |
| start r-factor (free) = 0.2424      final r-factor (free) = 0.2203          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3019 = 0.40 * 1.00 * 5.7841 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2014 = 0.40 * 1.00 * 5.5368 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.98   12.01    None  None   None       |
|    all(noH): 2823   0      0.00    74.98   12.01    None  None   None       |
|    Sol.    : 438    0      0.00    74.98   32.72    None  None   None       |
|    Mac.    : 2385   0      0.00    61.91   8.20     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.498: 1433   |   5:    37.490 -  44.988:  111        |
|      1:     7.498 -  14.996:  740   |   6:    44.988 -  52.486:   56        |
|      2:    14.996 -  22.494:  202   |   7:    52.486 -  59.984:   31        |
|      3:    22.494 -  29.992:  116   |   8:    59.984 -  67.483:    3        |
|      4:    29.992 -  37.490:  129   |   9:    67.483 -  74.981:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1706 r_free = 0.2203             target_work(ml) = 5.491         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1706 r_free = 0.2201             target_work(ml) = 5.491         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1706   r_free= 0.2201   ksol= 0.34   Bsol= 42.91   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,4.46,6.64,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.490831                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1693   r_free= 0.2189   ksol= 0.32   Bsol= 50.94   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.76,4.56,0.00,0.00,0.00); trace/3= 3.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.491587                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.815367              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.476  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.463241              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.234  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1693      final r-factor (work) = 0.1390          |
| start r-factor (free) = 0.2189      final r-factor (free) = 0.1833          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1093 = 1.82 * 0.50 * 5.5493 + 1.00 * 0.0723                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9628 = 1.82 * 0.50 * 5.4065 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1390      final r-factor (work) = 0.1316          |
| start r-factor (free) = 0.1833      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9219 = 1.46 * 1.00 * 5.4065 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7580 = 1.46 * 1.00 * 5.2919 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.17   12.95    None  None   None       |
|    all(noH): 2823   0      0.00    82.17   12.95    None  None   None       |
|    Sol.    : 438    0      0.69    82.17   37.93    None  None   None       |
|    Mac.    : 2385   0      0.00    79.23   8.37     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.217: 1565   |   5:    41.085 -  49.302:   98        |
|      1:     8.217 -  16.434:  630   |   6:    49.302 -  57.519:   65        |
|      2:    16.434 -  24.651:  186   |   7:    57.519 -  65.736:   45        |
|      3:    24.651 -  32.868:  107   |   8:    65.736 -  73.952:   23        |
|      4:    32.868 -  41.085:   96   |   9:    73.952 -  82.169:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1316 r_free = 0.1792             target_work(ml) = 5.283         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1315 r_free = 0.1792             target_work(ml) = 5.283         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1315   r_free= 0.1792   ksol= 0.32   Bsol= 50.94   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.76,4.56,0.00,0.00,0.00); trace/3= 3.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.282855                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1315   r_free= 0.1792   ksol= 0.33   Bsol= 57.47   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.25,2.48,4.28,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.282613                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.636994              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.060  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.351618              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.393  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1315      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1792      final r-factor (free) = 0.1699          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3865 = 1.64 * 0.50 * 5.2916 + 1.00 * 0.0554                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3528 = 1.64 * 0.50 * 5.2502 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1216      final r-factor (work) = 0.1205          |
| start r-factor (free) = 0.1699      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8606 = 0.35 * 1.00 * 5.2502 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8548 = 0.35 * 1.00 * 5.2211 + 1.00 * 0.0189                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.19   12.44    None  None   None       |
|    all(noH): 2823   0      0.00    81.19   12.44    None  None   None       |
|    Sol.    : 438    0      1.42    79.45   36.17    None  None   None       |
|    Mac.    : 2385   0      0.00    81.19   8.08     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 -   8.119: 1606   |   5:    40.597 -  48.716:   80        |
|      1:     8.119 -  16.239:  634   |   6:    48.716 -  56.836:   72        |
|      2:    16.239 -  24.358:  155   |   7:    56.836 -  64.955:   37        |
|      3:    24.358 -  32.478:  109   |   8:    64.955 -  73.075:   22        |
|      4:    32.478 -  40.597:  103   |   9:    73.075 -  81.194:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1205 r_free = 0.1658             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1204 r_free = 0.1656             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1656   ksol= 0.33   Bsol= 57.47   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.25,2.48,4.28,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207260                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1203   r_free= 0.1656   ksol= 0.33   Bsol= 57.47   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,2.46,4.25,0.00,0.00,0.00); trace/3= 3.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207222                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.348514              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.341  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.270172              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.842   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1146          |
| start r-factor (free) = 0.1656      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1863 = 2.35 * 0.50 * 5.2210 + 1.00 * 0.0555                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1517 = 2.35 * 0.50 * 5.1847 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6001 = 1.27 * 1.00 * 5.1847 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5909 = 1.27 * 1.00 * 5.1650 + 1.00 * 0.0305                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.01   12.48    None  None   None       |
|    all(noH): 2823   0      0.00    84.01   12.48    None  None   None       |
|    Sol.    : 438    0      1.19    79.54   36.54    None  None   None       |
|    Mac.    : 2385   0      0.00    84.01   8.06     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.401: 1657   |   5:    42.003 -  50.404:   81        |
|      1:     8.401 -  16.801:  583   |   6:    50.404 -  58.805:   68        |
|      2:    16.801 -  25.202:  159   |   7:    58.805 -  67.205:   34        |
|      3:    25.202 -  33.603:  111   |   8:    67.205 -  75.606:   19        |
|      4:    33.603 -  42.003:  106   |   9:    75.606 -  84.007:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1604             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1604             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1604   ksol= 0.33   Bsol= 57.47   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,2.46,4.25,0.00,0.00,0.00); trace/3= 3.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166652                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7317 0.99   1396  154 0.0997 0.1289      5.3872        5.54|
|  2:  4.7317 -  3.7752 0.99   1348  153 0.0859 0.1141      5.4395      5.6371|
|  3:  3.7752 -  3.3037 0.99   1316  141 0.1081 0.1497      5.4955       5.852|
|  4:  3.3037 -  3.0043 0.99   1312  151 0.1222 0.1750      5.4625      5.6381|
|  5:  3.0043 -  2.7904 0.99   1306  145 0.1337 0.1684      5.3384      5.5717|
|  6:  2.7904 -  2.6268 0.99   1301  142 0.1218 0.2043      5.2114      5.5116|
|  7:  2.6268 -  2.4958 0.99   1285  144 0.1322 0.1613      5.1979      5.3467|
|  8:  2.4958 -  2.3876 0.98   1279  142 0.1193 0.1692      5.1069      5.3532|
|  9:  2.3876 -  2.2961 0.98   1284  144 0.1239 0.1930      5.0827      5.3592|
| 10:  2.2961 -  2.2171 1.00   1290  141 0.1166 0.1648      4.9961      5.1972|
| 11:  2.2171 -  2.1480 0.98   1281  139 0.1178 0.1862      4.9786      5.3177|
| 12:  2.1480 -  2.0867 0.98   1254  144 0.1163 0.1769       4.908      5.2362|
| 13:  2.0867 -  2.0319 0.99   1287  141 0.1128 0.1691      4.7859      5.0243|
| 14:  2.0319 -  1.9825 0.53    691   78 0.0958 0.1573      4.6459      4.8613|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7317  1396   154  0.94   9.27   0.98     0.95       7215.11|
|  2:  4.7317 -  3.7752  1348   153  0.95   8.00   1.01     1.00       9156.43|
|  3:  3.7752 -  3.3037  1316   141  0.93  11.50   1.03     1.02      10692.83|
|  4:  3.3037 -  3.0043  1312   151  0.92  13.75   1.01     0.99      10568.73|
|  5:  3.0043 -  2.7904  1306   145  0.90  15.92   1.00     0.98       8494.61|
|  6:  2.7904 -  2.6268  1301   142  0.90  16.24   0.98     0.96       7184.38|
|  7:  2.6268 -  2.4958  1285   144  0.90  16.00   0.98     0.95       6434.12|
|  8:  2.4958 -  2.3876  1279   142  0.90  16.05   0.99     0.96       5777.12|
|  9:  2.3876 -  2.2961  1284   144  0.90  16.13   1.00     0.96       5585.56|
| 10:  2.2961 -  2.2171  1290   141  0.89  16.96   1.00     0.96       4884.70|
| 11:  2.2171 -  2.1480  1281   139  0.89  17.01   0.99     0.94       4721.18|
| 12:  2.1480 -  2.0867  1254   144  0.90  16.31   1.00     1.00       4239.75|
| 13:  2.0867 -  2.0319  1287   141  0.90  16.35   0.99     0.97       3377.41|
| 14:  2.0319 -  1.9825   691    78  0.92  13.47   0.98     0.95       2490.68|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2490.68 max =        10692.83 mean =      6656.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.47|
|phase err.(test): min =        0.00 max =           88.24 mean =        13.88|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1604   ksol= 0.33   Bsol= 55.50   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.56,1.22,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166667                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1604   ksol= 0.33   Bsol= 55.50   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.56,1.22,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166667                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7317 0.99   1396  154 0.0995 0.1287      5.3846      5.5379|
|  2:  4.7317 -  3.7752 0.99   1348  153 0.0856 0.1136      5.4372      5.6341|
|  3:  3.7752 -  3.3037 0.99   1316  141 0.1079 0.1497      5.4941      5.8519|
|  4:  3.3037 -  3.0043 0.99   1312  151 0.1223 0.1751      5.4633      5.6392|
|  5:  3.0043 -  2.7904 0.99   1306  145 0.1339 0.1686      5.3398      5.5732|
|  6:  2.7904 -  2.6268 0.99   1301  142 0.1219 0.2047      5.2128      5.5132|
|  7:  2.6268 -  2.4958 0.99   1285  144 0.1323 0.1613       5.199      5.3478|
|  8:  2.4958 -  2.3876 0.98   1279  142 0.1194 0.1693      5.1076      5.3536|
|  9:  2.3876 -  2.2961 0.98   1284  144 0.1239 0.1928      5.0832      5.3587|
| 10:  2.2961 -  2.2171 1.00   1290  141 0.1167 0.1650      4.9964      5.1981|
| 11:  2.2171 -  2.1480 0.98   1281  139 0.1179 0.1862       4.979      5.3179|
| 12:  2.1480 -  2.0867 0.98   1254  144 0.1164 0.1770       4.908      5.2362|
| 13:  2.0867 -  2.0319 0.99   1287  141 0.1128 0.1691      4.7861      5.0246|
| 14:  2.0319 -  1.9825 0.53    691   78 0.0959 0.1573      4.6463      4.8617|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7317  1396   154  0.94   9.24   0.98     0.95       7173.95|
|  2:  4.7317 -  3.7752  1348   153  0.95   7.97   1.02     1.00       9118.52|
|  3:  3.7752 -  3.3037  1316   141  0.93  11.48   1.03     1.03      10662.79|
|  4:  3.3037 -  3.0043  1312   151  0.92  13.76   1.01     0.99      10581.12|
|  5:  3.0043 -  2.7904  1306   145  0.90  15.95   1.00     0.99       8518.16|
|  6:  2.7904 -  2.6268  1301   142  0.90  16.27   0.98     0.96       7206.68|
|  7:  2.6268 -  2.4958  1285   144  0.90  16.02   0.99     0.96       6453.81|
|  8:  2.4958 -  2.3876  1279   142  0.90  16.07   1.00     0.97       5783.55|
|  9:  2.3876 -  2.2961  1284   144  0.90  16.14   1.01     0.97       5592.72|
| 10:  2.2961 -  2.2171  1290   141  0.89  16.97   1.01     0.96       4885.70|
| 11:  2.2171 -  2.1480  1281   139  0.89  17.02   1.00     0.95       4724.36|
| 12:  2.1480 -  2.0867  1254   144  0.90  16.32   1.01     1.00       4240.74|
| 13:  2.0867 -  2.0319  1287   141  0.90  16.36   1.00     0.97       3379.50|
| 14:  2.0319 -  1.9825   691    78  0.92  13.47   0.99     0.96       2493.02|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2493.02 max =        10662.79 mean =      6655.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.47|
|phase err.(test): min =        0.00 max =           88.24 mean =        13.88|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.15    87.15   15.62    None  None   None       |
|    all(noH): 2823   0      3.15    87.15   15.62    None  None   None       |
|    Sol.    : 438    0      4.34    82.69   39.69    None  None   None       |
|    Mac.    : 2385   0      3.15    87.15   11.21    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:     3.147 -  11.548: 1657   |   5:    45.150 -  53.551:   81        |
|      1:    11.548 -  19.948:  583   |   6:    53.551 -  61.951:   68        |
|      2:    19.948 -  28.349:  159   |   7:    61.951 -  70.352:   34        |
|      3:    28.349 -  36.750:  111   |   8:    70.352 -  78.753:   19        |
|      4:    36.750 -  45.150:  106   |   9:    78.753 -  87.153:    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)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.215 - 4.828
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 317
   mapped sites are within: 0.708 - 4.828

peak=   11.211 closest distance to " CB  VAL A 230 " =    1.462
peak=    8.932 closest distance to " CG2 VAL A 296 " =    1.375
peak=    5.984 closest distance to " CD2 LEU A   5 " =    1.180
peak=    5.895 closest distance to " CG  LEU A   5 " =    1.172
peak=    5.839 closest distance to " NH2 ARG A  56 " =    2.125
peak=    5.819 closest distance to " NE2 GLN A  11 " =    1.156
peak=    5.553 closest distance to " CG  PRO A  54 " =    1.363
peak=    5.515 closest distance to " O   HOH Z 142 " =    2.094
peak=    5.343 closest distance to " O   HOH Z   9 " =    1.813
peak=    5.318 closest distance to " CG  LEU A 228 " =    1.151
peak=    5.239 closest distance to " O   HOH Z 232 " =    2.328
peak=    5.100 closest distance to " CB  GLN A 223 " =    1.449
peak=    4.909 closest distance to " CB  GLN A 183 " =    1.252
peak=    4.900 closest distance to " O   HOH Z 427 " =    2.759
peak=    4.759 closest distance to " CB  PRO A  54 " =    0.980
peak=    4.657 closest distance to " CB  ASN A 148 " =    1.384
peak=    4.635 closest distance to " O   HOH Z 425 " =    1.476
peak=    4.502 closest distance to " CB  ASN A 142 " =    1.083
peak=    4.432 closest distance to " CB  ARG A 275 " =    0.972
peak=    4.426 closest distance to " CD1AILE A 234 " =    0.961
peak=    4.424 closest distance to " CB  ARG A  79 " =    1.483
peak=    4.410 closest distance to " O   HOH Z 265 " =    2.131
peak=    4.395 closest distance to " CG  PRO A 198 " =    1.209
peak=    4.370 closest distance to " ND2 ASN A 187 " =    1.639
peak=    4.348 closest distance to " CG  PRO A 213 " =    1.213
peak=    4.342 closest distance to " O   HOH Z 287 " =    1.990
peak=    4.312 closest distance to " CB  VAL A 265 " =    1.364
peak=    4.311 closest distance to " O   HOH Z 126 " =    2.093
peak=    4.302 closest distance to " O   HOH Z 346 " =    1.548
peak=    4.299 closest distance to " O   HOH Z  78 " =    1.655
peak=    4.295 closest distance to " CB  VAL A 230 " =    1.192
peak=    4.283 closest distance to " O   HOH Z 369 " =    2.199
peak=    4.270 closest distance to " CB  SER A  63 " =    1.286
peak=    4.270 closest distance to " CB BVAL A  41 " =    1.235
peak=    4.268 closest distance to " CB  TRP A 266 " =    1.099
peak=    4.233 closest distance to " O   SER A  87 " =    2.376
peak=    4.175 closest distance to " CG  LEU A 167 " =    1.250
peak=    4.171 closest distance to " O   HOH Z 303 " =    2.114
peak=    4.169 closest distance to " O   HOH Z 209 " =    2.337
peak=    4.162 closest distance to " NH2AARG A 190 " =    1.913
peak=    4.155 closest distance to " O   HOH Z 298 " =    1.723
peak=    4.128 closest distance to " CB  ARG A 190 " =    1.501
peak=    4.071 closest distance to " CG  PRO A 243 " =    1.142
peak=    4.062 closest distance to " CB  SER A   3 " =    1.333
peak=    4.059 closest distance to " O   PRO A 198 " =    1.565
peak=    4.032 closest distance to " O   HOH Z  61 " =    1.654
peak=    3.994 closest distance to " O   HOH Z 214 " =    2.265
peak=    3.978 closest distance to " O   HOH Z 188 " =    2.988
peak=    3.969 closest distance to " CB  ASN A  39 " =    0.966
peak=    3.968 closest distance to " O   HOH Z 422 " =    2.608
peak=    3.967 closest distance to " O   HOH Z 248 " =    1.445
peak=    3.963 closest distance to " CZ  PHE A 218 " =    1.122
peak=    3.949 closest distance to " O   HOH Z 411 " =    3.664
peak=    3.936 closest distance to " CB  GLU A 277 " =    3.595
peak=    3.929 closest distance to " CB  LYS A 117 " =    1.240
peak=    3.929 closest distance to " O   HOH Z 234 " =    3.687
peak=    3.918 closest distance to " CD  ARG A  66 " =    2.753
peak=    3.916 closest distance to " CG2 VAL A 257 " =    0.885
peak=    3.907 closest distance to " OG ASER A 258 " =    3.075
peak=    3.898 closest distance to " CA  TYR A  30 " =    0.997
peak=    3.887 closest distance to " CE  LYS A  76 " =    0.855
peak=    3.886 closest distance to " O   HOH Z  43 " =    1.910
peak=    3.880 closest distance to " CA  ALA A  51 " =    1.009
peak=    3.871 closest distance to " O   HOH Z 368 " =    2.111
peak=    3.869 closest distance to " O   HOH Z 353 " =    2.587
peak=    3.852 closest distance to " NH1 ARG A 138 " =    1.050
peak=    3.851 closest distance to " N   PHE A 130 " =    1.283
peak=    3.844 closest distance to " O   HOH Z 130 " =    1.038
peak=    3.826 closest distance to " CD2 LEU A 228 " =    1.133
peak=    3.823 closest distance to " CB  VAL A 202 " =    1.681
peak=    3.807 closest distance to " O   HOH Z 272 " =    1.792
peak=    3.787 closest distance to " OD1 ASN A  69 " =    2.525
peak=    3.786 closest distance to " O   HOH Z   1 " =    1.776
peak=    3.783 closest distance to " O   HOH Z   2 " =    1.530
peak=    3.778 closest distance to " O   HOH Z  78 " =    1.886
peak=    3.775 closest distance to " CB  GLN A  88 " =    1.261
peak=    3.775 closest distance to " CH2 TRP A 266 " =    1.126
peak=    3.761 closest distance to " CB  ARG A  79 " =    0.904
peak=    3.755 closest distance to " NZ  LYS A 117 " =    3.060
peak=    3.744 closest distance to " CB  SER A 216 " =    0.831
peak=    3.741 closest distance to " CD1 ILE A  33 " =    1.786
peak=    3.740 closest distance to " O   HOH Z   3 " =    2.004
peak=    3.738 closest distance to " CB  GLU A 152 " =    1.229
peak=    3.735 closest distance to " O   HOH Z 380 " =    1.751
peak=    3.732 closest distance to " O   HOH Z  10 " =    1.743
peak=    3.731 closest distance to " CB  TRP A 179 " =    1.441
peak=    3.725 closest distance to " OG BSER A 164 " =    2.172
peak=    3.713 closest distance to " CD  ARG A 159 " =    0.708
peak=    3.700 closest distance to " CB  ASP A 124 " =    0.775
peak=    3.696 closest distance to " O   HOH Z 251 " =    1.570
peak=    3.695 closest distance to " CD2 TRP A 179 " =    1.274
peak=    3.690 closest distance to " NH1AARG A 145 " =    1.178
peak=    3.675 closest distance to " OE2 GLU A   2 " =    1.921
peak=    3.662 closest distance to " CB  GLU A 128 " =    1.061
peak=    3.657 closest distance to " CA  SER A  87 " =    1.012
peak=    3.645 closest distance to " O   HOH Z 158 " =    3.196
peak=    3.644 closest distance to " O   HOH Z  30 " =    1.511
peak=    3.642 closest distance to " O   HOH Z 126 " =    1.730
peak=    3.638 closest distance to " CB  GLN A  89 " =    1.253
peak=    3.637 closest distance to " CA  VAL A 296 " =    1.070
peak=    3.636 closest distance to " O   HOH Z 193 " =    1.796
peak=    3.635 closest distance to " O   HOH Z 359 " =    1.394
peak=    3.633 closest distance to " O   HOH Z  59 " =    1.746
peak=    3.632 closest distance to " CB  SER A 212 " =    1.293
peak=    3.630 closest distance to " CG2AVAL A  72 " =    1.633
peak=    3.628 closest distance to " O   HOH Z 261 " =    1.864
peak=    3.627 closest distance to " CG BARG A 102 " =    1.867
peak=    3.615 closest distance to " CA  LYS A 117 " =    1.202
peak=    3.610 closest distance to " ND2 ASN A 249 " =    0.856
peak=    3.596 closest distance to " CD  ARG A 269 " =    1.012
peak=    3.575 closest distance to " O   HOH Z 180 " =    2.116
peak=    3.575 closest distance to " O   HOH Z 193 " =    1.687
peak=    3.570 closest distance to " O   HOH Z 290 " =    1.076
peak=    3.568 closest distance to " O   HOH Z  92 " =    2.453
peak=    3.561 closest distance to " CG2 ILE A  20 " =    1.527
peak=    3.556 closest distance to " CG  GLN A  88 " =    1.089
peak=    3.549 closest distance to " O  BHOH Z 338 " =    2.429
peak=    3.546 closest distance to " O   HOH Z 406 " =    1.492
peak=    3.546 closest distance to " CB  ASN A 110 " =    1.102
peak=    3.537 closest distance to " CA  PHE A 283 " =    1.175
peak=    3.534 closest distance to " O   HOH Z 368 " =    3.556
peak=    3.529 closest distance to " CB  HIS A 108 " =    0.847
peak=    3.526 closest distance to " O   HOH Z  88 " =    3.121
peak=    3.526 closest distance to " CG AARG A 275 " =    1.162
peak=    3.522 closest distance to " O   HOH Z 133 " =    2.668
peak=    3.517 closest distance to " O   HOH Z 238 " =    2.322
peak=    3.516 closest distance to " O   HOH Z 371 " =    2.810
peak=    3.515 closest distance to " CG2 ILE A 234 " =    0.963
peak=    3.512 closest distance to " O   HOH Z 423 " =    1.485
peak=    3.510 closest distance to " CB  PRO A  90 " =    1.151
peak=    3.506 closest distance to " O   HOH Z  97 " =    2.127
peak=    3.504 closest distance to " CE3 TRP A 150 " =    1.004
peak=    3.503 closest distance to " O   HOH Z   7 " =    1.243
peak=    3.502 closest distance to " O   HOH Z  40 " =    1.624
peak=    3.502 closest distance to " O   HOH Z 261 " =    1.576
peak=    3.492 closest distance to " O   HOH Z 403 " =    1.553
peak=    3.490 closest distance to " OE2 GLU A  53 " =    2.009
peak=    3.488 closest distance to " CB  ASP A 140 " =    0.945
peak=    3.488 closest distance to " N   ASN A  39 " =    1.234
peak=    3.487 closest distance to " O   HOH Z 126 " =    1.560
peak=    3.484 closest distance to " CD  LYS A 166 " =    1.333
peak=    3.484 closest distance to " CA  ARG A  36 " =    1.075
peak=    3.480 closest distance to " CB  LEU A 228 " =    1.260
peak=    3.475 closest distance to " CG1 ILE A 151 " =    1.164
peak=    3.469 closest distance to " O   HOH Z 303 " =    2.672
peak=    3.467 closest distance to " CA  ASN A 215 " =    1.106
peak=    3.466 closest distance to " O   HOH Z 366 " =    2.931
peak=    3.464 closest distance to " CB  ASN A 215 " =    1.224
peak=    3.462 closest distance to " N   ALA A 256 " =    1.026
peak=    3.459 closest distance to " O   HOH Z 352 " =    1.808
peak=    3.457 closest distance to " O   HOH Z 128 " =    2.125
peak=    3.455 closest distance to " CG1 VAL A 153 " =    0.961
peak=    3.453 closest distance to " O   PHE A 192 " =    1.386
peak=    3.452 closest distance to " CG1 ILE A  49 " =    1.490
peak=    3.449 closest distance to " CA  ARG A 195 " =    1.186
peak=    3.445 closest distance to " CB  ASN A 187 " =    1.110
peak=    3.445 closest distance to " O   HOH Z 280 " =    3.030
peak=    3.443 closest distance to " O   HOH Z  21 " =    1.759
peak=    3.439 closest distance to " O   HOH Z 419 " =    1.956
peak=    3.435 closest distance to " CB  THR A 157 " =    1.201
peak=    3.432 closest distance to " O   HOH Z 437 " =    1.682
peak=    3.431 closest distance to " O   HOH Z 193 " =    1.747
peak=    3.431 closest distance to " CE1 TYR A 186 " =    1.272
peak=    3.425 closest distance to " O   HOH Z 130 " =    1.975
peak=    3.423 closest distance to " O   HOH Z 392 " =    3.219
peak=    3.422 closest distance to " CG  MET A 185 " =    1.253
peak=    3.421 closest distance to " N   SER A 135 " =    1.334
peak=    3.420 closest distance to " O   HOH Z 421 " =    2.178
peak=    3.418 closest distance to " O   HOH Z 273 " =    2.968
peak=    3.417 closest distance to " O   HOH Z  97 " =    2.501
peak=    3.416 closest distance to " O   HOH Z 260 " =    1.515
peak=    3.414 closest distance to " CB  ALA A   9 " =    1.570
peak=    3.410 closest distance to " NE2 GLN A  73 " =    3.992
peak=    3.409 closest distance to " O   HOH Z  88 " =    3.403
peak=    3.407 closest distance to " ND1 HIS A  86 " =    1.711
peak=    3.405 closest distance to " CA  LYS A 290 " =    1.240
peak=    3.403 closest distance to " N   ASP A 162 " =    1.153
peak=    3.402 closest distance to " CB  SER A  26 " =    1.687
peak=    3.399 closest distance to " C   ALA A 299 " =    0.969
peak=    3.395 closest distance to " O   ASP A 124 " =    1.123
peak=    3.390 closest distance to " CA  THR A 264 " =    0.815
peak=    3.387 closest distance to " CG2 THR A 221 " =    1.118
peak=    3.383 closest distance to " CA  ALA A 158 " =    1.329
peak=    3.382 closest distance to " O   HOH Z 172 " =    3.214
peak=    3.382 closest distance to " CG2 ILE A 120 " =    1.278
peak=    3.381 closest distance to " CA  ALA A  21 " =    1.175
peak=    3.376 closest distance to " NZ  LYS A  48 " =    1.287
peak=    3.375 closest distance to " CB  VAL A 250 " =    1.099
peak=    3.373 closest distance to " O   HOH Z 435 " =    2.051
peak=    3.373 closest distance to " O   HOH Z 299 " =    4.188
peak=    3.372 closest distance to " N   ASN A 127 " =    1.282
peak=    3.364 closest distance to " O   HOH Z 148 " =    3.551
peak=    3.364 closest distance to " O   HOH Z 285 " =    2.346
peak=    3.361 closest distance to " CB  GLU A  46 " =    0.948
peak=    3.360 closest distance to " O   HOH Z 222 " =    2.353
peak=    3.346 closest distance to " CG  LEU A 281 " =    1.024
peak=    3.346 closest distance to " CA  ASN A 217 " =    1.203
peak=    3.342 closest distance to " O   HOH Z 425 " =    2.114
peak=    3.341 closest distance to " O   HOH Z 196 " =    1.346
peak=    3.339 closest distance to " CG  MET A 185 " =    0.999
peak=    3.338 closest distance to " CB  ALA A 104 " =    0.710
peak=    3.336 closest distance to " CD1 LEU A  96 " =    0.758
peak=    3.333 closest distance to " CA  ALA A 291 " =    0.827
peak=    3.332 closest distance to " CA  VAL A 125 " =    1.182
peak=    3.327 closest distance to " O   HOH Z   1 " =    1.718
peak=    3.327 closest distance to " O   PRO A 198 " =    1.230
peak=    3.320 closest distance to " NE2 HIS A 207 " =    1.236
peak=    3.319 closest distance to " CB  SER A  62 " =    1.068
peak=    3.316 closest distance to " O   HOH Z 175 " =    2.107
peak=    3.314 closest distance to " CB  SER A 273 " =    0.890
peak=    3.313 closest distance to " CA  LEU A 282 " =    1.140
peak=    3.312 closest distance to " O   HOH Z 405 " =    1.160
peak=    3.311 closest distance to " CB  MET A  40 " =    0.820
peak=    3.308 closest distance to " O   HOH Z  68 " =    2.209
peak=    3.308 closest distance to " NH2AARG A 145 " =    1.142
peak=    3.305 closest distance to " CB  THR A  31 " =    1.647
peak=    3.304 closest distance to " CB  LEU A 143 " =    1.191
peak=    3.304 closest distance to " CD2 LEU A 255 " =    1.607
peak=    3.300 closest distance to " OG BSER A 212 " =    2.848
peak=    3.299 closest distance to " O   HOH Z 305 " =    3.432
peak=    3.298 closest distance to " CD2 TYR A 186 " =    1.076
peak=    3.295 closest distance to " CB  ALA A 114 " =    1.454
peak=    3.293 closest distance to " O   HOH Z 329 " =    4.125
peak=    3.290 closest distance to " CB  THR A  82 " =    1.310
peak=    3.284 closest distance to " CA  GLY A 267 " =    0.928
peak=    3.282 closest distance to " CG2 VAL A 197 " =    1.082
peak=    3.278 closest distance to " CA  TYR A  30 " =    1.071
peak=    3.271 closest distance to " CG  LYS A 119 " =    1.154
peak=    3.265 closest distance to " O   HOH Z 325 " =    2.218
peak=    3.265 closest distance to " O   PRO A  90 " =    1.604
peak=    3.263 closest distance to " CD1 LEU A 228 " =    2.004
peak=    3.260 closest distance to " CG  ARG A 138 " =    1.281
peak=    3.259 closest distance to " CA  ASN A 127 " =    1.059
peak=    3.258 closest distance to " O   HOH Z 327 " =    1.930
peak=    3.255 closest distance to " CA  ASP A 162 " =    0.983
peak=    3.254 closest distance to " CD  GLN A 240 " =    1.576
peak=    3.252 closest distance to " OG  SER A  62 " =    2.939
peak=    3.251 closest distance to " O   HOH Z  61 " =    1.560
peak=    3.245 closest distance to " O   HOH Z  40 " =    1.890
peak=    3.244 closest distance to " CB  THR A 235 " =    1.253
peak=    3.240 closest distance to " O   HOH Z 116 " =    3.008
peak=    3.240 closest distance to " OG  SER A  62 " =    2.744
peak=    3.238 closest distance to " CA  ALA A 129 " =    1.438
peak=    3.234 closest distance to " CA  MET A 105 " =    0.969
peak=    3.231 closest distance to " CG  MET A 113 " =    1.208
peak=    3.229 closest distance to " CA  TYR A 116 " =    1.387
peak=    3.229 closest distance to " O   HOH Z 153 " =    3.775
peak=    3.226 closest distance to " CB  PHE A 204 " =    0.975
peak=    3.226 closest distance to " O   HOH Z 423 " =    2.459
peak=    3.225 closest distance to " CB  ALA A 248 " =    1.068
peak=    3.224 closest distance to " O   HOH Z 213 " =    2.013
peak=    3.223 closest distance to " O   HOH Z 409 " =    2.989
peak=    3.219 closest distance to " CD  LYS A  76 " =    1.817
peak=    3.219 closest distance to " CD  ARG A 195 " =    3.508
peak=    3.218 closest distance to " O   ALA A 158 " =    1.437
peak=    3.217 closest distance to " NE2 GLN A  73 " =    1.402
peak=    3.217 closest distance to " CG2 ILE A 239 " =    0.718
peak=    3.214 closest distance to " OG BSER A  99 " =    2.162
peak=    3.211 closest distance to " O   ASN A  74 " =    1.494
peak=    3.209 closest distance to " O   HOH Z 171 " =    4.174
peak=    3.207 closest distance to " O   HOH Z 109 " =    2.560
peak=    3.201 closest distance to " O   THR A 182 " =    1.418
peak=    3.198 closest distance to " CE  LYS A  48 " =    1.126
peak=    3.198 closest distance to " NH2AARG A 275 " =    3.464
peak=    3.195 closest distance to " CB  SER A 210 " =    0.802
peak=    3.191 closest distance to " O   HOH Z   4 " =    1.481
peak=    3.190 closest distance to " O   HOH Z 145 " =    1.912
peak=    3.188 closest distance to " O   HOH Z 263 " =    1.704
peak=    3.188 closest distance to " CA  ALA A 154 " =    1.056
peak=    3.186 closest distance to " CG  GLU A  37 " =    0.896
peak=    3.184 closest distance to " CZ3 TRP A  92 " =    1.278
peak=    3.183 closest distance to " CA  ILE A 234 " =    0.952
peak=    3.180 closest distance to " O   HOH Z 424 " =    2.480
peak=    3.178 closest distance to " O   HOH Z 389 " =    1.754
peak=    3.177 closest distance to " CG1 ILE A  33 " =    1.267
peak=    3.176 closest distance to " CB  VAL A 268 " =    0.841
peak=    3.173 closest distance to " CD2 LEU A 297 " =    0.916
peak=    3.170 closest distance to " O   MET A 105 " =    1.845
peak=    3.164 closest distance to " O   HOH Z 132 " =    2.499
peak=    3.160 closest distance to " O   HOH Z 147 " =    1.703
peak=    3.153 closest distance to " CD1 LEU A 300 " =    1.122
peak=    3.151 closest distance to " NH2BARG A 145 " =    2.034
peak=    3.149 closest distance to " O   HOH Z 389 " =    1.203
peak=    3.147 closest distance to " O   HOH Z 371 " =    3.304
peak=    3.144 closest distance to " OG1 THR A 264 " =    0.731
peak=    3.141 closest distance to " O   HOH Z 371 " =    1.581
peak=    3.138 closest distance to " OG1 THR A 279 " =    1.376
peak=    3.130 closest distance to " CB  TRP A 150 " =    1.359
peak=    3.129 closest distance to " O   HOH Z 130 " =    2.473
peak=    3.127 closest distance to " CA  VAL A  41 " =    0.786
peak=    3.125 closest distance to " CA  ARG A 102 " =    1.147
peak=    3.124 closest distance to " O   HOH Z 162 " =    3.685
peak=    3.122 closest distance to " CB  ALA A   1 " =    4.828
peak=    3.118 closest distance to " CB  LEU A 300 " =    0.863
peak=    3.115 closest distance to " CB  TYR A 116 " =    0.893
peak=    3.109 closest distance to " OG BSER A 164 " =    2.465
peak=    3.108 closest distance to " CB  ALA A 227 " =    1.003
peak=    3.108 closest distance to " O   HOH Z 128 " =    2.138
peak=    3.104 closest distance to " CD BLYS A 290 " =    1.125
peak=    3.098 closest distance to " O   HOH Z 233 " =    1.572
peak=    3.098 closest distance to " O   HOH Z  85 " =    2.088
peak=    3.096 closest distance to " O   HOH Z 148 " =    2.359
peak=    3.085 closest distance to " C   VAL A 153 " =    1.130
peak=    3.083 closest distance to " CG  ARG A 159 " =    0.927
peak=    3.080 closest distance to " CD1 ILE A 106 " =    0.874
peak=    3.069 closest distance to " CB  ASN A 173 " =    1.082
peak=    3.060 closest distance to " O   HOH Z 187 " =    2.233
peak=    3.057 closest distance to " CB  ARG A 139 " =    0.951
peak=    3.055 closest distance to " O   HOH Z 124 " =    2.204
peak=    3.054 closest distance to " O   HOH Z 154 " =    2.253
peak=    3.048 closest distance to " CB  GLN A 205 " =    1.101
peak=    3.022 closest distance to " O   HOH Z 412 " =    4.196
peak=    3.013 closest distance to " CB  ILE A  20 " =    1.354
peak=    2.964 closest distance to " O   HOH Z 238 " =    3.071

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.738 - 5.508
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 209
   mapped sites are within: 0.738 - 5.508

peak=   -4.828 closest distance to " CG2 VAL A 230 " =    0.738
peak=   -4.450 closest distance to " OG BSER A 134 " =    1.249
peak=   -4.355 closest distance to " CD  ARG A  14 " =    3.235
peak=   -4.347 closest distance to " CD  ARG A 156 " =    2.055
peak=   -4.272 closest distance to " O   HOH Z 266 " =    5.508
peak=   -4.185 closest distance to " CB  PRO A 243 " =    2.687
peak=   -4.172 closest distance to " O   VAL A  67 " =    2.545
peak=   -4.145 closest distance to " CB  PHE A 192 " =    1.900
peak=   -4.140 closest distance to " CZ2 TRP A  92 " =    2.877
peak=   -4.139 closest distance to " O   HOH Z 231 " =    1.968
peak=   -4.080 closest distance to " CG2 VAL A 202 " =    2.728
peak=   -4.061 closest distance to " CD  GLN A  58 " =    1.042
peak=   -3.989 closest distance to " N   ALA A  43 " =    2.580
peak=   -3.983 closest distance to " O   HOH Z 185 " =    2.314
peak=   -3.981 closest distance to " O   HOH Z 211 " =    1.179
peak=   -3.955 closest distance to " CD  GLN A 223 " =    2.234
peak=   -3.855 closest distance to " CB  ALA A  43 " =    2.628
peak=   -3.851 closest distance to " C   HIS A 108 " =    1.219
peak=   -3.803 closest distance to " O   HOH Z 351 " =    1.500
peak=   -3.788 closest distance to " O   HOH Z 394 " =    1.533
peak=   -3.780 closest distance to " CE2 TYR A  30 " =    2.699
peak=   -3.773 closest distance to " CG2 VAL A 296 " =    1.558
peak=   -3.769 closest distance to " CD1 LEU A 255 " =    2.828
peak=   -3.747 closest distance to " CB  ALA A 161 " =    2.549
peak=   -3.730 closest distance to " CE BMET A  47 " =    1.282
peak=   -3.729 closest distance to " O   HOH Z  44 " =    2.336
peak=   -3.721 closest distance to " CA  GLY A 241 " =    2.318
peak=   -3.717 closest distance to " O   HOH Z 166 " =    2.094
peak=   -3.716 closest distance to " CB  ALA A 248 " =    2.074
peak=   -3.709 closest distance to " N   THR A 157 " =    1.446
peak=   -3.673 closest distance to " O   HOH Z  73 " =    2.247
peak=   -3.670 closest distance to " O   HOH Z 359 " =    3.106
peak=   -3.661 closest distance to " O   HOH Z 290 " =    1.184
peak=   -3.656 closest distance to " O   HOH Z 166 " =    2.125
peak=   -3.639 closest distance to " OG  SER A  97 " =    2.257
peak=   -3.638 closest distance to " O   PRO A 198 " =    1.185
peak=   -3.636 closest distance to " O   HOH Z 102 " =    1.542
peak=   -3.619 closest distance to " CG1 VAL A 112 " =    2.886
peak=   -3.617 closest distance to " O   PRO A 163 " =    2.003
peak=   -3.615 closest distance to " CB  ALA A 248 " =    2.358
peak=   -3.615 closest distance to " ND2 ASN A  45 " =    1.308
peak=   -3.609 closest distance to " NH2 ARG A  79 " =    2.070
peak=   -3.600 closest distance to " CD  PRO A 213 " =    2.057
peak=   -3.597 closest distance to " CD2 LEU A 237 " =    2.793
peak=   -3.595 closest distance to " O   HOH Z 131 " =    4.051
peak=   -3.593 closest distance to " CZ3 TRP A 179 " =    1.230
peak=   -3.593 closest distance to " ND2 ASN A  45 " =    1.994
peak=   -3.591 closest distance to " C   MET A 188 " =    1.462
peak=   -3.590 closest distance to " O   HOH Z  52 " =    1.496
peak=   -3.587 closest distance to " OG  SER A  87 " =    1.372
peak=   -3.585 closest distance to " O   HOH Z 350 " =    1.791
peak=   -3.584 closest distance to " O   HOH Z 191 " =    5.482
peak=   -3.578 closest distance to " CG1 VAL A 112 " =    2.620
peak=   -3.571 closest distance to " N   THR A  52 " =    1.721
peak=   -3.569 closest distance to " CB  VAL A 230 " =    1.146
peak=   -3.559 closest distance to " CG2 VAL A 296 " =    1.094
peak=   -3.557 closest distance to " O   HOH Z  11 " =    1.826
peak=   -3.555 closest distance to " ND2 ASN A 249 " =    2.484
peak=   -3.542 closest distance to " CA  ASP A 298 " =    1.077
peak=   -3.541 closest distance to " CE3 TRP A 150 " =    2.187
peak=   -3.526 closest distance to " CD1 LEU A 101 " =    2.326
peak=   -3.526 closest distance to " O   HOH Z 357 " =    2.015
peak=   -3.521 closest distance to " O   VAL A 189 " =    2.543
peak=   -3.519 closest distance to " CA  GLY A 203 " =    2.467
peak=   -3.513 closest distance to " CB  PRO A 280 " =    2.156
peak=   -3.512 closest distance to " CD2 LEU A   5 " =    1.124
peak=   -3.508 closest distance to " O   HOH Z 140 " =    1.624
peak=   -3.507 closest distance to " O   HOH Z 111 " =    1.641
peak=   -3.505 closest distance to " CA  ASN A 127 " =    1.094
peak=   -3.502 closest distance to " OH  TYR A 172 " =    1.755
peak=   -3.502 closest distance to " CA  VAL A  67 " =    2.902
peak=   -3.498 closest distance to " OXT GLY A 302 " =    3.024
peak=   -3.480 closest distance to " CE  MET A 105 " =    2.384
peak=   -3.472 closest distance to " N   ALA A 248 " =    1.550
peak=   -3.469 closest distance to " O   HOH Z  43 " =    1.802
peak=   -3.465 closest distance to " OG  SER A  62 " =    4.358
peak=   -3.458 closest distance to " ND2 ASN A 187 " =    1.538
peak=   -3.458 closest distance to " CZ2 TRP A 274 " =    0.943
peak=   -3.457 closest distance to " O   SER A  22 " =    2.358
peak=   -3.451 closest distance to " CD2 TYR A 293 " =    1.941
peak=   -3.447 closest distance to " CE2 PHE A 218 " =    2.499
peak=   -3.446 closest distance to " OE1 GLN A  88 " =    0.977
peak=   -3.444 closest distance to " CG  TRP A 266 " =    1.888
peak=   -3.441 closest distance to " O   GLY A  80 " =    2.500
peak=   -3.439 closest distance to " CB  ALA A 114 " =    2.511
peak=   -3.438 closest distance to " ND2 ASN A 252 " =    1.927
peak=   -3.437 closest distance to " N   ALA A 226 " =    2.081
peak=   -3.433 closest distance to " O   HOH Z 389 " =    1.431
peak=   -3.428 closest distance to " O   GLY A 203 " =    2.463
peak=   -3.422 closest distance to " O   HOH Z 114 " =    2.932
peak=   -3.417 closest distance to " O   HOH Z 286 " =    1.687
peak=   -3.415 closest distance to " O   HOH Z 281 " =    2.666
peak=   -3.409 closest distance to " O   HOH Z 103 " =    1.763
peak=   -3.408 closest distance to " O   ARG A 145 " =    1.442
peak=   -3.406 closest distance to " O   HOH Z  51 " =    1.018
peak=   -3.396 closest distance to " O   HOH Z 389 " =    2.151
peak=   -3.396 closest distance to " CD2 HIS A 207 " =    2.270
peak=   -3.391 closest distance to " O   HOH Z 198 " =    1.948
peak=   -3.389 closest distance to " CB  PRO A 163 " =    2.418
peak=   -3.385 closest distance to " NH2AARG A 275 " =    5.200
peak=   -3.381 closest distance to " NE2 GLN A 278 " =    1.817
peak=   -3.373 closest distance to " O   HOH Z  65 " =    1.228
peak=   -3.372 closest distance to " CA  ASP A  27 " =    2.423
peak=   -3.369 closest distance to " CD1 ILE A 199 " =    2.481
peak=   -3.366 closest distance to " O   HOH Z 147 " =    2.023
peak=   -3.362 closest distance to " CG2 ILE A 151 " =    2.574
peak=   -3.362 closest distance to " O   SER A 135 " =    1.402
peak=   -3.360 closest distance to " OD1 ASN A 187 " =    1.603
peak=   -3.358 closest distance to " CB  TYR A  15 " =    2.194
peak=   -3.358 closest distance to " O   GLY A  17 " =    1.151
peak=   -3.349 closest distance to " C   LEU A 222 " =    0.834
peak=   -3.347 closest distance to " O   HOH Z 295 " =    1.590
peak=   -3.340 closest distance to " O   HOH Z 359 " =    1.605
peak=   -3.335 closest distance to " O   HOH Z 318 " =    2.086
peak=   -3.335 closest distance to " O   HOH Z 313 " =    1.596
peak=   -3.333 closest distance to " CZ  PHE A 192 " =    2.815
peak=   -3.330 closest distance to " O   HOH Z 243 " =    1.968
peak=   -3.325 closest distance to " CB  ALA A  10 " =    2.326
peak=   -3.322 closest distance to " CG1 VAL A 125 " =    2.000
peak=   -3.318 closest distance to " O   ASP A  27 " =    1.937
peak=   -3.313 closest distance to " O   HOH Z 189 " =    2.131
peak=   -3.312 closest distance to " CG1 VAL A 250 " =    2.749
peak=   -3.309 closest distance to " N   SER A 276 " =    1.377
peak=   -3.304 closest distance to " O   PHE A 218 " =    1.605
peak=   -3.298 closest distance to " OE2 GLU A 152 " =    1.239
peak=   -3.296 closest distance to " C   LEU A 143 " =    1.079
peak=   -3.293 closest distance to " O   SER A 271 " =    2.164
peak=   -3.290 closest distance to " O   HOH Z 138 " =    1.345
peak=   -3.288 closest distance to " CB  PRO A 213 " =    2.197
peak=   -3.288 closest distance to " CE2 TRP A  70 " =    2.200
peak=   -3.279 closest distance to " O   HOH Z  38 " =    1.946
peak=   -3.279 closest distance to " CE  LYS A  76 " =    2.619
peak=   -3.273 closest distance to " NE2 GLN A 278 " =    1.842
peak=   -3.272 closest distance to " CD1 LEU A 228 " =    2.279
peak=   -3.269 closest distance to " CB  ALA A 291 " =    2.207
peak=   -3.267 closest distance to " O   HOH Z 231 " =    1.328
peak=   -3.262 closest distance to " O   HOH Z 134 " =    4.002
peak=   -3.262 closest distance to " O   HOH Z 371 " =    2.300
peak=   -3.260 closest distance to " O   ALA A  10 " =    1.754
peak=   -3.256 closest distance to " O   HOH Z 412 " =    4.243
peak=   -3.253 closest distance to " O   HOH Z 285 " =    2.136
peak=   -3.251 closest distance to " O   HOH Z 345 " =    2.106
peak=   -3.250 closest distance to " O   SER A 210 " =    1.866
peak=   -3.249 closest distance to " O   HOH Z 165 " =    2.114
peak=   -3.243 closest distance to " CG  ASP A 231 " =    0.810
peak=   -3.234 closest distance to " CD2 TYR A 247 " =    2.517
peak=   -3.232 closest distance to " OH  TYR A 214 " =    1.230
peak=   -3.231 closest distance to " C   ALA A 158 " =    1.334
peak=   -3.226 closest distance to " CG  GLU A 277 " =    1.282
peak=   -3.224 closest distance to " O   HOH Z 253 " =    3.901
peak=   -3.220 closest distance to " CB  ALA A   7 " =    2.200
peak=   -3.217 closest distance to " O   HOH Z 236 " =    1.413
peak=   -3.214 closest distance to " N   HIS A 115 " =    2.176
peak=   -3.213 closest distance to " CD2 PHE A 225 " =    1.132
peak=   -3.213 closest distance to " CA  GLY A 241 " =    3.099
peak=   -3.205 closest distance to " O   HOH Z 216 " =    1.338
peak=   -3.201 closest distance to " CE1 PHE A  59 " =    2.001
peak=   -3.200 closest distance to " CG1 VAL A 197 " =    2.368
peak=   -3.193 closest distance to " CA  SER A 135 " =    1.369
peak=   -3.192 closest distance to " O   HOH Z 111 " =    4.378
peak=   -3.187 closest distance to " O   HOH Z 100 " =    1.141
peak=   -3.187 closest distance to " N   ALA A 248 " =    1.861
peak=   -3.187 closest distance to " O   HOH Z 407 " =    3.007
peak=   -3.182 closest distance to " O   HOH Z 166 " =    1.535
peak=   -3.181 closest distance to " CZ  TYR A 169 " =    1.701
peak=   -3.178 closest distance to " CB  ASP A 132 " =    2.383
peak=   -3.177 closest distance to " O   HOH Z 292 " =    1.566
peak=   -3.177 closest distance to " O   HOH Z 353 " =    2.050
peak=   -3.176 closest distance to " CB  ALA A 291 " =    2.299
peak=   -3.172 closest distance to " CB  ASP A 132 " =    2.294
peak=   -3.171 closest distance to " O   HOH Z 108 " =    1.536
peak=   -3.171 closest distance to " O   GLY A  80 " =    2.537
peak=   -3.167 closest distance to " O   GLN A 240 " =    2.531
peak=   -3.165 closest distance to " CD  LYS A 289 " =    2.408
peak=   -3.162 closest distance to " O   ASN A 301 " =    1.583
peak=   -3.162 closest distance to " O   TRP A  70 " =    1.449
peak=   -3.162 closest distance to " CB  ASN A  39 " =    2.250
peak=   -3.158 closest distance to " O   PRO A 198 " =    1.382
peak=   -3.158 closest distance to " O   HOH Z 252 " =    3.952
peak=   -3.156 closest distance to " CA  GLY A 133 " =    1.952
peak=   -3.154 closest distance to " CD1 ILE A  33 " =    2.524
peak=   -3.150 closest distance to " OD2 ASP A 191 " =    1.326
peak=   -3.150 closest distance to " CG2 VAL A 296 " =    1.955
peak=   -3.146 closest distance to " CG2 ILE A 263 " =    2.329
peak=   -3.142 closest distance to " CB  HIS A  86 " =    1.085
peak=   -3.138 closest distance to " O   MET A  40 " =    2.838
peak=   -3.138 closest distance to " O   HOH Z 193 " =    1.460
peak=   -3.135 closest distance to " CG  PHE A 283 " =    2.639
peak=   -3.134 closest distance to " OH  TYR A 247 " =    1.884
peak=   -3.125 closest distance to " C   ARG A 269 " =    1.447
peak=   -3.125 closest distance to " O   HOH Z  60 " =    2.068
peak=   -3.125 closest distance to " CG  GLN A 103 " =    2.432
peak=   -3.124 closest distance to " NE2 GLN A 194 " =    1.848
peak=   -3.116 closest distance to " ND2BASN A 224 " =    1.664
peak=   -3.113 closest distance to " CB  ASP A 171 " =    2.258
peak=   -3.098 closest distance to " O   HOH Z 250 " =    1.644
peak=   -3.097 closest distance to " CB  GLN A  11 " =    1.859
peak=   -3.097 closest distance to " OG BSER A 134 " =    1.726
peak=   -3.089 closest distance to " NH2 ARG A 219 " =    1.677
peak=   -3.085 closest distance to " O   HOH Z   9 " =    3.084
peak=   -3.085 closest distance to " OD1 ASP A 200 " =    1.651
peak=   -3.064 closest distance to " O   ALA A  51 " =    1.335
peak=   -3.062 closest distance to " CB  TRP A  85 " =    2.541
peak=   -3.060 closest distance to " CD2 PHE A  61 " =    1.981
peak=   -3.056 closest distance to " CD1 PHE A  61 " =    2.966
peak=   -3.044 closest distance to " O   ALA A 227 " =    1.578
peak=   -3.032 closest distance to " O   ARG A  24 " =    1.654
peak=   -3.019 closest distance to " OD1 ASN A 301 " =    1.967
peak=   -3.012 closest distance to " CB  ALA A 244 " =    2.306

================= 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    :  0.4579 0.4398   6.256973e+00   6.228725e+00
   1_bss:  0.4496 0.4268   6.251697e+00   6.216287e+00
   1_xyz:  0.3503 0.3684   6.087930e+00   6.109817e+00
   1_adp:  0.2963 0.3419   5.960167e+00   6.057982e+00
   1_occ:  0.2958 0.3418   5.959201e+00   6.058727e+00
   2_bss:  0.2906 0.3361   5.958398e+00   6.056358e+00
   2_xyz:  0.1932 0.2424   5.601058e+00   5.775069e+00
   2_adp:  0.1706 0.2203   5.491046e+00   5.683567e+00
   2_occ:  0.1706 0.2201   5.490831e+00   5.684090e+00
   3_bss:  0.1693 0.2189   5.491587e+00   5.684615e+00
   3_xyz:  0.1390 0.1833   5.318633e+00   5.528838e+00
   3_adp:  0.1316 0.1792   5.283150e+00   5.507552e+00
   3_occ:  0.1315 0.1792   5.282855e+00   5.507379e+00
   4_bss:  0.1315 0.1792   5.282613e+00   5.506778e+00
   4_xyz:  0.1216 0.1699   5.222738e+00   5.457241e+00
   4_adp:  0.1205 0.1658   5.207715e+00   5.433925e+00
   4_occ:  0.1204 0.1656   5.207260e+00   5.433484e+00
   5_bss:  0.1203 0.1656   5.207222e+00   5.433482e+00
   5_xyz:  0.1146 0.1600   5.168664e+00   5.407363e+00
   5_adp:  0.1139 0.1604   5.167251e+00   5.410231e+00
   5_occ:  0.1138 0.1604   5.166652e+00   5.409933e+00
   5_bss:  0.1137 0.1604   5.166667e+00   5.410016e+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:  0.354  20.000   6.883   8.677  10.445   0.000   0.000   0.000
   1_xyz:  0.354  20.000   6.883   8.677  10.445   0.000   0.000   0.000
   1_adp:  0.354  20.000   6.883   8.677  10.445   0.000   0.000   0.000
   1_occ:  0.354  20.000   6.883   8.677  10.445   0.000   0.000   0.000
   2_bss:  0.341  42.911   3.446   4.457   6.639   0.000   0.000   0.000
   2_xyz:  0.341  42.911   3.446   4.457   6.639   0.000   0.000   0.000
   2_adp:  0.341  42.911   3.446   4.457   6.639   0.000   0.000   0.000
   2_occ:  0.341  42.911   3.446   4.457   6.639   0.000   0.000   0.000
   3_bss:  0.321  50.945   2.368   2.757   4.560   0.000   0.000   0.000
   3_xyz:  0.321  50.945   2.368   2.757   4.560   0.000   0.000   0.000
   3_adp:  0.321  50.945   2.368   2.757   4.560   0.000   0.000   0.000
   3_occ:  0.321  50.945   2.368   2.757   4.560   0.000   0.000   0.000
   4_bss:  0.331  57.468   2.253   2.477   4.278   0.000   0.000   0.000
   4_xyz:  0.331  57.468   2.253   2.477   4.278   0.000   0.000   0.000
   4_adp:  0.331  57.468   2.253   2.477   4.278   0.000   0.000   0.000
   4_occ:  0.331  57.468   2.253   2.477   4.278   0.000   0.000   0.000
   5_bss:  0.332  57.468   2.340   2.464   4.253   0.000   0.000   0.000
   5_xyz:  0.332  57.468   2.340   2.464   4.253   0.000   0.000   0.000
   5_adp:  0.332  57.468   2.340   2.464   4.253   0.000   0.000   0.000
   5_occ:  0.332  57.468   2.340   2.464   4.253   0.000   0.000   0.000
   5_bss:  0.325  55.502  -0.662  -0.562   1.224  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.496 0.5152  0.5884    57408.350
   1_bss:  50.263 0.5164  0.7628    54994.117
   1_xyz:  40.203 0.6391  0.9104    36937.530
   1_adp:  35.634 0.6937  1.0052    30781.785
   1_occ:  35.682 0.6930  1.0031    30801.389
   2_bss:  35.375 0.6964  0.8800    30408.239
   2_xyz:  23.706 0.8243  1.0015    14584.094
   2_adp:  20.857 0.8535  1.0172    11954.765
   2_occ:  20.877 0.8533  1.0170    11949.380
   3_bss:  20.842 0.8538  0.9601    12005.160
   3_xyz:  17.036 0.8894  0.9809     8537.051
   3_adp:  16.531 0.8941  0.9777     8215.591
   3_occ:  16.527 0.8941  0.9778     8211.851
   4_bss:  16.519 0.8942  0.9699     8210.408
   4_xyz:  15.502 0.9026  0.9746     7351.460
   4_adp:  14.940 0.9076  0.9738     7037.555
   4_occ:  14.933 0.9076  0.9739     7031.386
   5_bss:  14.932 0.9077  0.9746     7032.431
   5_xyz:  14.388 0.9120  0.9768     6647.839
   5_adp:  14.417 0.9119  0.9721     6661.215
   5_occ:  14.410 0.9120  0.9719     6656.839
   5_bss:  14.414 0.9120  0.9762     6655.799
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3878e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3878e+01
   1_xyz:   1.605  0.012  0.104 18.049  0.006  4.111   1.2732e-01
   1_adp:   1.605  0.012  0.104 18.049  0.006  4.111   1.2732e-01
   1_occ:   1.605  0.012  0.104 18.049  0.006  4.111   1.2732e-01
   2_bss:   1.605  0.012  0.104 18.049  0.006  4.111   1.2732e-01
   2_xyz:   1.078  0.008  0.081 16.230  0.004  4.125   7.2293e-02
   2_adp:   1.078  0.008  0.081 16.230  0.004  4.125   7.2293e-02
   2_occ:   1.078  0.008  0.081 16.230  0.004  4.125   7.2293e-02
   3_bss:   1.078  0.008  0.081 16.230  0.004  4.125   7.2293e-02
   3_xyz:   0.928  0.006  0.072 15.777  0.003  4.123   5.5358e-02
   3_adp:   0.928  0.006  0.072 15.777  0.003  4.123   5.5358e-02
   3_occ:   0.928  0.006  0.072 15.777  0.003  4.123   5.5358e-02
   4_bss:   0.928  0.006  0.072 15.777  0.003  4.123   5.5358e-02
   4_xyz:   0.935  0.006  0.074 15.606  0.003  4.127   5.5531e-02
   4_adp:   0.935  0.006  0.074 15.606  0.003  4.127   5.5531e-02
   4_occ:   0.935  0.006  0.074 15.606  0.003  4.127   5.5531e-02
   5_bss:   0.935  0.006  0.074 15.606  0.003  4.127   5.5531e-02
   5_xyz:   1.012  0.008  0.081 15.467  0.004  4.111   6.3510e-02
   5_adp:   1.012  0.008  0.081 15.467  0.004  4.111   6.3510e-02
   5_occ:   1.012  0.008  0.081 15.467  0.004  4.111   6.3510e-02
   5_bss:   1.012  0.008  0.081 15.467  0.004  4.111   6.3510e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9852e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9852e+00
   1_xyz:  12.925  0.157  0.392 85.954  0.030  2.156   9.3211e-02
   1_adp:  12.925  0.157  0.392 85.954  0.030  2.156   9.3211e-02
   1_occ:  12.925  0.157  0.392 85.954  0.030  2.156   9.3211e-02
   2_bss:  12.925  0.157  0.392 85.954  0.030  2.156   9.3211e-02
   2_xyz:   6.638  0.086  0.290 85.601  0.039  2.299   6.5773e-02
   2_adp:   6.638  0.086  0.290 85.601  0.039  2.299   6.5773e-02
   2_occ:   6.638  0.086  0.290 85.601  0.039  2.299   6.5773e-02
   3_bss:   6.638  0.086  0.290 85.601  0.039  2.299   6.5773e-02
   3_xyz:   7.010  0.042  0.347 84.970  0.028  2.327   3.9588e-02
   3_adp:   7.010  0.042  0.347 84.970  0.028  2.327   3.9588e-02
   3_occ:   7.010  0.042  0.347 84.970  0.028  2.327   3.9588e-02
   4_bss:   7.010  0.042  0.347 84.970  0.028  2.327   3.9588e-02
   4_xyz:   7.875  0.046  0.350 81.789  0.035  2.383   3.1897e-02
   4_adp:   7.875  0.046  0.350 81.789  0.035  2.383   3.1897e-02
   4_occ:   7.875  0.046  0.350 81.789  0.035  2.383   3.1897e-02
   5_bss:   7.875  0.046  0.350 81.789  0.035  2.383   3.1897e-02
   5_xyz:   6.645  0.046  0.443 83.943  0.038  2.317   4.3978e-02
   5_adp:   6.645  0.046  0.443 83.943  0.038  2.317   4.3978e-02
   5_occ:   6.645  0.046  0.443 83.943  0.038  2.317   4.3978e-02
   5_bss:   6.645  0.046  0.443 83.943  0.038  2.317   4.3978e-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:  69.80   0.00  11.98  58.60   0.00   9.16  69.80   0.00  27.35
   1_occ:  69.80   0.00  11.98  58.60   0.00   9.16  69.80   0.00  27.35
   2_bss:  69.80   0.00  11.98  58.60   0.00   9.16  69.80   0.00  27.35
   2_xyz:  69.80   0.00  11.98  58.60   0.00   9.16  69.80   0.00  27.35
   2_adp:  74.98   0.00  12.01  61.91   0.00   8.20  74.98   0.00  32.72
   2_occ:  74.98   0.00  12.01  61.91   0.00   8.20  74.98   0.00  32.72
   3_bss:  74.98   0.00  12.01  61.91   0.00   8.20  74.98   0.00  32.72
   3_xyz:  74.98   0.00  12.01  61.91   0.00   8.20  74.98   0.00  32.72
   3_adp:  82.17   0.00  12.95  79.23   0.00   8.37  82.17   0.69  37.93
   3_occ:  82.17   0.00  12.95  79.23   0.00   8.37  82.17   0.69  37.93
   4_bss:  82.17   0.00  12.95  79.23   0.00   8.37  82.17   0.69  37.93
   4_xyz:  82.17   0.00  12.95  79.23   0.00   8.37  82.17   0.69  37.93
   4_adp:  81.19   0.00  12.44  81.19   0.00   8.08  79.45   1.42  36.17
   4_occ:  81.19   0.00  12.44  81.19   0.00   8.08  79.45   1.42  36.17
   5_bss:  81.19   0.00  12.44  81.19   0.00   8.08  79.45   1.42  36.17
   5_xyz:  81.19   0.00  12.44  81.19   0.00   8.08  79.45   1.42  36.17
   5_adp:  84.01   0.00  12.48  84.01   0.00   8.06  79.54   1.19  36.54
   5_occ:  84.01   0.00  12.48  84.01   0.00   8.06  79.54   1.19  36.54
   5_bss:  87.15   3.15  15.62  87.15   3.15  11.21  82.69   4.34  39.69
------------------------------------------------------------------------
 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:    1.236    0.011    0.404
   1_adp:    1.236    0.011    0.404
   1_occ:    1.236    0.011    0.404
   2_bss:    1.236    0.011    0.404
   2_xyz:    1.494    0.036    0.548
   2_adp:    1.494    0.036    0.548
   2_occ:    1.494    0.036    0.548
   3_bss:    1.494    0.036    0.548
   3_xyz:    1.587    0.041    0.583
   3_adp:    1.587    0.041    0.583
   3_occ:    1.587    0.041    0.583
   4_bss:    1.587    0.041    0.583
   4_xyz:    1.681    0.056    0.610
   4_adp:    1.681    0.056    0.610
   4_occ:    1.681    0.056    0.610
   5_bss:    1.681    0.056    0.610
   5_xyz:    1.677    0.026    0.618
   5_adp:    1.677    0.026    0.618
   5_occ:    1.677    0.026    0.618
   5_bss:    1.677    0.026    0.618
------------------------------------------------------------------------

CPU time actual refinement: 334.19


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_646/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_646/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_646/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_646/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_646/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.03 
  Macro-tasks:
    bulk solvent and scale       = 41.37  
    individual site refinement   = 136.91 
    weights calculation          = 31.74  
    collect and process          = 6.59   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 216.74 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 102.92 
    alpha_beta                      = 8.12   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.50 
    fmodel                         = 7.11   
    r_factors                      = 0.27   
    phase_errors                   = 10.80  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 245.96 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.689 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    659 calls, 102.62 s
gradients_fft:          604 calls, 100.06 s

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

# Date 2008-01-16 Time 02:04:27 PST -0800 (1200477867.27 s)
Start R-work = 0.4579, R-free = 0.4398 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1777 (no bulk solvent and anisotropic scale)

Start R-work = 0.4496, R-free = 0.4268
Final R-work = 0.1137, R-free = 0.1604