# Date 2008-01-16 Time 02:38:50 PST -0800 (1200479930.24 s)
#phil __OFF__

Command line arguments: "../917.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 = 5714
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 917

-------------------------------------------------------------------------------
  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: (70.9525, 47.1647, 85.9581, 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: 3.29, 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: (70.9525, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.9911
Completeness in resolution range: 0.963125
Completeness with d_max=infinity: 0.960151

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9911

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: (70.9525, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.9911
Completeness in resolution range: 0.963125
Completeness with d_max=infinity: 0.960151

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2605 [2129/2157]  1918   211   9.9%
  bin  2:  4.2605 -  3.3943 [2051/2067]  1844   207  10.1%
  bin  3:  3.3943 -  2.9690 [2021/2040]  1817   204  10.1%
  bin  4:  2.9690 -  2.6992 [2017/2047]  1820   197   9.8%
  bin  5:  2.6992 -  2.5067 [1992/2011]  1792   200  10.0%
  bin  6:  2.5067 -  2.3595 [1981/2006]  1781   200  10.1%
  bin  7:  2.3595 -  2.2417 [1954/1987]  1761   193   9.9%
  bin  8:  2.2417 -  2.1444 [1975/2006]  1779   196   9.9%
  bin  9:  2.1444 -  2.0621 [1983/2025]  1783   200  10.1%
  bin 10:  2.0621 -  1.9911 [1486/1993]  1335   151  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_917/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2189
        3.04 -     3.66: 4636
        3.66 -     4.28: 8988
        4.28 -     4.90: 12311
  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
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.940 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.341 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28130 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_917/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_917/model_refine_001.geo

CPU time processing inputs: 9.08


============================ 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 = 70.9525 47.16465 85.95805 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: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4222   r_free= 0.4072   ksol= 0.00   Bsol= 0.00   scale= 0.825    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.212149                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7519 0.99   1385  154 0.3597 0.3377       6.513      6.4092|
|  2:  4.7519 -  3.7915 0.99   1340  146 0.3138 0.3325      6.6104      6.6662|
|  3:  3.7915 -  3.3180 0.99   1303  147 0.3607 0.3377      6.5302      6.5316|
|  4:  3.3180 -  3.0173 0.99   1305  147 0.3945 0.3538      6.4275      6.3213|
|  5:  3.0173 -  2.8025 0.99   1292  140 0.4407 0.4293      6.2971      6.3315|
|  6:  2.8025 -  2.6382 0.99   1280  148 0.4437 0.4755       6.214      6.2093|
|  7:  2.6382 -  2.5067 0.99   1286  137 0.4728 0.4519      6.2106      6.1518|
|  8:  2.5067 -  2.3980 0.98   1266  147 0.4685 0.4401      6.1305      6.1054|
|  9:  2.3980 -  2.3061 0.98   1275  142 0.4693 0.4710      6.0882      6.0888|
| 10:  2.3061 -  2.2267 0.99   1261  135 0.4760 0.4748      6.0749        6.04|
| 11:  2.2267 -  2.1573 0.99   1270  143 0.4779 0.4418      6.0142      6.0106|
| 12:  2.1573 -  2.0958 0.97   1247  138 0.4826 0.4705      5.9596      5.9941|
| 13:  2.0958 -  2.0408 0.99   1266  139 0.5042 0.5079      5.8767      5.8538|
| 14:  2.0408 -  1.9911 0.66    854   96 0.4908 0.4203      5.8253      5.6751|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7519  1385   154  0.75  30.12   0.82     0.77      54947.48|
|  2:  4.7519 -  3.7915  1340   146  0.79  27.08   0.92     0.83      67413.50|
|  3:  3.7915 -  3.3180  1303   147  0.73  33.12   0.87     0.81      69823.17|
|  4:  3.3180 -  3.0173  1305   147  0.67  37.81   0.84     0.74      63644.31|
|  5:  3.0173 -  2.8025  1292   140  0.57  46.15   0.78     0.65      57869.79|
|  6:  2.8025 -  2.6382  1280   148  0.55  47.79   0.77     0.62      52759.51|
|  7:  2.6382 -  2.5067  1286   137  0.55  48.52   0.76     0.60      48105.36|
|  8:  2.5067 -  2.3980  1266   147  0.53  49.46   0.76     0.61      43575.12|
|  9:  2.3980 -  2.3061  1275   142  0.54  48.89   0.75     0.60      38682.23|
| 10:  2.3061 -  2.2267  1261   135  0.53  49.93   0.79     0.60      36021.10|
| 11:  2.2267 -  2.1573  1270   143  0.51  51.69   0.78     0.57      34118.28|
| 12:  2.1573 -  2.0958  1247   138  0.48  53.78   0.78     0.56      34160.45|
| 13:  2.0958 -  2.0408  1266   139  0.46  55.22   0.75     0.55      29593.71|
| 14:  2.0408 -  1.9911   854    96  0.54  49.39   0.73     0.58      22125.30|
|alpha:            min =        0.55 max =            0.83 mean =         0.65|
|beta:             min =    22125.30 max =        69823.17 mean =     47466.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.97 mean =        44.61|
|phase err.(test): min =        0.00 max =           89.95 mean =        44.56|
|-----------------------------------------------------------------------------|

============================== 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 = 7.422441              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.615   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.553449              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.089   (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:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1498 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2616 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3882 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5033 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6581 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7649 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.015 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.633 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    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: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4304   r_free= 0.4140   ksol= 0.00   Bsol= 0.00   scale= 0.794    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.217980                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4134   r_free= 0.3960   ksol= 0.34   Bsol= 20.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.06,8.55,7.97,0.00,0.00,0.00); trace/3= 8.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.208064                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.030502              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.725   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.570167              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.246   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4134      final r-factor (work) = 0.3000          |
| start r-factor (free) = 0.3960      final r-factor (free) = 0.3296          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.9071 = 7.03 * 0.50 * 6.2277 + 1.00 * 54.0151                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3169 = 7.03 * 0.50 * 6.0312 + 1.00 * 0.1156                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3000      final r-factor (work) = 0.2341          |
| start r-factor (free) = 0.3296      final r-factor (free) = 0.2708          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4536 = 0.57 * 1.00 * 6.0312 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3406 = 0.57 * 1.00 * 5.8398 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    51.22   9.76     None  None   None       |
|    all(noH): 2823   0      0.00    51.22   9.76     None  None   None       |
|    Sol.    : 438    0      0.00    51.22   26.01    None  None   None       |
|    Mac.    : 2385   0      0.00    46.15   6.78     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.122: 1216   |   5:    25.610 -  30.732:  118        |
|      1:     5.122 -  10.244:  760   |   6:    30.732 -  35.854:   83        |
|      2:    10.244 -  15.366:  303   |   7:    35.854 -  40.976:   65        |
|      3:    15.366 -  20.488:  123   |   8:    40.976 -  46.098:   30        |
|      4:    20.488 -  25.610:  118   |   9:    46.098 -  51.219:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2341 r_free = 0.2708             target_work(ml) = 5.754         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2335 r_free = 0.2704             target_work(ml) = 5.752         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2335   r_free= 0.2704   ksol= 0.34   Bsol= 20.00   scale= 1.077   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.06,8.55,7.97,0.00,0.00,0.00); trace/3= 8.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.752173                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2292   r_free= 0.2633   ksol= 0.34   Bsol= 50.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.64,4.91,5.12,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.749911                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.972101              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.868   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.301075              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.278  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2292      final r-factor (work) = 0.1538          |
| start r-factor (free) = 0.2633      final r-factor (free) = 0.1932          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7388 = 3.97 * 0.50 * 5.8526 + 1.00 * 0.1152                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1335 = 3.97 * 0.50 * 5.5716 + 1.00 * 0.0680                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1538      final r-factor (work) = 0.1407          |
| start r-factor (free) = 0.1932      final r-factor (free) = 0.1824          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7078 = 0.30 * 1.00 * 5.5716 + 1.00 * 0.0303                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7233 = 0.30 * 1.00 * 5.3536 + 1.00 * 0.1115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.99   10.20    None  None   None       |
|    all(noH): 2823   0      0.00    79.99   10.20    None  None   None       |
|    Sol.    : 438    0      0.00    53.27   28.70    None  None   None       |
|    Mac.    : 2385   0      0.00    79.99   6.81     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 -   7.999: 1739   |   5:    39.994 -  47.993:   66        |
|      1:     7.999 -  15.998:  534   |   6:    47.993 -  55.992:    8        |
|      2:    15.998 -  23.997:  170   |   7:    55.992 -  63.991:    0        |
|      3:    23.997 -  31.995:  141   |   8:    63.991 -  71.990:    0        |
|      4:    31.995 -  39.994:  164   |   9:    71.990 -  79.988:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1407 r_free = 0.1824             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1405 r_free = 0.1823             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1405   r_free= 0.1823   ksol= 0.34   Bsol= 50.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.64,4.91,5.12,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.322830                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1401   r_free= 0.1818   ksol= 0.34   Bsol= 50.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.57,3.84,4.44,0.00,0.00,0.00); trace/3= 3.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.323792                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.815769              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.825  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.189460              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.918   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1401      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1818      final r-factor (free) = 0.1671          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9338 = 1.82 * 0.50 * 5.3595 + 1.00 * 0.0680                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8475 = 1.82 * 0.50 * 5.2755 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1671      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5672 = 2.19 * 1.00 * 5.2755 + 1.00 * 0.0167                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4201 = 2.19 * 1.00 * 5.2092 + 1.00 * 0.0147                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.73   11.47    None  None   None       |
|    all(noH): 2823   0      0.00    76.73   11.47    None  None   None       |
|    Sol.    : 438    0      0.06    76.73   34.79    None  None   None       |
|    Mac.    : 2385   0      0.00    75.03   7.18     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 -   7.673: 1685   |   5:    38.363 -  46.035:   86        |
|      1:     7.673 -  15.345:  544   |   6:    46.035 -  53.708:   80        |
|      2:    15.345 -  23.018:  157   |   7:    53.708 -  61.380:   49        |
|      3:    23.018 -  30.690:  102   |   8:    61.380 -  69.053:   17        |
|      4:    30.690 -  38.363:   95   |   9:    69.053 -  76.725:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1197 r_free = 0.1633             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1197 r_free = 0.1633             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1633   ksol= 0.34   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.57,3.84,4.44,0.00,0.00,0.00); trace/3= 3.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.198371                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1633   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.57,3.84,4.44,0.00,0.00,0.00); trace/3= 3.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.197768                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.614884              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.203  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.190163              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.693  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1633      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8678 = 2.61 * 0.50 * 5.2085 + 1.00 * 0.0580                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8304 = 2.61 * 0.50 * 5.1715 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0271 = 0.19 * 1.00 * 5.1715 + 1.00 * 0.0437                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1357 = 0.19 * 1.00 * 5.1652 + 1.00 * 1.1534                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.59   10.92    None  None   None       |
|    all(noH): 2823   0      0.00    73.59   10.92    None  None   None       |
|    Sol.    : 438    0      0.66    68.37   32.25    None  None   None       |
|    Mac.    : 2385   0      0.00    73.59   7.00     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:     0.000 -   7.359: 1687   |   5:    36.797 -  44.156:   75        |
|      1:     7.359 -  14.719:  548   |   6:    44.156 -  51.516:   73        |
|      2:    14.719 -  22.078:  161   |   7:    51.516 -  58.875:   39        |
|      3:    22.078 -  29.438:  109   |   8:    58.875 -  66.234:   13        |
|      4:    29.438 -  36.797:  111   |   9:    66.234 -  73.594:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1136 r_free = 0.1571             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1135 r_free = 0.1572             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1572   ksol= 0.33   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.57,3.84,4.44,0.00,0.00,0.00); trace/3= 3.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.155870                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1575   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.57,3.84,4.44,0.00,0.00,0.00); trace/3= 3.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157309                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.650916              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.116  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 26.629722             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.730   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3330 = 1.65 * 0.50 * 5.1657 + 1.00 * 0.0690                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3190 = 1.65 * 0.50 * 5.1617 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1579      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 137.5129 = 26.63 * 1.00 * 5.1617 + 1.00 * 0.0580                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 137.3062 = 26.63 * 1.00 * 5.1556 + 1.00 * 0.0150                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.47   11.42    None  None   None       |
|    all(noH): 2823   0      0.00    86.47   11.42    None  None   None       |
|    Sol.    : 438    0      0.28    81.46   34.62    None  None   None       |
|    Mac.    : 2385   0      0.00    86.47   7.16     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 -   8.647: 1817   |   5:    43.234 -  51.881:   92        |
|      1:     8.647 -  17.294:  462   |   6:    51.881 -  60.527:   56        |
|      2:    17.294 -  25.940:  150   |   7:    60.527 -  69.174:   19        |
|      3:    25.940 -  34.587:  110   |   8:    69.174 -  77.821:    8        |
|      4:    34.587 -  43.234:  103   |   9:    77.821 -  86.468:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1599             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1600             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1600   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.57,3.84,4.44,0.00,0.00,0.00); trace/3= 3.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164791                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7519 0.99   1385  154 0.1004 0.1315      5.3886      5.5184|
|  2:  4.7519 -  3.7915 0.99   1340  146 0.0874 0.1087       5.446      5.6223|
|  3:  3.7915 -  3.3180 0.99   1303  147 0.1061 0.1512      5.4795      5.8599|
|  4:  3.3180 -  3.0173 0.99   1305  147 0.1208 0.1540      5.4622       5.595|
|  5:  3.0173 -  2.8025 0.99   1292  140 0.1346 0.1800      5.3471      5.5706|
|  6:  2.8025 -  2.6382 0.99   1280  148 0.1224 0.1880       5.231       5.498|
|  7:  2.6382 -  2.5067 0.99   1286  137 0.1286 0.1670      5.1979       5.388|
|  8:  2.5067 -  2.3980 0.98   1266  147 0.1209 0.1748      5.1005       5.361|
|  9:  2.3980 -  2.3061 0.98   1275  142 0.1194 0.1885      5.0734      5.3788|
| 10:  2.3061 -  2.2267 0.99   1261  135 0.1128 0.1708      4.9832      5.2042|
| 11:  2.2267 -  2.1573 0.99   1270  143 0.1165 0.1799      4.9605      5.3094|
| 12:  2.1573 -  2.0958 0.97   1247  138 0.1131 0.1630      4.9022      5.1372|
| 13:  2.0958 -  2.0408 0.99   1266  139 0.1170 0.1828      4.8236      5.1265|
| 14:  2.0408 -  1.9911 0.66    854   96 0.1054 0.1847      4.6939      4.9716|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7519  1385   154  0.94   8.96   0.97     0.95       7020.60|
|  2:  4.7519 -  3.7915  1340   146  0.95   7.82   1.01     0.99       8877.77|
|  3:  3.7915 -  3.3180  1303   147  0.93  11.32   1.02     1.02      10507.32|
|  4:  3.3180 -  3.0173  1305   147  0.92  13.75   1.01     0.99      10532.75|
|  5:  3.0173 -  2.8025  1292   140  0.89  16.53   0.99     0.96       8695.54|
|  6:  2.8025 -  2.6382  1280   148  0.90  16.18   0.98     0.95       7506.22|
|  7:  2.6382 -  2.5067  1286   137  0.90  15.87   0.99     0.96       6598.61|
|  8:  2.5067 -  2.3980  1266   147  0.90  16.01   0.99     0.96       5762.59|
|  9:  2.3980 -  2.3061  1275   142  0.90  16.10   1.00     0.97       5494.52|
| 10:  2.3061 -  2.2267  1261   135  0.90  15.83   1.00     0.95       4577.62|
| 11:  2.2267 -  2.1573  1270   143  0.89  16.81   0.99     0.95       4499.22|
| 12:  2.1573 -  2.0958  1247   138  0.92  14.98   1.01     0.99       4108.58|
| 13:  2.0958 -  2.0408  1266   139  0.89  16.94   1.00     0.98       3674.71|
| 14:  2.0408 -  1.9911   854    96  0.91  15.59   0.98     0.94       2776.56|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2776.56 max =        10532.75 mean =      6597.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.70 mean =        14.38|
|phase err.(test): min =        0.00 max =           87.94 mean =        13.92|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1600   ksol= 0.33   Bsol= 53.91   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,-0.14,0.52,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164751                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1600   ksol= 0.33   Bsol= 53.91   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,-0.14,0.52,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164751                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7519 0.99   1385  154 0.1004 0.1315      5.3885      5.5183|
|  2:  4.7519 -  3.7915 0.99   1340  146 0.0874 0.1087       5.446      5.6224|
|  3:  3.7915 -  3.3180 0.99   1303  147 0.1061 0.1512      5.4796      5.8599|
|  4:  3.3180 -  3.0173 0.99   1305  147 0.1208 0.1540      5.4622      5.5949|
|  5:  3.0173 -  2.8025 0.99   1292  140 0.1347 0.1801       5.347      5.5707|
|  6:  2.8025 -  2.6382 0.99   1280  148 0.1224 0.1878      5.2309      5.4973|
|  7:  2.6382 -  2.5067 0.99   1286  137 0.1286 0.1670      5.1977       5.388|
|  8:  2.5067 -  2.3980 0.98   1266  147 0.1209 0.1747      5.1004      5.3608|
|  9:  2.3980 -  2.3061 0.98   1275  142 0.1193 0.1884      5.0733      5.3786|
| 10:  2.3061 -  2.2267 0.99   1261  135 0.1128 0.1709      4.9833      5.2046|
| 11:  2.2267 -  2.1573 0.99   1270  143 0.1165 0.1800      4.9606      5.3097|
| 12:  2.1573 -  2.0958 0.97   1247  138 0.1131 0.1629      4.9025      5.1374|
| 13:  2.0958 -  2.0408 0.99   1266  139 0.1170 0.1829      4.8235      5.1271|
| 14:  2.0408 -  1.9911 0.66    854   96 0.1055 0.1845      4.6935      4.9706|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7519  1385   154  0.94   8.95   0.97     0.95       7018.42|
|  2:  4.7519 -  3.7915  1340   146  0.95   7.82   1.01     0.99       8876.68|
|  3:  3.7915 -  3.3180  1303   147  0.93  11.32   1.02     1.02      10508.92|
|  4:  3.3180 -  3.0173  1305   147  0.92  13.75   1.01     0.99      10532.29|
|  5:  3.0173 -  2.8025  1292   140  0.89  16.52   0.99     0.96       8690.99|
|  6:  2.8025 -  2.6382  1280   148  0.90  16.17   0.98     0.95       7503.76|
|  7:  2.6382 -  2.5067  1286   137  0.90  15.86   0.99     0.96       6594.96|
|  8:  2.5067 -  2.3980  1266   147  0.90  16.01   0.99     0.96       5760.78|
|  9:  2.3980 -  2.3061  1275   142  0.90  16.09   1.00     0.97       5493.84|
| 10:  2.3061 -  2.2267  1261   135  0.90  15.84   1.00     0.95       4578.95|
| 11:  2.2267 -  2.1573  1270   143  0.89  16.81   0.99     0.95       4502.17|
| 12:  2.1573 -  2.0958  1247   138  0.92  14.98   1.00     0.99       4112.19|
| 13:  2.0958 -  2.0408  1266   139  0.89  16.94   1.00     0.98       3674.26|
| 14:  2.0408 -  1.9911   854    96  0.91  15.58   0.98     0.94       2772.59|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2772.59 max =        10532.29 mean =      6596.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.70 mean =        14.38|
|phase err.(test): min =        0.00 max =           87.94 mean =        13.92|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.91    90.38   15.33    None  None   None       |
|    all(noH): 2823   0      3.91    90.38   15.33    None  None   None       |
|    Sol.    : 438    0      4.19    85.37   38.53    None  None   None       |
|    Mac.    : 2385   0      3.91    90.38   11.07    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:     3.914 -  12.561: 1817   |   5:    47.148 -  55.795:   92        |
|      1:    12.561 -  21.208:  462   |   6:    55.795 -  64.441:   56        |
|      2:    21.208 -  29.854:  150   |   7:    64.441 -  73.088:   19        |
|      3:    29.854 -  38.501:  110   |   8:    73.088 -  81.735:    8        |
|      4:    38.501 -  47.148:  103   |   9:    81.735 -  90.382:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.321 - 4.732
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 313
   mapped sites are within: 0.703 - 4.732

peak=   10.305 closest distance to " CG2 VAL A 230 " =    1.316
peak=    7.319 closest distance to " CG2 VAL A 296 " =    1.119
peak=    6.250 closest distance to " NH2 ARG A  56 " =    2.264
peak=    6.161 closest distance to " CG  LEU A   5 " =    1.188
peak=    5.818 closest distance to " CB  GLN A 223 " =    1.421
peak=    5.656 closest distance to " CG  LEU A 228 " =    1.149
peak=    5.554 closest distance to " CG  PRO A  54 " =    1.275
peak=    5.448 closest distance to " CD2 LEU A   5 " =    1.166
peak=    5.349 closest distance to " CB  PRO A  54 " =    0.970
peak=    5.255 closest distance to " CB  VAL A 230 " =    1.210
peak=    4.859 closest distance to " CB  SER A  63 " =    1.331
peak=    4.851 closest distance to " CB  VAL A 296 " =    1.062
peak=    4.836 closest distance to " CG  PRO A 213 " =    1.224
peak=    4.788 closest distance to " CB  GLN A 183 " =    1.312
peak=    4.782 closest distance to " NE2 GLN A  11 " =    1.066
peak=    4.761 closest distance to " CG  PRO A 198 " =    1.206
peak=    4.716 closest distance to " CB  ARG A 275 " =    0.884
peak=    4.657 closest distance to " O   HOH Z 232 " =    2.358
peak=    4.569 closest distance to " O   HOH Z 126 " =    2.050
peak=    4.514 closest distance to " O   HOH Z 298 " =    1.836
peak=    4.509 closest distance to " O   HOH Z 369 " =    2.197
peak=    4.471 closest distance to " CB  GLU A 128 " =    1.047
peak=    4.418 closest distance to " CG  PRO A 243 " =    1.135
peak=    4.372 closest distance to " C   PRO A 198 " =    1.566
peak=    4.360 closest distance to " O   HOH Z 316 " =    3.046
peak=    4.332 closest distance to " OD1 ASN A  69 " =    2.630
peak=    4.323 closest distance to " CB  ASN A 148 " =    1.316
peak=    4.322 closest distance to " CD2 LEU A 228 " =    1.187
peak=    4.312 closest distance to " CA  TYR A  30 " =    0.933
peak=    4.308 closest distance to " O   HOH Z 427 " =    2.990
peak=    4.306 closest distance to " O   HOH Z  44 " =    2.279
peak=    4.277 closest distance to " CB  TRP A 266 " =    0.957
peak=    4.261 closest distance to " O   HOH Z  78 " =    1.719
peak=    4.244 closest distance to " O   HOH Z 272 " =    1.874
peak=    4.244 closest distance to " O   HOH Z 142 " =    1.530
peak=    4.229 closest distance to " O   HOH Z  54 " =    2.380
peak=    4.182 closest distance to " O   HOH Z 368 " =    2.220
peak=    4.101 closest distance to " CB  SER A   3 " =    1.296
peak=    4.077 closest distance to " CZ  PHE A 218 " =    1.065
peak=    4.071 closest distance to " O   HOH Z 423 " =    1.727
peak=    4.069 closest distance to " O   HOH Z  43 " =    2.007
peak=    4.067 closest distance to " CB  VAL A 265 " =    1.261
peak=    4.015 closest distance to " O   HOH Z 189 " =    2.752
peak=    4.011 closest distance to " O   HOH Z 203 " =    1.763
peak=    3.996 closest distance to " O   HOH Z 303 " =    2.062
peak=    3.980 closest distance to " O   HOH Z 158 " =    3.113
peak=    3.975 closest distance to " O   SER A  87 " =    2.314
peak=    3.963 closest distance to " O   HOH Z  63 " =    1.959
peak=    3.960 closest distance to " O   HOH Z 234 " =    3.606
peak=    3.945 closest distance to " O   HOH Z  61 " =    1.639
peak=    3.936 closest distance to " O   HOH Z  68 " =    2.183
peak=    3.929 closest distance to " CA  THR A 264 " =    0.706
peak=    3.928 closest distance to " O   HOH Z  15 " =    2.225
peak=    3.917 closest distance to " O   HOH Z 236 " =    1.864
peak=    3.911 closest distance to " CB  GLU A 152 " =    1.195
peak=    3.911 closest distance to " O   HOH Z 193 " =    1.799
peak=    3.885 closest distance to " CB  GLU A 277 " =    3.651
peak=    3.884 closest distance to " O   HOH Z 403 " =    1.702
peak=    3.883 closest distance to " CB  ARG A 190 " =    1.651
peak=    3.877 closest distance to " O   MET A 105 " =    1.837
peak=    3.877 closest distance to " O   HOH Z 280 " =    2.912
peak=    3.873 closest distance to " O   HOH Z 346 " =    1.616
peak=    3.869 closest distance to " ND2 ASN A 187 " =    1.408
peak=    3.856 closest distance to " CZ  PHE A 192 " =    0.975
peak=    3.852 closest distance to " O   HOH Z 261 " =    2.054
peak=    3.849 closest distance to " CD  ARG A  66 " =    2.655
peak=    3.836 closest distance to " CA  ASN A 215 " =    1.257
peak=    3.835 closest distance to " CD  ARG A 159 " =    0.776
peak=    3.831 closest distance to " CG2 VAL A 257 " =    0.859
peak=    3.830 closest distance to " CB  ASP A 140 " =    0.971
peak=    3.830 closest distance to " ND2 ASN A 249 " =    1.874
peak=    3.826 closest distance to " CB  VAL A 202 " =    1.618
peak=    3.823 closest distance to " CB  TRP A 179 " =    1.423
peak=    3.819 closest distance to " CD BLYS A 290 " =    1.007
peak=    3.817 closest distance to " CG1BVAL A  72 " =    1.680
peak=    3.815 closest distance to " CB  ARG A  79 " =    1.440
peak=    3.810 closest distance to " CB AVAL A  41 " =    1.116
peak=    3.807 closest distance to " O   HOH Z 411 " =    3.735
peak=    3.798 closest distance to " NH2 ARG A 156 " =    1.122
peak=    3.791 closest distance to " N   ASN A  39 " =    1.221
peak=    3.791 closest distance to " CG1 ILE A  33 " =    1.313
peak=    3.774 closest distance to " O   HOH Z 263 " =    1.623
peak=    3.772 closest distance to " O   HOH Z  88 " =    3.249
peak=    3.767 closest distance to " CD  ARG A 269 " =    0.977
peak=    3.756 closest distance to " CA  ALA A  51 " =    0.989
peak=    3.751 closest distance to " O   HOH Z  97 " =    2.042
peak=    3.741 closest distance to " O   HOH Z 344 " =    2.985
peak=    3.733 closest distance to " CA  ARG A 195 " =    1.195
peak=    3.732 closest distance to " CB  LEU A 228 " =    1.306
peak=    3.726 closest distance to " O   HOH Z 402 " =    1.464
peak=    3.724 closest distance to " O   HOH Z 214 " =    2.141
peak=    3.716 closest distance to " NH1AARG A 145 " =    1.096
peak=    3.714 closest distance to " O   HOH Z 245 " =    1.322
peak=    3.708 closest distance to " O   HOH Z 425 " =    1.331
peak=    3.700 closest distance to " CB  ASN A  39 " =    0.892
peak=    3.697 closest distance to " CB  ASN A 187 " =    1.408
peak=    3.697 closest distance to " CA  ALA A  21 " =    1.221
peak=    3.677 closest distance to " O   HOH Z  59 " =    2.131
peak=    3.660 closest distance to " O   HOH Z 197 " =    3.037
peak=    3.654 closest distance to " CA  LYS A 117 " =    1.250
peak=    3.654 closest distance to " CG  MET A 185 " =    1.196
peak=    3.647 closest distance to " CB  ARG A 139 " =    0.848
peak=    3.646 closest distance to " O   HOH Z 112 " =    1.662
peak=    3.646 closest distance to " O   HOH Z 247 " =    1.328
peak=    3.640 closest distance to " CE1 TYR A 186 " =    1.305
peak=    3.632 closest distance to " CD2 LEU A   5 " =    0.740
peak=    3.630 closest distance to " CB  LEU A 143 " =    1.176
peak=    3.628 closest distance to " CG1 VAL A 153 " =    0.904
peak=    3.624 closest distance to " CA  ARG A  36 " =    1.072
peak=    3.621 closest distance to " CD1 LEU A 300 " =    1.136
peak=    3.619 closest distance to " O   TRP A 274 " =    1.845
peak=    3.615 closest distance to " OD2 ASP A 286 " =    2.841
peak=    3.603 closest distance to " O   HOH Z 290 " =    0.970
peak=    3.602 closest distance to " CD  LYS A 166 " =    1.343
peak=    3.601 closest distance to " CB  SER A 216 " =    0.818
peak=    3.600 closest distance to " CG1 VAL A 296 " =    1.229
peak=    3.600 closest distance to " O   HOH Z 193 " =    2.069
peak=    3.598 closest distance to " CB  ALA A 291 " =    1.389
peak=    3.595 closest distance to " CG  LEU A 167 " =    1.158
peak=    3.592 closest distance to " O   HOH Z  97 " =    2.601
peak=    3.588 closest distance to " CB  ALA A   9 " =    1.599
peak=    3.587 closest distance to " CD1 LEU A  96 " =    0.703
peak=    3.577 closest distance to " CA  THR A 221 " =    0.926
peak=    3.576 closest distance to " CB  ALA A 248 " =    1.443
peak=    3.573 closest distance to " O   HOH Z 134 " =    1.382
peak=    3.573 closest distance to " NZ  LYS A 117 " =    3.239
peak=    3.571 closest distance to " CB  SER A 212 " =    1.116
peak=    3.564 closest distance to " O   HOH Z 145 " =    2.118
peak=    3.557 closest distance to " O   HOH Z 371 " =    3.267
peak=    3.557 closest distance to " O   HOH Z 426 " =    1.550
peak=    3.554 closest distance to " CG2 THR A 221 " =    1.176
peak=    3.549 closest distance to " O   HOH Z  80 " =    1.701
peak=    3.548 closest distance to " O   HOH Z 133 " =    1.692
peak=    3.546 closest distance to " CA  ALA A 295 " =    1.092
peak=    3.543 closest distance to " O   HOH Z 437 " =    1.892
peak=    3.538 closest distance to " CA  MET A  40 " =    1.130
peak=    3.534 closest distance to " O   HOH Z 273 " =    2.723
peak=    3.533 closest distance to " CB  SER A 273 " =    0.855
peak=    3.528 closest distance to " ND1 HIS A  81 " =    1.679
peak=    3.528 closest distance to " O   HOH Z 147 " =    1.722
peak=    3.524 closest distance to " O   HOH Z 345 " =    3.378
peak=    3.523 closest distance to " CA  ALA A 158 " =    1.234
peak=    3.519 closest distance to " OG BSER A 164 " =    2.232
peak=    3.513 closest distance to " O   HOH Z 368 " =    3.597
peak=    3.507 closest distance to " O   HOH Z 128 " =    2.147
peak=    3.507 closest distance to " CE  LYS A  76 " =    0.838
peak=    3.506 closest distance to " CB  ASN A 142 " =    1.091
peak=    3.504 closest distance to " O   HOH Z 128 " =    2.099
peak=    3.502 closest distance to " N   VAL A 126 " =    1.388
peak=    3.500 closest distance to " O   HOH Z  48 " =    1.702
peak=    3.499 closest distance to " O   HOH Z 193 " =    1.641
peak=    3.486 closest distance to " O   HOH Z  21 " =    1.700
peak=    3.485 closest distance to " O   HOH Z 285 " =    3.084
peak=    3.468 closest distance to " O   HOH Z 180 " =    2.122
peak=    3.468 closest distance to " CB  THR A 157 " =    1.173
peak=    3.467 closest distance to " O   HOH Z 250 " =    1.345
peak=    3.466 closest distance to " CA  ASP A 140 " =    1.207
peak=    3.464 closest distance to " O   ASP A 124 " =    1.083
peak=    3.461 closest distance to " O   HOH Z 135 " =    1.892
peak=    3.461 closest distance to " CB  THR A  31 " =    1.699
peak=    3.460 closest distance to " CA  VAL A  41 " =    0.838
peak=    3.458 closest distance to " O   HOH Z 383 " =    2.086
peak=    3.457 closest distance to " O   HOH Z  20 " =    1.611
peak=    3.453 closest distance to " CA  ALA A 291 " =    0.901
peak=    3.451 closest distance to " CB  MET A  47 " =    1.074
peak=    3.435 closest distance to " CG1 ILE A 151 " =    0.966
peak=    3.426 closest distance to " O   HOH Z 329 " =    3.869
peak=    3.424 closest distance to " CG  MET A 185 " =    1.128
peak=    3.422 closest distance to " O   ALA A 165 " =    1.464
peak=    3.422 closest distance to " O   HOH Z  19 " =    2.359
peak=    3.420 closest distance to " CB  ALA A 161 " =    0.840
peak=    3.415 closest distance to " CB  PRO A 198 " =    1.099
peak=    3.413 closest distance to " O   HOH Z 171 " =    2.430
peak=    3.402 closest distance to " O   HOH Z 403 " =    1.392
peak=    3.395 closest distance to " CB  VAL A 268 " =    0.809
peak=    3.393 closest distance to " O   HOH Z 248 " =    1.691
peak=    3.392 closest distance to " CB  HIS A 108 " =    0.815
peak=    3.391 closest distance to " CD  ARG A  66 " =    2.537
peak=    3.391 closest distance to " O   HOH Z  63 " =    1.289
peak=    3.390 closest distance to " CB  MET A  40 " =    0.811
peak=    3.380 closest distance to " CG1 ILE A  49 " =    1.517
peak=    3.374 closest distance to " CG  GLN A  88 " =    1.057
peak=    3.370 closest distance to " CA  LEU A 282 " =    1.049
peak=    3.370 closest distance to " CB  LYS A 117 " =    1.162
peak=    3.368 closest distance to " O   HOH Z 417 " =    2.203
peak=    3.360 closest distance to " O   HOH Z 295 " =    1.480
peak=    3.357 closest distance to " CD2 HIS A  81 " =    1.010
peak=    3.355 closest distance to " CA  SER A  87 " =    1.068
peak=    3.354 closest distance to " O   HOH Z 172 " =    3.623
peak=    3.352 closest distance to " O   HOH Z  49 " =    2.531
peak=    3.347 closest distance to " O   HOH Z 132 " =    2.700
peak=    3.344 closest distance to " O   HOH Z 102 " =    1.275
peak=    3.344 closest distance to " CG2 THR A 220 " =    0.939
peak=    3.343 closest distance to " CA  LYS A 290 " =    1.244
peak=    3.338 closest distance to " O   ALA A 158 " =    1.419
peak=    3.337 closest distance to " CB  TRP A 150 " =    1.390
peak=    3.335 closest distance to " OG  SER A  22 " =    2.816
peak=    3.334 closest distance to " CD2 TRP A 179 " =    1.401
peak=    3.333 closest distance to " CB  LEU A 255 " =    0.772
peak=    3.326 closest distance to " OG1 THR A 294 " =    2.359
peak=    3.325 closest distance to " CA  ASP A 191 " =    0.938
peak=    3.323 closest distance to " O   HOH Z 291 " =    1.609
peak=    3.320 closest distance to " CD  LYS A 119 " =    1.446
peak=    3.320 closest distance to " CZ  PHE A  38 " =    1.226
peak=    3.317 closest distance to " CB  ASN A 110 " =    1.264
peak=    3.315 closest distance to " O   HOH Z 422 " =    2.689
peak=    3.313 closest distance to " O   HOH Z 407 " =    2.447
peak=    3.309 closest distance to " NE2 HIS A 207 " =    1.374
peak=    3.309 closest distance to " O   HOH Z 435 " =    1.976
peak=    3.307 closest distance to " O   HOH Z 108 " =    2.649
peak=    3.307 closest distance to " CG2 VAL A 202 " =    1.078
peak=    3.302 closest distance to " O   HOH Z 133 " =    2.439
peak=    3.301 closest distance to " CA  ALA A 299 " =    0.978
peak=    3.299 closest distance to " O   HOH Z 227 " =    1.641
peak=    3.297 closest distance to " CA  GLY A 211 " =    1.329
peak=    3.289 closest distance to " N   SER A 135 " =    1.413
peak=    3.286 closest distance to " O   GLN A 278 " =    1.537
peak=    3.286 closest distance to " CG2 THR A 294 " =    1.744
peak=    3.281 closest distance to " CD1 ILE A 106 " =    0.918
peak=    3.279 closest distance to " O   HOH Z  40 " =    1.662
peak=    3.275 closest distance to " OH  TYR A 214 " =    1.216
peak=    3.275 closest distance to " O   HOH Z 189 " =    2.927
peak=    3.272 closest distance to " O   HOH Z  10 " =    1.820
peak=    3.271 closest distance to " CB  ARG A  79 " =    0.894
peak=    3.269 closest distance to " N   PHE A 130 " =    1.256
peak=    3.266 closest distance to " CB  ALA A  34 " =    0.792
peak=    3.265 closest distance to " O   HOH Z 359 " =    3.818
peak=    3.263 closest distance to " NH2 ARG A 219 " =    1.822
peak=    3.260 closest distance to " CD1 ILE A  33 " =    1.606
peak=    3.260 closest distance to " CB  ALA A 242 " =    0.884
peak=    3.256 closest distance to " O   HOH Z   4 " =    1.836
peak=    3.255 closest distance to " O   HOH Z 423 " =    3.022
peak=    3.254 closest distance to " CB  GLU A  46 " =    1.031
peak=    3.250 closest distance to " O   HOH Z 366 " =    3.037
peak=    3.249 closest distance to " NZ  LYS A  76 " =    1.555
peak=    3.247 closest distance to " O   HOH Z  48 " =    1.344
peak=    3.244 closest distance to " CA  SER A 146 " =    1.719
peak=    3.243 closest distance to " ND2 ASN A 110 " =    1.673
peak=    3.243 closest distance to " CA  ALA A 233 " =    1.519
peak=    3.233 closest distance to " CG2 VAL A 197 " =    1.095
peak=    3.231 closest distance to " CD2 LEU A 297 " =    0.837
peak=    3.229 closest distance to " CB  ALA A 137 " =    1.143
peak=    3.228 closest distance to " O   HOH Z 116 " =    1.789
peak=    3.227 closest distance to " O   HOH Z 353 " =    2.730
peak=    3.223 closest distance to " O   HOH Z 313 " =    1.696
peak=    3.222 closest distance to " CD2 LEU A 255 " =    1.599
peak=    3.220 closest distance to " C   TYR A 214 " =    1.474
peak=    3.219 closest distance to " CD1 LEU A   5 " =    1.390
peak=    3.218 closest distance to " O   HOH Z 216 " =    2.710
peak=    3.217 closest distance to " O   HOH Z 417 " =    3.136
peak=    3.213 closest distance to " ND1 HIS A  86 " =    1.723
peak=    3.212 closest distance to " O   HOH Z 155 " =    3.336
peak=    3.209 closest distance to " O   HOH Z 420 " =    1.828
peak=    3.208 closest distance to " CE  LYS A  48 " =    1.086
peak=    3.206 closest distance to " CE1 HIS A 108 " =    1.169
peak=    3.201 closest distance to " CB  ALA A 104 " =    0.718
peak=    3.199 closest distance to " CB  ILE A 120 " =    1.332
peak=    3.199 closest distance to " CB  GLN A  89 " =    1.186
peak=    3.198 closest distance to " O   HOH Z 250 " =    1.350
peak=    3.194 closest distance to " CG  GLN A  77 " =    2.345
peak=    3.190 closest distance to " O   HOH Z 187 " =    2.308
peak=    3.187 closest distance to " CA  GLN A 194 " =    1.232
peak=    3.185 closest distance to " CG2AVAL A 121 " =    2.357
peak=    3.182 closest distance to " CG  LEU A 281 " =    1.082
peak=    3.182 closest distance to " O   HOH Z 305 " =    3.609
peak=    3.182 closest distance to " O   HOH Z 425 " =    2.028
peak=    3.182 closest distance to " CB  SER A  26 " =    1.707
peak=    3.181 closest distance to " CG BARG A 102 " =    1.849
peak=    3.179 closest distance to " O   HOH Z 421 " =    1.774
peak=    3.172 closest distance to " O   HOH Z 327 " =    1.837
peak=    3.171 closest distance to " O   HOH Z 409 " =    3.397
peak=    3.168 closest distance to " N   ASN A 127 " =    1.246
peak=    3.168 closest distance to " O   HOH Z 238 " =    2.335
peak=    3.168 closest distance to " O   HOH Z 296 " =    1.632
peak=    3.167 closest distance to " CA  VAL A 126 " =    0.886
peak=    3.167 closest distance to " CA  ASN A 176 " =    1.085
peak=    3.165 closest distance to " CA  ALA A 154 " =    0.987
peak=    3.164 closest distance to " O   HOH Z 261 " =    1.423
peak=    3.157 closest distance to " CB  ALA A   1 " =    4.732
peak=    3.155 closest distance to " CB  GLN A 278 " =    0.926
peak=    3.154 closest distance to " NH1 ARG A  14 " =    0.935
peak=    3.151 closest distance to " O   HOH Z 163 " =    1.419
peak=    3.151 closest distance to " O   HOH Z 156 " =    3.374
peak=    3.150 closest distance to " CB  ASN A 215 " =    1.148
peak=    3.137 closest distance to " N   GLN A 278 " =    1.112
peak=    3.137 closest distance to " CA  MET A 105 " =    1.041
peak=    3.130 closest distance to " OE1 GLU A 152 " =    0.862
peak=    3.130 closest distance to " O   THR A  31 " =    1.546
peak=    3.121 closest distance to " O   HOH Z 302 " =    1.944
peak=    3.115 closest distance to " CB  TYR A 116 " =    0.825
peak=    3.114 closest distance to " CA  GLY A  80 " =    0.926
peak=    3.111 closest distance to " CD1 LEU A 228 " =    1.856
peak=    3.096 closest distance to " O   HOH Z 325 " =    2.254
peak=    3.095 closest distance to " O   HOH Z 201 " =    3.195
peak=    3.093 closest distance to " O   HOH Z 124 " =    1.213
peak=    3.091 closest distance to " CE2 TYR A 186 " =    0.850
peak=    3.090 closest distance to " CA  ILE A 106 " =    0.768
peak=    3.086 closest distance to " CB  GLN A 205 " =    1.041
peak=    3.085 closest distance to " CG  GLU A  37 " =    0.778
peak=    3.066 closest distance to " N   ASP A 162 " =    1.311
peak=    3.063 closest distance to " O   HOH Z 391 " =    2.950
peak=    3.059 closest distance to " O   HOH Z 128 " =    2.024
peak=    3.035 closest distance to " CB  PRO A 243 " =    1.413
peak=    3.024 closest distance to " O   HOH Z 175 " =    2.128

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.792 - 5.506
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 208
   mapped sites are within: 0.792 - 5.506

peak=   -5.013 closest distance to " CG2 VAL A 230 " =    0.868
peak=   -4.473 closest distance to " CD  ARG A 156 " =    2.023
peak=   -4.469 closest distance to " O   HOH Z 266 " =    4.954
peak=   -4.333 closest distance to " SG  CYS A 254 " =    3.273
peak=   -4.149 closest distance to " CB  PRO A 243 " =    2.649
peak=   -4.143 closest distance to " CB  ALA A 161 " =    2.630
peak=   -4.078 closest distance to " CG  ASP A 231 " =    0.792
peak=   -4.055 closest distance to " OE1 GLN A 223 " =    2.095
peak=   -3.981 closest distance to " C   HIS A 108 " =    1.124
peak=   -3.961 closest distance to " O   HOH Z 231 " =    1.977
peak=   -3.917 closest distance to " O   HOH Z 118 " =    3.182
peak=   -3.913 closest distance to " CG2BVAL A  41 " =    2.634
peak=   -3.901 closest distance to " CE2 TYR A  30 " =    2.773
peak=   -3.896 closest distance to " O   PRO A 163 " =    2.160
peak=   -3.876 closest distance to " OG BSER A 134 " =    1.113
peak=   -3.868 closest distance to " O   HOH Z 196 " =    2.200
peak=   -3.857 closest distance to " O   HOH Z 166 " =    1.921
peak=   -3.848 closest distance to " O   HOH Z 351 " =    1.474
peak=   -3.829 closest distance to " NE2 GLN A  88 " =    2.054
peak=   -3.828 closest distance to " N   ALA A 226 " =    2.114
peak=   -3.811 closest distance to " O   HOH Z  11 " =    1.923
peak=   -3.806 closest distance to " CG1 VAL A 296 " =    1.285
peak=   -3.784 closest distance to " CD2 LEU A 300 " =    2.767
peak=   -3.780 closest distance to " OG  SER A  97 " =    2.257
peak=   -3.780 closest distance to " CA  ASP A 298 " =    1.016
peak=   -3.779 closest distance to " ND2 ASN A  45 " =    1.016
peak=   -3.777 closest distance to " NH2AARG A 275 " =    5.250
peak=   -3.777 closest distance to " CG1 VAL A 265 " =    2.407
peak=   -3.777 closest distance to " CD  GLN A  58 " =    1.118
peak=   -3.753 closest distance to " CG1 VAL A 112 " =    2.937
peak=   -3.745 closest distance to " CG2 VAL A 296 " =    1.447
peak=   -3.742 closest distance to " OXT GLY A 302 " =    2.946
peak=   -3.735 closest distance to " C   ALA A 158 " =    1.257
peak=   -3.729 closest distance to " O   HOH Z  43 " =    1.690
peak=   -3.688 closest distance to " O   HOH Z 290 " =    1.233
peak=   -3.666 closest distance to " CB  PHE A 192 " =    1.882
peak=   -3.651 closest distance to " CG1 VAL A 112 " =    2.637
peak=   -3.643 closest distance to " O   HOH Z  52 " =    1.622
peak=   -3.641 closest distance to " O   HOH Z 435 " =    2.771
peak=   -3.640 closest distance to " OD1 ASN A 187 " =    1.604
peak=   -3.635 closest distance to " CG1 VAL A 250 " =    2.718
peak=   -3.614 closest distance to " O   HOH Z 350 " =    1.746
peak=   -3.613 closest distance to " O   HOH Z 198 " =    2.358
peak=   -3.609 closest distance to " O   HOH Z 394 " =    1.547
peak=   -3.608 closest distance to " CZ3 TRP A 179 " =    1.201
peak=   -3.604 closest distance to " O   HOH Z  19 " =    2.278
peak=   -3.586 closest distance to " CD1 LEU A 228 " =    2.328
peak=   -3.579 closest distance to " O   HOH Z 102 " =    1.677
peak=   -3.572 closest distance to " O   HOH Z  13 " =    1.416
peak=   -3.567 closest distance to " O   VAL A  67 " =    2.745
peak=   -3.566 closest distance to " CE3 TRP A 150 " =    2.108
peak=   -3.563 closest distance to " N   ALA A  43 " =    2.507
peak=   -3.562 closest distance to " O   HOH Z 389 " =    1.912
peak=   -3.558 closest distance to " O   HOH Z 426 " =    1.657
peak=   -3.549 closest distance to " CE  MET A 105 " =    2.149
peak=   -3.549 closest distance to " CG  TRP A 266 " =    1.843
peak=   -3.547 closest distance to " CB  ALA A  43 " =    2.545
peak=   -3.545 closest distance to " CG  ARG A 269 " =    2.445
peak=   -3.540 closest distance to " ND2 ASN A 187 " =    1.711
peak=   -3.537 closest distance to " CD  ARG A 139 " =    1.587
peak=   -3.536 closest distance to " CD2 LEU A 167 " =    1.714
peak=   -3.535 closest distance to " SD BMET A  47 " =    0.966
peak=   -3.533 closest distance to " O   HOH Z 103 " =    1.831
peak=   -3.529 closest distance to " O   HOH Z 185 " =    2.339
peak=   -3.529 closest distance to " O   GLY A 203 " =    2.358
peak=   -3.517 closest distance to " CD1 LEU A 101 " =    2.490
peak=   -3.515 closest distance to " O   PRO A 198 " =    1.227
peak=   -3.514 closest distance to " N   GLN A  58 " =    1.707
peak=   -3.509 closest distance to " OD1 ASN A 148 " =    1.479
peak=   -3.508 closest distance to " CB  PRO A 280 " =    2.085
peak=   -3.506 closest distance to " O   HOH Z 292 " =    4.550
peak=   -3.500 closest distance to " CA  GLY A 203 " =    2.392
peak=   -3.496 closest distance to " OG ASER A 134 " =    1.231
peak=   -3.491 closest distance to " CD  LYS A 289 " =    2.530
peak=   -3.490 closest distance to " O   HOH Z 283 " =    2.152
peak=   -3.483 closest distance to " CB  ALA A 248 " =    2.042
peak=   -3.477 closest distance to " CG  PHE A 283 " =    2.852
peak=   -3.473 closest distance to " CG  GLU A 277 " =    1.091
peak=   -3.469 closest distance to " C   ASN A 187 " =    1.845
peak=   -3.463 closest distance to " CB  PRO A 163 " =    2.612
peak=   -3.450 closest distance to " O   HOH Z 222 " =    1.513
peak=   -3.446 closest distance to " CB  ASP A 132 " =    2.309
peak=   -3.443 closest distance to " NH2 ARG A  66 " =    1.824
peak=   -3.441 closest distance to " CA  GLY A 241 " =    3.096
peak=   -3.435 closest distance to " O   HOH Z 311 " =    3.772
peak=   -3.426 closest distance to " O   HOH Z  10 " =    1.529
peak=   -3.423 closest distance to " OG BSER A 134 " =    1.770
peak=   -3.415 closest distance to " O   VAL A 189 " =    2.555
peak=   -3.413 closest distance to " C   ASN A 285 " =    2.448
peak=   -3.411 closest distance to " N   THR A 157 " =    1.475
peak=   -3.411 closest distance to " O   HOH Z 407 " =    3.081
peak=   -3.407 closest distance to " O   HOH Z 353 " =    2.105
peak=   -3.407 closest distance to " CG  HIS A  86 " =    0.857
peak=   -3.405 closest distance to " O   HOH Z  17 " =    1.573
peak=   -3.397 closest distance to " OH  TYR A 169 " =    0.991
peak=   -3.394 closest distance to " O   HOH Z 372 " =    2.263
peak=   -3.393 closest distance to " O   HOH Z  38 " =    1.559
peak=   -3.391 closest distance to " OG  SER A  62 " =    1.727
peak=   -3.388 closest distance to " NH2 ARG A  79 " =    2.021
peak=   -3.384 closest distance to " O   HOH Z 241 " =    1.312
peak=   -3.382 closest distance to " C   LEU A 222 " =    0.868
peak=   -3.380 closest distance to " ND2 ASN A  45 " =    1.640
peak=   -3.374 closest distance to " NE2 GLN A 103 " =    1.783
peak=   -3.369 closest distance to " CG  ASP A  50 " =    2.435
peak=   -3.368 closest distance to " CZ  TYR A 169 " =    1.700
peak=   -3.367 closest distance to " O   SER A 271 " =    2.121
peak=   -3.365 closest distance to " N   VAL A 230 " =    1.103
peak=   -3.365 closest distance to " CE2 PHE A 218 " =    2.606
peak=   -3.363 closest distance to " CB  ASN A  39 " =    2.155
peak=   -3.363 closest distance to " CB  ALA A 291 " =    2.209
peak=   -3.355 closest distance to " O   HOH Z 165 " =    1.873
peak=   -3.353 closest distance to " O   HOH Z  44 " =    2.103
peak=   -3.343 closest distance to " O   HOH Z  63 " =    1.103
peak=   -3.334 closest distance to " CB  VAL A 230 " =    1.064
peak=   -3.333 closest distance to " O   HOH Z 243 " =    2.061
peak=   -3.324 closest distance to " C   LEU A 143 " =    1.082
peak=   -3.319 closest distance to " O   HOH Z 210 " =    1.099
peak=   -3.319 closest distance to " CG1 VAL A 197 " =    2.313
peak=   -3.317 closest distance to " O   LEU A 167 " =    1.473
peak=   -3.313 closest distance to " O   HOH Z 310 " =    1.787
peak=   -3.309 closest distance to " O   HOH Z  47 " =    1.633
peak=   -3.309 closest distance to " C   MET A 188 " =    1.469
peak=   -3.308 closest distance to " N   SER A 212 " =    1.874
peak=   -3.305 closest distance to " CD1 LEU A 101 " =    2.882
peak=   -3.303 closest distance to " O   HOH Z 252 " =    4.039
peak=   -3.302 closest distance to " NH1 ARG A 195 " =    2.608
peak=   -3.297 closest distance to " O   HOH Z 111 " =    2.324
peak=   -3.293 closest distance to " CG  GLU A  53 " =    1.432
peak=   -3.291 closest distance to " O   HOH Z  11 " =    2.205
peak=   -3.291 closest distance to " O   HOH Z 275 " =    1.475
peak=   -3.285 closest distance to " O   GLY A 211 " =    1.413
peak=   -3.285 closest distance to " O   HOH Z  60 " =    2.109
peak=   -3.284 closest distance to " O   HOH Z 113 " =    2.142
peak=   -3.280 closest distance to " OG  SER A  87 " =    1.488
peak=   -3.279 closest distance to " NZ  LYS A 119 " =    3.500
peak=   -3.266 closest distance to " O   HOH Z 191 " =    5.506
peak=   -3.264 closest distance to " N   SER A 276 " =    1.308
peak=   -3.262 closest distance to " CB  TYR A  15 " =    2.235
peak=   -3.260 closest distance to " CA  ASN A 127 " =    1.075
peak=   -3.256 closest distance to " O   HOH Z 388 " =    2.075
peak=   -3.255 closest distance to " CZ  PHE A  59 " =    1.588
peak=   -3.252 closest distance to " O   HOH Z 431 " =    1.722
peak=   -3.248 closest distance to " CD1 LEU A  25 " =    2.448
peak=   -3.243 closest distance to " O   HOH Z 359 " =    3.145
peak=   -3.235 closest distance to " CG2 VAL A 112 " =    2.523
peak=   -3.235 closest distance to " CG1 VAL A 296 " =    1.291
peak=   -3.232 closest distance to " CD1 PHE A  59 " =    1.893
peak=   -3.232 closest distance to " CG  MET A 105 " =    0.945
peak=   -3.232 closest distance to " CD2 PHE A  61 " =    2.448
peak=   -3.231 closest distance to " O   HOH Z  98 " =    2.169
peak=   -3.228 closest distance to " O   HOH Z 198 " =    1.584
peak=   -3.227 closest distance to " O   HOH Z 211 " =    1.645
peak=   -3.227 closest distance to " O   HOH Z 295 " =    1.485
peak=   -3.225 closest distance to " O   ARG A  24 " =    2.101
peak=   -3.223 closest distance to " O   GLU A  44 " =    1.583
peak=   -3.219 closest distance to " ND2 ASN A  60 " =    1.759
peak=   -3.218 closest distance to " OE1 GLN A  88 " =    1.079
peak=   -3.218 closest distance to " CB  ALA A  10 " =    2.244
peak=   -3.218 closest distance to " CD1 TYR A 247 " =    2.353
peak=   -3.215 closest distance to " OG  SER A 206 " =    1.766
peak=   -3.211 closest distance to " CB  ALA A 291 " =    2.315
peak=   -3.211 closest distance to " O   HOH Z 234 " =    4.229
peak=   -3.209 closest distance to " CD2 TYR A 293 " =    2.044
peak=   -3.207 closest distance to " O   HOH Z 177 " =    1.694
peak=   -3.206 closest distance to " OD1 ASP A 191 " =    1.448
peak=   -3.203 closest distance to " CB  ALA A 248 " =    2.420
peak=   -3.200 closest distance to " O   HOH Z 193 " =    1.753
peak=   -3.197 closest distance to " CA  GLY A 133 " =    2.285
peak=   -3.195 closest distance to " N   SER A   3 " =    2.059
peak=   -3.192 closest distance to " O   LYS A 117 " =    1.666
peak=   -3.192 closest distance to " O   GLY A  17 " =    1.321
peak=   -3.190 closest distance to " CD  PRO A 213 " =    2.170
peak=   -3.185 closest distance to " CE BMET A  47 " =    1.903
peak=   -3.181 closest distance to " NH1 ARG A  36 " =    2.047
peak=   -3.180 closest distance to " O   HOH Z 423 " =    2.065
peak=   -3.173 closest distance to " O   GLY A  80 " =    2.521
peak=   -3.171 closest distance to " CD  ARG A 195 " =    5.126
peak=   -3.167 closest distance to " O   HOH Z 380 " =    4.852
peak=   -3.159 closest distance to " OG  SER A  26 " =    1.394
peak=   -3.159 closest distance to " OXT GLY A 302 " =    3.439
peak=   -3.155 closest distance to " CG1 VAL A 230 " =    1.907
peak=   -3.151 closest distance to " C   ASP A 231 " =    2.585
peak=   -3.147 closest distance to " CG  LEU A 228 " =    1.047
peak=   -3.146 closest distance to " CB  ASP A 132 " =    2.317
peak=   -3.146 closest distance to " O   HOH Z 184 " =    1.533
peak=   -3.140 closest distance to " O   HOH Z 341 " =    1.183
peak=   -3.139 closest distance to " CD2 TYR A 247 " =    2.277
peak=   -3.136 closest distance to " CD1 ILE A 199 " =    2.553
peak=   -3.135 closest distance to " CD2 LEU A 237 " =    2.846
peak=   -3.130 closest distance to " CB  LEU A  83 " =    2.320
peak=   -3.129 closest distance to " O   HOH Z 148 " =    3.604
peak=   -3.126 closest distance to " CB  ASP A 171 " =    2.278
peak=   -3.122 closest distance to " CD1 ILE A 151 " =    2.327
peak=   -3.110 closest distance to " O   HOH Z   6 " =    1.780
peak=   -3.102 closest distance to " ND2 ASN A  60 " =    1.458
peak=   -3.101 closest distance to " O   HOH Z 396 " =    1.675
peak=   -3.100 closest distance to " N   ALA A 248 " =    1.615
peak=   -3.099 closest distance to " O   HOH Z 139 " =    3.004
peak=   -3.096 closest distance to " O   PRO A 198 " =    1.363
peak=   -3.089 closest distance to " O   HOH Z 389 " =    4.605
peak=   -3.089 closest distance to " O   HOH Z 298 " =    2.760
peak=   -3.084 closest distance to " CD  PRO A 243 " =    2.127
peak=   -3.080 closest distance to " NE2 GLN A  88 " =    1.037
peak=   -3.068 closest distance to " O   THR A  18 " =    1.564
peak=   -3.066 closest distance to " O   HOH Z 128 " =    2.546
peak=   -3.058 closest distance to " CA  TYR A  68 " =    2.891
peak=   -3.055 closest distance to " O   HOH Z 166 " =    1.540

================= 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    :  0.4222 0.4072   6.212149e+00   6.187092e+00
   1_bss:  0.4134 0.3960   6.208064e+00   6.174067e+00
   1_xyz:  0.3000 0.3296   5.970775e+00   6.037268e+00
   1_adp:  0.2341 0.2708   5.753591e+00   5.877955e+00
   1_occ:  0.2335 0.2704   5.752173e+00   5.878253e+00
   2_bss:  0.2292 0.2633   5.749911e+00   5.871671e+00
   2_xyz:  0.1538 0.1932   5.398354e+00   5.590460e+00
   2_adp:  0.1407 0.1824   5.323609e+00   5.531240e+00
   2_occ:  0.1405 0.1823   5.322830e+00   5.530688e+00
   3_bss:  0.1401 0.1818   5.323792e+00   5.531211e+00
   3_xyz:  0.1257 0.1671   5.231646e+00   5.454102e+00
   3_adp:  0.1197 0.1633   5.198801e+00   5.431938e+00
   3_occ:  0.1197 0.1633   5.198371e+00   5.431483e+00
   4_bss:  0.1197 0.1633   5.197768e+00   5.431170e+00
   4_xyz:  0.1124 0.1595   5.157746e+00   5.408180e+00
   4_adp:  0.1136 0.1571   5.156092e+00   5.393964e+00
   4_occ:  0.1135 0.1572   5.155870e+00   5.394119e+00
   5_bss:  0.1139 0.1575   5.157309e+00   5.393849e+00
   5_xyz:  0.1150 0.1579   5.163968e+00   5.398389e+00
   5_adp:  0.1133 0.1599   5.164799e+00   5.410189e+00
   5_occ:  0.1133 0.1600   5.164791e+00   5.410293e+00
   5_bss:  0.1133 0.1600   5.164751e+00   5.410270e+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:  0.339  20.002   8.056   8.546   7.970   0.000   0.000   0.000
   1_xyz:  0.339  20.002   8.056   8.546   7.970   0.000   0.000   0.000
   1_adp:  0.339  20.002   8.056   8.546   7.970   0.000   0.000   0.000
   1_occ:  0.339  20.002   8.056   8.546   7.970   0.000   0.000   0.000
   2_bss:  0.339  50.001   4.636   4.915   5.125   0.000   0.000   0.000
   2_xyz:  0.339  50.001   4.636   4.915   5.125   0.000   0.000   0.000
   2_adp:  0.339  50.001   4.636   4.915   5.125   0.000   0.000   0.000
   2_occ:  0.339  50.001   4.636   4.915   5.125   0.000   0.000   0.000
   3_bss:  0.341  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   3_xyz:  0.341  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   3_adp:  0.341  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   3_occ:  0.341  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   4_bss:  0.327  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   4_xyz:  0.327  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   4_adp:  0.327  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   4_occ:  0.327  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   5_bss:  0.328  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   5_xyz:  0.328  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   5_adp:  0.328  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   5_occ:  0.328  50.001   3.571   3.839   4.435   0.000   0.000   0.000
   5_bss:  0.328  53.915  -0.379  -0.145   0.524   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.602 0.5893  0.6513    47467.926
   1_bss:  44.432 0.5892  0.8326    45210.332
   1_xyz:  35.240 0.6977  0.9590    29544.979
   1_adp:  26.756 0.7939  1.0462    18728.949
   1_occ:  26.760 0.7938  1.0460    18727.525
   2_bss:  26.490 0.7966  0.9320    18403.079
   2_xyz:  18.446 0.8762  0.9915     9594.550
   2_adp:  16.974 0.8901  1.0018     8534.362
   2_occ:  16.962 0.8902  1.0016     8523.872
   3_bss:  16.978 0.8901  0.9675     8560.365
   3_xyz:  15.212 0.9053  0.9731     7250.637
   3_adp:  14.798 0.9088  0.9740     6901.692
   3_occ:  14.786 0.9089  0.9739     6896.877
   4_bss:  14.786 0.9089  0.9738     6890.512
   4_xyz:  14.314 0.9127  0.9754     6588.592
   4_adp:  13.978 0.9156  0.9772     6443.877
   4_occ:  13.983 0.9155  0.9769     6444.393
   5_bss:  13.995 0.9154  0.9761     6440.675
   5_xyz:  14.045 0.9151  0.9752     6461.027
   5_adp:  14.335 0.9127  0.9705     6594.740
   5_occ:  14.337 0.9127  0.9705     6598.299
   5_bss:  14.336 0.9127  0.9693     6597.509
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4015e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4015e+01
   1_xyz:   1.505  0.011  0.100 17.719  0.006  4.125   1.1555e-01
   1_adp:   1.505  0.011  0.100 17.719  0.006  4.125   1.1555e-01
   1_occ:   1.505  0.011  0.100 17.719  0.006  4.125   1.1555e-01
   2_bss:   1.505  0.011  0.100 17.719  0.006  4.125   1.1555e-01
   2_xyz:   1.052  0.008  0.078 16.126  0.004  4.128   6.8008e-02
   2_adp:   1.052  0.008  0.078 16.126  0.004  4.128   6.8008e-02
   2_occ:   1.052  0.008  0.078 16.126  0.004  4.128   6.8008e-02
   3_bss:   1.052  0.008  0.078 16.126  0.004  4.128   6.8008e-02
   3_xyz:   0.965  0.007  0.077 15.575  0.003  4.134   5.7967e-02
   3_adp:   0.965  0.007  0.077 15.575  0.003  4.134   5.7967e-02
   3_occ:   0.965  0.007  0.077 15.575  0.003  4.134   5.7967e-02
   4_bss:   0.965  0.007  0.077 15.575  0.003  4.134   5.7967e-02
   4_xyz:   1.069  0.009  0.088 15.672  0.004  4.138   6.8955e-02
   4_adp:   1.069  0.009  0.088 15.672  0.004  4.138   6.8955e-02
   4_occ:   1.069  0.009  0.088 15.672  0.004  4.138   6.8955e-02
   5_bss:   1.069  0.009  0.088 15.672  0.004  4.138   6.8955e-02
   5_xyz:   0.965  0.007  0.078 15.318  0.003  4.139   5.8206e-02
   5_adp:   0.965  0.007  0.078 15.318  0.003  4.139   5.8206e-02
   5_occ:   0.965  0.007  0.078 15.318  0.003  4.139   5.8206e-02
   5_bss:   0.965  0.007  0.078 15.318  0.003  4.139   5.8206e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0039e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0039e+00
   1_xyz:  12.792  0.137  0.429 88.264  0.041  2.270   8.7703e-02
   1_adp:  12.792  0.137  0.429 88.264  0.041  2.270   8.7703e-02
   1_occ:  12.792  0.137  0.429 88.264  0.041  2.270   8.7703e-02
   2_bss:  12.792  0.137  0.429 88.264  0.041  2.270   8.7703e-02
   2_xyz:   8.073  0.075  0.362 83.344  0.038  2.353   5.2378e-02
   2_adp:   8.073  0.075  0.362 83.344  0.038  2.353   5.2378e-02
   2_occ:   8.073  0.075  0.362 83.344  0.038  2.353   5.2378e-02
   3_bss:   8.073  0.075  0.362 83.344  0.038  2.353   5.2378e-02
   3_xyz:   7.106  0.042  0.486 82.948  0.039  2.395   3.2796e-02
   3_adp:   7.106  0.042  0.486 82.948  0.039  2.395   3.2796e-02
   3_occ:   7.106  0.042  0.486 82.948  0.039  2.395   3.2796e-02
   4_bss:   7.106  0.042  0.486 82.948  0.039  2.395   3.2796e-02
   4_xyz:   7.376  0.044  0.626 83.080  0.040  2.291   4.7711e-02
   4_adp:   7.376  0.044  0.626 83.080  0.040  2.291   4.7711e-02
   4_occ:   7.376  0.044  0.626 83.080  0.040  2.291   4.7711e-02
   5_bss:   7.376  0.044  0.626 83.080  0.040  2.291   4.7711e-02
   5_xyz:   7.303  0.045  0.497 82.907  0.039  2.363   3.6459e-02
   5_adp:   7.303  0.045  0.497 82.907  0.039  2.363   3.6459e-02
   5_occ:   7.303  0.045  0.497 82.907  0.039  2.363   3.6459e-02
   5_bss:   7.303  0.045  0.497 82.907  0.039  2.363   3.6459e-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:  51.22   0.00   9.76  46.15   0.00   6.78  51.22   0.00  26.01
   1_occ:  51.22   0.00   9.76  46.15   0.00   6.78  51.22   0.00  26.01
   2_bss:  51.22   0.00   9.76  46.15   0.00   6.78  51.22   0.00  26.01
   2_xyz:  51.22   0.00   9.76  46.15   0.00   6.78  51.22   0.00  26.01
   2_adp:  79.99   0.00  10.20  79.99   0.00   6.81  53.27   0.00  28.70
   2_occ:  79.99   0.00  10.20  79.99   0.00   6.81  53.27   0.00  28.70
   3_bss:  79.99   0.00  10.20  79.99   0.00   6.81  53.27   0.00  28.70
   3_xyz:  79.99   0.00  10.20  79.99   0.00   6.81  53.27   0.00  28.70
   3_adp:  76.73   0.00  11.47  75.03   0.00   7.18  76.73   0.06  34.79
   3_occ:  76.73   0.00  11.47  75.03   0.00   7.18  76.73   0.06  34.79
   4_bss:  76.73   0.00  11.47  75.03   0.00   7.18  76.73   0.06  34.79
   4_xyz:  76.73   0.00  11.47  75.03   0.00   7.18  76.73   0.06  34.79
   4_adp:  73.59   0.00  10.92  73.59   0.00   7.00  68.37   0.66  32.25
   4_occ:  73.59   0.00  10.92  73.59   0.00   7.00  68.37   0.66  32.25
   5_bss:  73.59   0.00  10.92  73.59   0.00   7.00  68.37   0.66  32.25
   5_xyz:  73.59   0.00  10.92  73.59   0.00   7.00  68.37   0.66  32.25
   5_adp:  86.47   0.00  11.42  86.47   0.00   7.16  81.46   0.28  34.62
   5_occ:  86.47   0.00  11.42  86.47   0.00   7.16  81.46   0.28  34.62
   5_bss:  90.38   3.91  15.33  90.38   3.91  11.07  85.37   4.19  38.53
------------------------------------------------------------------------
 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:    1.177    0.016    0.404
   1_adp:    1.177    0.016    0.404
   1_occ:    1.177    0.016    0.404
   2_bss:    1.177    0.016    0.404
   2_xyz:    1.400    0.017    0.499
   2_adp:    1.400    0.017    0.499
   2_occ:    1.400    0.017    0.499
   3_bss:    1.400    0.017    0.499
   3_xyz:    1.446    0.058    0.520
   3_adp:    1.446    0.058    0.520
   3_occ:    1.446    0.058    0.520
   4_bss:    1.446    0.058    0.520
   4_xyz:    1.435    0.041    0.536
   4_adp:    1.435    0.041    0.536
   4_occ:    1.435    0.041    0.536
   5_bss:    1.435    0.041    0.536
   5_xyz:    1.491    0.052    0.542
   5_adp:    1.491    0.052    0.542
   5_occ:    1.491    0.052    0.542
   5_bss:    1.491    0.052    0.542
------------------------------------------------------------------------

CPU time actual refinement: 317.21


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_917/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_917/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_917/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_917/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_917/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 317.05 
  Macro-tasks:
    bulk solvent and scale       = 41.85  
    individual site refinement   = 130.62 
    weights calculation          = 31.38  
    collect and process          = 6.56   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.53 
  Micro-tasks:
    mask                            = 1.70   
    f_calc                          = 94.61  
    alpha_beta                      = 8.19   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 106.10 
    fmodel                         = 7.33   
    r_factors                      = 0.23   
    phase_errors                   = 11.09  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 230.71 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.471 micro seconds
Total CPU time: 5.51 minutes
from_scatterers_fft:    629 calls, 94.18 s
gradients_fft:          574 calls, 92.72 s

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

# Date 2008-01-16 Time 02:44:20 PST -0800 (1200480260.25 s)
Start R-work = 0.4222, R-free = 0.4072 (no bulk solvent and anisotropic scale)
Final R-work = 0.1297, R-free = 0.1752 (no bulk solvent and anisotropic scale)

Start R-work = 0.4134, R-free = 0.3960
Final R-work = 0.1133, R-free = 0.1600